diff --git a/.github/workflows/node.js.yml b/.github/workflows/node.js.yml index 8d1d7653e..6acf81b86 100644 --- a/.github/workflows/node.js.yml +++ b/.github/workflows/node.js.yml @@ -11,11 +11,73 @@ jobs: uses: actions/setup-node@v3 with: node-version: '16.14.0' + - name: Check versions + run: | + main_version=$(grep -E '^# 3DBIONOTES-WS v[0-9.]+' README.md | sed -E 's/^# 3DBIONOTES-WS v([0-9.]+)$/\1/') + viewer_protvista_version=$(cat app/views/webserver/viewer.html.haml | grep -Eo 'protvista-pdb-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}') + viewer_pdbe_molstar_version=$(cat app/views/webserver/viewer.html.haml | grep -Eo 'pdbe-molstar-plugin-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}') + cd app/assets/javascripts/covid19 + bio_covid19_version=$(cat package.json | jq -r '.version') + cd ../3dbio_viewer + bio_viewer_version=$(cat package.json | jq -r '.version') + protvista_version=$(cat package.json | jq -r '.dependencies["@3dbionotes/protvista-pdb"]') + pdbe_molstar_version=$(cat package.json | jq -r '.dependencies["@3dbionotes/pdbe-molstar"]') + index_protvista_version=$(cat public/index.html | grep -Eo 'protvista-pdb-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}') + index_pdbe_molstar_version=$(cat public/index.html | grep -Eo 'pdbe-molstar-plugin-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}') + if [ "$bio_viewer_version" != "$bio_covid19_version" ] || + [ "$main_version" != "$bio_covid19_version" ]; then + echo "3dbio_viewer version doesn't match with covid19 version" + echo "3dbio_viewer: $bio_viewer_version" + echo "covid19: $bio_covid19_version" + echo "README.md version: $main_version" + exit 1 + fi + + if [ "$viewer_protvista_version" != "$index_protvista_version" ] || + [ "$viewer_pdbe_molstar_version" != "$index_pdbe_molstar_version" ] || + [ "$(echo "$index_protvista_version" | sed 's/protvista-pdb-//')" != "$protvista_version" ] || + [ "$(echo "$index_pdbe_molstar_version" | sed 's/pdbe-molstar-plugin-//')" != "$pdbe_molstar_version" ]; then + echo "Versions don't match:" + echo "Viewer and index protvista: $viewer_protvista_version, $index_protvista_version" + echo "Viewer and index pdbe-molstar: $viewer_pdbe_molstar_version, $index_pdbe_molstar_version" + echo "3dbio_viewer dependency and index protvista: $protvista_version, $(echo "$index_protvista_version" | sed 's/protvista-pdb-//')" + echo "3dbio_viewer dependency and index pdbe-molstar: $pdbe_molstar_version, $(echo "$index_pdbe_molstar_version" | sed 's/pdbe-molstar-plugin-//'), " + exit 1 + fi + + echo "3dbio_viewer versions match" + echo "README.md version: $main_version" + echo "3DBIONOTES version: $bio_viewer_version" + echo "protvista-pdb version: $protvista_version" + echo "pdbe-molstar version: $pdbe_molstar_version" - name: Install and build (3dbio_viewer) run: | cd app/assets/javascripts/3dbio_viewer yarn install yarn build + - name: Check build dependency versions (3dbioviewer) + run: | + cd app/assets/javascripts/3dbio_viewer + index_protvista_version=$(cat public/index.html | grep -Eo 'protvista-pdb-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}') + index_pdbe_molstar_version=$(cat public/index.html | grep -Eo 'pdbe-molstar-plugin-[0-9.]+-est-[0-9]+(-beta.[0-9]+){0,1}' | awk '{print $1}') + build_pdbe_molstar_file="build/pdbe-molstar/$index_pdbe_molstar_version.js" + if [ -f "$build_pdbe_molstar_file" ]; then + echo "Build file $build_pdbe_molstar_file exists." + else + echo "Build file $build_pdbe_molstar_file does not exist." + exit 1 + fi + + build_protvista_file="build/protvista-pdb/$index_protvista_version.js" + if [ -f "$build_protvista_file" ]; then + echo "Build file $build_protvista_file exists." + else + echo "Build file $build_protvista_file does not exist." + exit 1 + fi + - name: Run tests (3dbio_viewer) + run: | + cd app/assets/javascripts/3dbio_viewer yarn test:nowatch - name: Install and build (covid19) run: | diff --git a/app/assets/javascripts/3dbio_viewer/package.json b/app/assets/javascripts/3dbio_viewer/package.json index 7200677cb..01a6bf1d0 100644 --- a/app/assets/javascripts/3dbio_viewer/package.json +++ b/app/assets/javascripts/3dbio_viewer/package.json @@ -4,7 +4,7 @@ "private": true, "dependencies": { "@3dbionotes/pdbe-molstar": "3.1.0-est-2", - "@3dbionotes/protvista-pdb": "2.0.1-est-2", + "@3dbionotes/protvista-pdb": "2.0.1-est-2-beta.1", "@material-ui/core": "^4.11.2", "@material-ui/data-grid": "4.0.0-alpha.35", "@material-ui/icons": "^4.11.2", @@ -14,6 +14,7 @@ "classnames": "^2.2.6", "d2-ui-components": "^2.4.0", "data-loader": "^3.0.0", + "file-saver": "^2.0.5", "fluture": "^13.0.1", "jszip": "^3.10.1", "purify-ts": "^1.1.0", @@ -42,8 +43,10 @@ "@types/axios": "^0.14.0", "@types/classnames": "^2.2.11", "@types/express": "^4.17.11", + "@types/file-saver": "^2.0.7", "@types/hookrouter": "^2.2.5", "@types/jest": "^26.0.15", + "@types/mime-types": "^2.1.4", "@types/node": "^12.0.0", "@types/react": "17.0.2", "@types/react-dom": "17.0.2", @@ -114,4 +117,4 @@ "\\.(jpg|jpeg|png|svg)$": "/config/fileMock.js" } } -} \ No newline at end of file +} diff --git a/app/assets/javascripts/3dbio_viewer/public/index.html b/app/assets/javascripts/3dbio_viewer/public/index.html index 5a4a50a1c..65d29b896 100644 --- a/app/assets/javascripts/3dbio_viewer/public/index.html +++ b/app/assets/javascripts/3dbio_viewer/public/index.html @@ -17,7 +17,7 @@ type="text/css" /> - + 3dbio Viewer diff --git a/app/assets/javascripts/3dbio_viewer/src/compositionRoot.ts b/app/assets/javascripts/3dbio_viewer/src/compositionRoot.ts index 28e03e4a3..2fc7c481a 100644 --- a/app/assets/javascripts/3dbio_viewer/src/compositionRoot.ts +++ b/app/assets/javascripts/3dbio_viewer/src/compositionRoot.ts @@ -21,6 +21,11 @@ import { BionotesOrganismRepository } from "./data/repositories/BionotesOrganism import { ExportAllAnnotationsUseCase } from "./domain/usecases/ExportAllAnnotationsUseCase"; import { AnnotationsExportApiRepository } from "./data/repositories/AnnotationsExportApiRepository"; import { ExportAnnotationsUseCase } from "./domain/usecases/ExportAnnotationsUseCase"; +import { GetPartialNMRTargetUseCase } from "./domain/usecases/GetPartialNMRTargetUseCase"; +import { SaveNMRTargetUseCase } from "./domain/usecases/SaveNMRTargetUseCase"; +import { NMRApiRepository } from "./data/repositories/NMRApiRepository"; +import { GetSourcesUseCase } from "./domain/usecases/GetSourcesUseCase"; +import { SourcesApiRepository } from "./data/repositories/SourcesApiRepository"; export function getCompositionRoot() { const pdbRepository = new ApiPdbRepository(); @@ -33,8 +38,11 @@ export function getCompositionRoot() { const ontologyRepository = new BionotesOntologyRepository(); const organismRepository = new BionotesOrganismRepository(); const annotationsExportRepository = new AnnotationsExportApiRepository(); + const nmrRepository = new NMRApiRepository(); + const sourcesRepository = new SourcesApiRepository(); return { + getSources: new GetSourcesUseCase(sourcesRepository), getPdb: new GetPdbUseCase(pdbRepository, ontologyRepository, organismRepository), getPdbInfo: new GetPdbInfoUseCase(pdbInfoRepository), searchDbModels: new SearchDbModelsUseCase(dbModelRepository), @@ -50,6 +58,8 @@ export function getCompositionRoot() { exportAnnotations: new ExportAnnotationsUseCase(annotationsExportRepository), buildNetwork: new BuildNetworkUseCase(networkRepository), getNetwork: new GetNetworkUseCase(networkRepository), + getPartialNMR: new GetPartialNMRTargetUseCase(nmrRepository), + saveNMR: new SaveNMRTargetUseCase(nmrRepository), }; } diff --git a/app/assets/javascripts/3dbio_viewer/src/data/NMRScreening.ts b/app/assets/javascripts/3dbio_viewer/src/data/NMRScreening.ts new file mode 100644 index 000000000..bddb7e77c --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/data/NMRScreening.ts @@ -0,0 +1,79 @@ +import _ from "lodash"; +import { Codec, GetType, nullType, number, oneOf, string } from "purify-ts"; +import { NMRFragmentTarget } from "../domain/entities/Protein"; +import { commonLigand, pdbLigandC } from "./PdbLigands"; + +const featureTypeCodec = Codec.interface({ + dataSource: string, + name: string, // binding | not binding + description: string, + externalLink: string, +}); + +export const nmrFragmentCodec = Codec.interface({ + name: string, + description: string, + externalLink: string, + pdbentry: nullType, + uniprotentry: string, + ligandentity: oneOf([Codec.interface(commonLigand), pdbLigandC]), + details: Codec.interface({ + type: string, // binding | notbinding + entity: string, // NMR target + }), + start: number, + end: number, + featureType: featureTypeCodec, +}); + +export type NMRScreeningFragment = GetType; + +export function getNMR(nmrScreenings: NMRScreeningFragment[]): NMRFragmentTarget[] { + const fragments = nmrScreenings.map(nmr => ({ + ...nmr, + binding: !nmr.details.type.toLowerCase().includes("not"), + })); + + const targets = _(fragments) + .groupBy(i => i.details.entity) + .toPairs() + .value(); + + return targets.flatMap(([name, targetFragments]) => { + const fragments = targetFragments.map( + ({ name, description, externalLink, binding, ligandentity, start, end }) => ({ + name, + description, + externalLink, + binding, + ligand: { + ...ligandentity, + inChI: ligandentity.IUPACInChIkey, + smiles: ligandentity.canonicalSMILES, + pubchemId: ligandentity.pubChemCompoundId, + formula: ligandentity.formula, + imageDataResource: undefined, + }, + start, + end, + }) + ); + + const start = _.first(fragments.map(({ start }) => start)); + const end = _.first(fragments.map(({ end }) => end)); + const uniprotId = _.first(targetFragments.map(({ uniprotentry }) => uniprotentry)); + if (!start || !end || !uniprotId) return []; + + return [ + { + name, + uniprotId, + fragments, + bindingCount: fragments.filter(({ binding }) => binding).length, + notBindingCount: fragments.filter(({ binding }) => !binding).length, + start, + end, + }, + ]; + }); +} diff --git a/app/assets/javascripts/3dbio_viewer/src/data/NMRTarget.ts b/app/assets/javascripts/3dbio_viewer/src/data/NMRTarget.ts new file mode 100644 index 000000000..203369e56 --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/data/NMRTarget.ts @@ -0,0 +1,11 @@ +import _ from "lodash"; +import { Codec, GetType, number, string } from "purify-ts"; + +export const nmrTargetCodec = Codec.interface({ + entity: string, + start: number, + end: number, + uniprot_acc: string, +}); + +export type NMRTarget = GetType; diff --git a/app/assets/javascripts/3dbio_viewer/src/data/Ontologies.ts b/app/assets/javascripts/3dbio_viewer/src/data/Ontologies.ts index 31f0e1ddb..cda3f0126 100644 --- a/app/assets/javascripts/3dbio_viewer/src/data/Ontologies.ts +++ b/app/assets/javascripts/3dbio_viewer/src/data/Ontologies.ts @@ -1,14 +1,10 @@ -import { array, Codec, GetType, nullType, number, oneOf, string } from "purify-ts"; - -function maybeNull(type: Codec) { - return oneOf([type, nullType]); -} +import { array, Codec, GetType, nullable, number, string } from "purify-ts"; function getOntologiesResponse(codec: Codec) { return Codec.interface({ count: number, - next: maybeNull(string), - previous: maybeNull(string), + next: nullable(string), + previous: nullable(string), results: codec, }); } diff --git a/app/assets/javascripts/3dbio_viewer/src/data/Organisms.ts b/app/assets/javascripts/3dbio_viewer/src/data/Organisms.ts index f71d93e18..7de7481cf 100644 --- a/app/assets/javascripts/3dbio_viewer/src/data/Organisms.ts +++ b/app/assets/javascripts/3dbio_viewer/src/data/Organisms.ts @@ -1,16 +1,12 @@ import _ from "lodash"; -import { array, Codec, GetType, nullType, number, oneOf, string } from "purify-ts"; +import { array, Codec, GetType, nullable, number, string } from "purify-ts"; import { Organism } from "../domain/entities/LigandImageData"; -function maybeNull(type: Codec) { - return oneOf([type, nullType]); -} - function getOrganismsResponse(codec: Codec) { return Codec.interface({ count: number, - next: maybeNull(string), - previous: maybeNull(string), + next: nullable(string), + previous: nullable(string), results: codec, }); } diff --git a/app/assets/javascripts/3dbio_viewer/src/data/PdbLigands.ts b/app/assets/javascripts/3dbio_viewer/src/data/PdbLigands.ts index eff8497b0..a4189f3b0 100644 --- a/app/assets/javascripts/3dbio_viewer/src/data/PdbLigands.ts +++ b/app/assets/javascripts/3dbio_viewer/src/data/PdbLigands.ts @@ -121,18 +121,22 @@ const imageDataC = Codec.interface({ assays: array(assayC), }); -export const pdbLigandC = Codec.interface({ +export const commonLigand = { IUPACInChIkey: string, - dbId: string, - pubChemCompoundId: string, name: string, formula: string, formula_weight: number, imageLink: string, externalLink: string, + pubChemCompoundId: string, IUPACInChI: string, isomericSMILES: string, canonicalSMILES: string, +}; + +export const pdbLigandC = Codec.interface({ + ...commonLigand, + dbId: string, imageData: optional(array(imageDataC)), //it shouldn't be an array... }); @@ -256,6 +260,9 @@ export function getPdbLigand(pdbLigandOptions: PdbLigandsOptions): PdbLigand { name: ligand.name, inChI: ligand.IUPACInChIkey, imageDataResource: idr, + smiles: ligand.canonicalSMILES, + formula: ligand.formula, + pubchemId: ligand.pubChemCompoundId, }; } diff --git a/app/assets/javascripts/3dbio_viewer/src/data/codec-utils.ts b/app/assets/javascripts/3dbio_viewer/src/data/codec-utils.ts new file mode 100644 index 000000000..3b633f935 --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/data/codec-utils.ts @@ -0,0 +1,21 @@ +import { Codec, array, nullable, number, optional, string } from "purify-ts"; + +export function paginationCodec(type: Codec): Codec> { + return Codec.interface({ + count: number, + next: optional(nullable(string)), + previous: optional(nullable(string)), + results: array(type), + }); +} + +export function getResults(pagination?: Pagination) { + return pagination?.results ?? []; +} + +export type Pagination = { + count: number; + next: string | null | undefined; + previous: string | null | undefined; + results: K[]; +}; diff --git a/app/assets/javascripts/3dbio_viewer/src/data/repositories/BionotesPdbInfoRepository.ts b/app/assets/javascripts/3dbio_viewer/src/data/repositories/BionotesPdbInfoRepository.ts index 8c9c69c00..eac0fa6b6 100644 --- a/app/assets/javascripts/3dbio_viewer/src/data/repositories/BionotesPdbInfoRepository.ts +++ b/app/assets/javascripts/3dbio_viewer/src/data/repositories/BionotesPdbInfoRepository.ts @@ -8,52 +8,55 @@ import { routes } from "../../routes"; import { Future } from "../../utils/future"; import { RequestError, getFromUrl } from "../request-utils"; import { emdbsFromPdbUrl, getEmdbsFromMapping, PdbEmdbMapping } from "./mapping"; +import { Maybe } from "../../utils/ts-utils"; import i18n from "../../domain/utils/i18n"; export class BionotesPdbInfoRepository implements PdbInfoRepository { get(pdbId: PdbId): FutureData { - const proteinMappingUrl = `${routes.bionotes}/api/mappings/PDB/Uniprot/${pdbId}`; + const proteinMappingUrl = `${routes.ebi}/pdbe/api/mappings/uniprot/${pdbId}`; const fallbackMappingUrl = `${routes.ebi}/pdbe/api/pdb/entry/polymer_coverage/${pdbId}/`; const emdbMapping = `${emdbsFromPdbUrl}/${pdbId}`; const data$ = { - uniprotMapping: getFromUrl(proteinMappingUrl).flatMapError((err) => buildError("serviceUnavailable", err)), - fallbackMapping: getFromUrl(fallbackMappingUrl).flatMapError((err) => buildError("noData", err)), + uniprotMapping: getFromUrl>( + proteinMappingUrl + ).flatMapError(_err => Future.success, Error>(undefined)), + fallbackMapping: getFromUrl(fallbackMappingUrl).flatMapError(err => + buildError("noData", err) + ), emdbMapping: getFromUrl(emdbMapping), }; return Future.joinObj(data$).flatMap(data => { const { uniprotMapping, emdbMapping, fallbackMapping } = data; - const proteinsMapping = uniprotMapping[pdbId.toLowerCase()]; + const proteinsMapping = uniprotMapping && uniprotMapping[pdbId.toLowerCase()]?.UniProt; const fallback = fallbackMapping[pdbId.toLowerCase()]; - if (!proteinsMapping) { + if (!proteinsMapping && !fallback) { const err = `Uniprot mapping not found for ${pdbId}`; return buildError("noData", { message: err }); } - if (!fallback) { - const err = `No fallback chains found for ${pdbId}`; - return buildError("noData", { message: err }); - } - const emdbIds = getEmdbsFromMapping(emdbMapping, pdbId); - if (proteinsMapping instanceof Array) { - return Future.success(buildPdbInfo({ - id: pdbId, - emdbs: emdbIds.map(emdbId => ({ id: emdbId })), - ligands: [], - proteins: [], - proteinsMapping: undefined, - chains: fallback.molecules.flatMap(({ chains }) => chains).map(chain => ({ - id: chain.struct_asym_id, - shortName: chain.struct_asym_id, - name: chain.struct_asym_id, - chainId: chain.struct_asym_id, - protein: undefined - })) - })); - } + if (!proteinsMapping && fallback) + return Future.success( + buildPdbInfo({ + id: pdbId, + emdbs: emdbIds.map(emdbId => ({ id: emdbId })), + ligands: [], + proteins: [], + proteinsMapping: undefined, + chains: fallback.molecules + .flatMap(({ chains }) => chains) + .map(chain => ({ + id: chain.struct_asym_id, + shortName: chain.struct_asym_id, + name: chain.struct_asym_id, + chainId: chain.struct_asym_id, + protein: undefined, + })), + }) + ); const proteins = _(proteinsMapping).keys().join(","); const proteinsInfoUrl = `${routes.bionotes}/api/lengths/UniprotMulti/${proteins}`; @@ -61,6 +64,13 @@ export class BionotesPdbInfoRepository implements PdbInfoRepository { ? getFromUrl(proteinsInfoUrl) : Future.success({}); + const proteinsMappingChains = _.mapValues(proteinsMapping, v => + v.mappings.map(({ struct_asym_id, chain_id }) => ({ + structAsymId: struct_asym_id, + chainId: chain_id, + })) + ); + return proteinsInfo$.map(proteinsInfo => { const proteins = _(proteinsInfo) .toPairs() @@ -78,7 +88,7 @@ export class BionotesPdbInfoRepository implements PdbInfoRepository { ligands: [], chains: [], proteins, - proteinsMapping, + proteinsMapping: proteinsMappingChains, }); }); }); @@ -90,22 +100,35 @@ type ErrorType = "serviceUnavailable" | "noData"; function buildError(type: ErrorType, err: RequestError): FutureData { console.error(err.message); switch (type) { - case "serviceUnavailable": return Future.error({ - message: i18n.t( - "We apologize. Some of the services we rely on are temporarily unavailable. Our team is working to resolve the issue, and we appreciate your patience. Please try again later." - ), - }); - case "noData": return Future.error({ - message: i18n.t(`No data found for this PDB. But you can try and visualize another PDB. If you believe this is incorrect, please contact us using the "Send Feedback" button below.`), - }) + case "serviceUnavailable": + return Future.error({ + message: i18n.t( + "We apologize. Some of the services we rely on are temporarily unavailable. Our team is working to resolve the issue, and we appreciate your patience. Please try again later." + ), + }); + case "noData": + return Future.error({ + message: i18n.t( + `No data found for this PDB. But you can try and visualize another PDB. If you believe this is incorrect, please contact us using the "Send Feedback" button below.` + ), + }); } } -type UniprotFromPdbMapping = Record | unknown[]>; +export type UniprotMapping = Record< + ProteinId, + { mappings: { chain_id: ChainId; struct_asym_id: ChainId }[] } +>; + +type Uniprot = { + UniProt: UniprotMapping; +}; + +type UniprotFromPdbMapping = Record; type PolymerMolecules = { chains: { struct_asym_id: string }[]; -}[] +}[]; type ChainsFromPolymer = Record; diff --git a/app/assets/javascripts/3dbio_viewer/src/data/repositories/NMRApiRepository.ts b/app/assets/javascripts/3dbio_viewer/src/data/repositories/NMRApiRepository.ts new file mode 100644 index 000000000..b5779c734 --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/data/repositories/NMRApiRepository.ts @@ -0,0 +1,200 @@ +import _, { pick } from "lodash"; +import FileSaver from "file-saver"; +import { routes } from "../../routes"; +import { lookup } from "mime-types"; +import { FutureData } from "../../domain/entities/FutureData"; +import { NMRPagination, NMRRepository } from "../../domain/repositories/NMRRepository"; +import { nmrFragmentCodec, NMRScreeningFragment } from "../NMRScreening"; +import { getResults, Pagination, paginationCodec } from "../codec-utils"; +import { RequestError, getValidatedJSON } from "../request-utils"; +import { + BasicNMRFragmentTarget, + NMRFragment, + NMRFragmentTarget, +} from "../../domain/entities/Protein"; +import { Future } from "../../utils/future"; +import i18n from "../../domain/utils/i18n"; +import { PdbLigand } from "../../domain/entities/Pdb"; + +export class NMRApiRepository implements NMRRepository { + getPartialNMRTarget( + target: BasicNMRFragmentTarget, + pagination: NMRPagination + ): FutureData<{ target: NMRFragmentTarget; pagination: NMRPagination }> { + const { uniprotId, start, end } = target; + const { bionotesStaging } = routes; + const nmrTarget$ = getValidatedJSON>( + `${bionotesStaging}/bws/api/nmr/${uniprotId}?start=${start}&end=${end}&limit=${ + pagination.pageSize + }&page=${pagination.page + 1}`, + paginationCodec(nmrFragmentCodec) + ).flatMap(p => + getNMRTarget(uniprotId, getResults(p)).map(target => ({ + pagination: p + ? { ...pagination, page: pagination.page - 1, count: p.count } + : pagination, + target, + })) + ); + + return nmrTarget$; + } + + getNMRTarget(target: BasicNMRFragmentTarget): FutureData { + const { uniprotId, start, end } = target; + const { bionotesStaging } = routes; + const chunkSize = 50; + const targetChunk$ = (page: number) => + getValidatedJSON>( + `${bionotesStaging}/bws/api/nmr/${uniprotId}?start=${start}&end=${end}&limit=${chunkSize}&page=${ + page + 1 + }`, + paginationCodec(nmrFragmentCodec) + ).flatMap(pagination => getNMRTarget(uniprotId, getResults(pagination))); + + const nmrTarget$ = getValidatedJSON>( + `${bionotesStaging}/bws/api/nmr/${uniprotId}?start=${start}&end=${end}&limit=1`, + paginationCodec(nmrFragmentCodec) + ) + .flatMap(pagination => { + const pages = Math.ceil((pagination?.count ?? 0) / chunkSize); + return Future.sequential(_.times(pages).map(page => targetChunk$(page))); + }) + .flatMap( + (targets): Future => + _.isEmpty(targets) + ? Future.error({ message: "No targets" }) + : Future.success(targets) + ) + .map(targets => + targets.reduce((acc, v) => ({ + ...acc, + bindingCount: acc.bindingCount + v.bindingCount, + notBindingCount: acc.notBindingCount + v.notBindingCount, + fragments: [...acc.fragments, ...v.fragments], + })) + ); + + return nmrTarget$; + } + + saveNMRTarget(target: NMRFragmentTarget) { + const targetKeys: Array = [ + "name", + "uniprotId", + "start", + "end", + "fragments", + ]; + + const fragmentKeys: Array = ["name", "ligand", "binding"]; + + const ligandKeys: Array = [ + "formula", + "inChI", + "name", + "pubchemId", + "smiles", + ]; + + const fragments = target.fragments.map(f => { + const fragment = { + ...f, + ligand: pick(f.ligand, ligandKeys), + }; + + return pick(fragment, fragmentKeys); + }); + + const targetWithPickedProps = { + ...target, + fragments, + }; + + const content = pick(targetWithPickedProps, targetKeys); + const contents = JSON.stringify(content, null, 4); + + return this.save({ + contents, + name: `${target.name.toLowerCase().replaceAll(/\s/g, "-")}`, + extension: "json", + }); + } + + private save(options: { name: string; contents: string; extension: string }) { + const { name, extension, contents } = options; + const filename = `${name}.${extension}`; + const mimeType = lookup(filename); + const blob = new Blob([contents], { type: mimeType || undefined }); + FileSaver.saveAs(blob, filename); + } +} + +export function getNMRTarget( + uniprotId: string, + nmrScreenings: NMRScreeningFragment[] +): FutureData { + const fragments = nmrScreenings.map(nmr => ({ + ...nmr, + binding: !nmr.details.type.toLowerCase().includes("not"), + })); + + const targets = _(fragments) + .groupBy(i => i.details.entity) + .toPairs() + .value(); + + const target = targets[0]; + if (!target) + return Future.error({ + message: i18n.t("NMR Error: no target found", { nsSeparator: false }), + }); + if (targets.length > 1) + return Future.error({ + message: i18n.t( + `NMR Error: target should only be one. Instead received ${targets.length}.`, + { nsSeparator: false } + ), + }); + + const [targetName, targetFragments] = target; + + const tFragments = targetFragments.map( + ({ name, description, externalLink, binding, ligandentity, start, end }) => ({ + name, + description, + externalLink, + binding, + ligand: { + ...ligandentity, + inChI: ligandentity.IUPACInChIkey, + smiles: ligandentity.canonicalSMILES, + pubchemId: ligandentity.pubChemCompoundId, + formula: ligandentity.formula, + imageDataResource: undefined, + }, + start, + end, + }) + ); + + const start = _.first(fragments.map(({ start }) => start)); + const end = _.first(fragments.map(({ end }) => end)); + if (!start || !end) + return Future.error({ + message: i18n.t( + "NMR Unexpected Error: no start / no end on fragments. Unable to get target.", + { nsSeparator: false } + ), + }); + + return Future.success({ + name: targetName, + uniprotId, + fragments: tFragments, + bindingCount: fragments.filter(({ binding }) => binding).length, + notBindingCount: fragments.filter(({ binding }) => !binding).length, + start, + end, + }); +} diff --git a/app/assets/javascripts/3dbio_viewer/src/data/repositories/SourcesApiRepository.ts b/app/assets/javascripts/3dbio_viewer/src/data/repositories/SourcesApiRepository.ts new file mode 100644 index 000000000..a2175c61a --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/data/repositories/SourcesApiRepository.ts @@ -0,0 +1,37 @@ +import { Codec, string } from "purify-ts"; +import { FutureData } from "../../domain/entities/FutureData"; +import { Source } from "../../domain/entities/Source"; +import { SourcesRepository } from "../../domain/repositories/SourcesRepository"; +import { routes } from "../../routes"; +import { getValidatedJSON } from "../request-utils"; +import { getResults, paginationCodec } from "../codec-utils"; + +export class SourcesApiRepository implements SourcesRepository { + get(): FutureData { + const { bionotesStaging: api } = routes; + + const nmr$ = getValidatedJSON( + `${api}/bws/api/nmr/source/`, + paginationCodec(nmrMethodCodec) + ).map(getResults); + + return nmr$.map(nmr => { + // Manually adding NMR + // BWS should be grouped in only one endpoint for all sources, and grouping even methods + const nmrSource: Source = { + name: "NMR", + description: "The COVID19-NMR Consortium", + externalLink: "https://covid19-nmr.de/", + methods: nmr, + }; + + return [nmrSource]; + }); + } +} + +const nmrMethodCodec = Codec.interface({ + name: string, + description: string, + externalLink: string, +}); diff --git a/app/assets/javascripts/3dbio_viewer/src/data/repositories/protvista/ApiPdbRepository.ts b/app/assets/javascripts/3dbio_viewer/src/data/repositories/protvista/ApiPdbRepository.ts index ad7abe32f..29bc6509c 100644 --- a/app/assets/javascripts/3dbio_viewer/src/data/repositories/protvista/ApiPdbRepository.ts +++ b/app/assets/javascripts/3dbio_viewer/src/data/repositories/protvista/ApiPdbRepository.ts @@ -47,11 +47,15 @@ import { pdbEntryResponseC, PdbLigandsResponse, } from "../../PdbLigands"; +import { getResults, Pagination, paginationCodec } from "../../codec-utils"; import { getPublicationsCodec, EntryPublications, getPublications } from "../../PdbPublications"; +import { getNMRSubtrack } from "./tracks/nmr"; +import { NMRTarget, nmrTargetCodec } from "../../NMRTarget"; interface Data { uniprot: UniprotResponse; pdbEmdbsEmValidations: PdbEmdbEmValidations[]; + nmrTargets: NMRTarget[]; features: Features; cv19Tracks: Cv19Tracks; pdbAnnotations: PdbAnnotations; @@ -124,6 +128,7 @@ export class ApiPdbRepository implements PdbRepository { pdbRedoFragments: on(data.pdbRedo, pdbRedo => getPdbRedoFragments(pdbRedo, chainId)), epitomesFragments: on(data.iedb, getEpitomesFragments), molprobityFragments: on(data.molprobity, molprobity => getMolprobityFragments(molprobity, chainId)), + nmrFragments: on(data.nmrTargets, nmr => getNMRSubtrack(nmr)), }; const fragmentsList = { ...proteinFragments, ...fragments }; @@ -222,10 +227,18 @@ function getData(options: PdbOptions): FutureData> { pdbEntryResponseC ).map(pdbEntryResponse => pdbEntryResponse?.results) + const nmrTargets = onF(proteinId, proteinId => + getValidatedJSON>( + `${bioUrlDev}/bws/api/nmr/targets/${proteinId}/`, + paginationCodec(nmrTargetCodec) + ).map(pagination => getResults(pagination)) + ); + // Move URLS to each track module? //prettier-ignore const data$: DataRequests = { uniprot: onF(proteinId, proteinId => getXML(`${routes.uniprot}/uniprotkb/${proteinId}.xml`)), + nmrTargets, pdbEmdbsEmValidations, features: onF(proteinId, proteinId => getJSON(`${ebiProteinsApiUrl}/features/${proteinId}`)), cv19Tracks: onF(proteinId, proteinId => getJSON(`${bioUrl}/cv19_annotations/${proteinId}_annotations.json`)), diff --git a/app/assets/javascripts/3dbio_viewer/src/data/repositories/protvista/tracks/nmr.ts b/app/assets/javascripts/3dbio_viewer/src/data/repositories/protvista/tracks/nmr.ts new file mode 100644 index 000000000..3f5813b8c --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/data/repositories/protvista/tracks/nmr.ts @@ -0,0 +1,12 @@ +import { Fragments } from "../../../../domain/entities/Fragment2"; +import { NMRTarget } from "../../../NMRTarget"; +import { subtracks } from "../definitions"; + +export function getNMRSubtrack(target: NMRTarget[]): Fragments { + return target.map(t => ({ + subtrack: subtracks.nmr, + start: t.start, + end: t.end, + description: t.entity, + })); +} diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/definitions/subtracks.ts b/app/assets/javascripts/3dbio_viewer/src/domain/definitions/subtracks.ts index 2db415d68..b2799dd78 100644 --- a/app/assets/javascripts/3dbio_viewer/src/domain/definitions/subtracks.ts +++ b/app/assets/javascripts/3dbio_viewer/src/domain/definitions/subtracks.ts @@ -482,6 +482,17 @@ export const subtracks = recordOf()({ description: i18n.t(""), }, + nmr: { + id: "nmr" as const, + name: i18n.t("NMR-based fragment screening"), + source: "https://onlinelibrary.wiley.com/doi/10.1002/anie.202205858", + description: i18n.t( + "List of binding/not-binding fragments from an NMR screening study in which a well-defined fragment library was used to identify hits against SCoV2 proteins." + ), + color: "#673ab7", + isBlast: false, + }, + // Functional mapping ligands functionalMappingLigands: { id: "functional-mapping-ligands" as const, diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/definitions/tracks.ts b/app/assets/javascripts/3dbio_viewer/src/domain/definitions/tracks.ts index fa55993f1..80fb2c60f 100644 --- a/app/assets/javascripts/3dbio_viewer/src/domain/definitions/tracks.ts +++ b/app/assets/javascripts/3dbio_viewer/src/domain/definitions/tracks.ts @@ -140,11 +140,7 @@ export const trackDefinitions = { description: i18n.t( "Different validation methods and local quality of the map-to-models fit in cryo-EM" ), - subtracks: [ - subtracks.deepRes, - subtracks.monoRes, - subtracks.blocRes, - ], + subtracks: [subtracks.deepRes, subtracks.monoRes, subtracks.blocRes], }), validationMapToModel: definition({ id: "em-validation-map-to-model" as const, @@ -152,11 +148,7 @@ export const trackDefinitions = { description: i18n.t( "Different validation methods and local quality of the map-to-models fit in cryo-EM" ), - subtracks: [ - subtracks.fscQ, - subtracks.mapQ, - subtracks.daq, - ], + subtracks: [subtracks.fscQ, subtracks.mapQ, subtracks.daq], }), pockets: definition({ id: "pockets" as const, @@ -187,6 +179,11 @@ export const trackDefinitions = { name: i18n.t("Ligands"), subtracks: [subtracks.ligands], }), + nmr: definition({ + id: "nmr" as const, + name: i18n.t("Ligand interaction"), + subtracks: [subtracks.nmr], + }), functionalMappingLigands: definition({ id: "functional-mapping-ligands" as const, name: i18n.t("Functional mapping ligands"), diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/entities/Pdb.ts b/app/assets/javascripts/3dbio_viewer/src/domain/entities/Pdb.ts index e899b44c8..65dd4b9f2 100644 --- a/app/assets/javascripts/3dbio_viewer/src/domain/entities/Pdb.ts +++ b/app/assets/javascripts/3dbio_viewer/src/domain/entities/Pdb.ts @@ -39,7 +39,10 @@ export interface Pdb { export interface PdbLigand { name: string; inChI: string; //IUPACInChIkey - imageDataResource?: LigandImageData; + imageDataResource: Maybe; + smiles: string; + formula: string; + pubchemId: string; } export type PdbId = string; diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/entities/PdbInfo.ts b/app/assets/javascripts/3dbio_viewer/src/domain/entities/PdbInfo.ts index bd96e96e6..59e028ab8 100644 --- a/app/assets/javascripts/3dbio_viewer/src/domain/entities/PdbInfo.ts +++ b/app/assets/javascripts/3dbio_viewer/src/domain/entities/PdbInfo.ts @@ -2,7 +2,7 @@ import _ from "lodash"; import { Maybe } from "../../utils/ts-utils"; import { Ligand } from "./Ligand"; import { Emdb } from "./Pdb"; -import { ChainId, Protein, ProteinId } from "./Protein"; +import { ChainId, Protein } from "./Protein"; import { UploadData } from "./UploadData"; export interface PdbInfo { @@ -19,9 +19,14 @@ type Chain = { protein: Maybe; }; +type ChainIds = { + structAsymId: string; + chainId: string; +}; + interface BuildPdbInfoOptions extends PdbInfo { proteins: Protein[]; - proteinsMapping: Maybe>; + proteinsMapping: Maybe>; } export function buildPdbInfo(options: BuildPdbInfoOptions): PdbInfo { @@ -33,13 +38,13 @@ export function buildPdbInfo(options: BuildPdbInfoOptions): PdbInfo { const protein = proteinById[proteinId]; if (!protein) return []; - return chainIds.map(chainId => { - const shortName = _([chainId, protein.gen]).compact().join(" - "); + return chainIds.map(({ structAsymId, chainId: _chainId }) => { + const shortName = _([structAsymId, protein.gen]).compact().join(" - "); return { - id: [proteinId, chainId].join("-"), + id: [proteinId, structAsymId].join("-"), shortName, name: _([shortName, protein.name]).compact().join(", "), - chainId, + chainId: structAsymId, protein, }; }); diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/entities/Protein.ts b/app/assets/javascripts/3dbio_viewer/src/domain/entities/Protein.ts index 34646c020..6b9b52796 100644 --- a/app/assets/javascripts/3dbio_viewer/src/domain/entities/Protein.ts +++ b/app/assets/javascripts/3dbio_viewer/src/domain/entities/Protein.ts @@ -1,3 +1,4 @@ +import { PdbLigand } from "./Pdb"; import { Link } from "./Link"; export interface Protein { @@ -8,6 +9,32 @@ export interface Protein { genBank?: string[]; } +export interface NMRTarget { + name: string; + uniprotId: string; + start: number; + end: number; +} + +export interface BasicNMRFragmentTarget { + uniprotId: string; + start: number; + end: number; +} + +export interface NMRFragmentTarget extends BasicNMRFragmentTarget { + name: string; + fragments: NMRFragment[]; + bindingCount: number; + notBindingCount: number; +} + +export interface NMRFragment { + name: string; + binding: boolean; + ligand: PdbLigand; +} + export type ProteinId = string; export type ChainId = string; @@ -23,9 +50,9 @@ export function getProteinEntityLinks(protein: Protein, entity: ProteinEntity): case "geneBank": { return protein.genBank ? protein.genBank?.map(id => ({ - name: id ?? "-", - url: `https://www.ncbi.nlm.nih.gov/gene/${id}`, - })) + name: id ?? "-", + url: `https://www.ncbi.nlm.nih.gov/gene/${id}`, + })) : []; } } diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/entities/Source.ts b/app/assets/javascripts/3dbio_viewer/src/domain/entities/Source.ts new file mode 100644 index 000000000..4e884298e --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/domain/entities/Source.ts @@ -0,0 +1,20 @@ +import { Maybe } from "../../utils/ts-utils"; + +type Reference = { + name: string; + description: string; + externalLink: string; +}; + +type Method = Reference; + +export type Source = Reference & { + name: SourceName; + methods: Method[]; +}; + +type SourceName = "CERES" | "CSTF" | "PDB-REDO" | "IDR" | "NMR"; + +export function getSource(sources: Source[], source: SourceName): Maybe { + return sources.find(s => s.name === source); +} diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/repositories/NMRRepository.ts b/app/assets/javascripts/3dbio_viewer/src/domain/repositories/NMRRepository.ts new file mode 100644 index 000000000..6b8395e88 --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/domain/repositories/NMRRepository.ts @@ -0,0 +1,17 @@ +import { FutureData } from "../entities/FutureData"; +import { BasicNMRFragmentTarget, NMRFragmentTarget } from "../entities/Protein"; + +export interface NMRRepository { + getPartialNMRTarget: ( + target: BasicNMRFragmentTarget, + pagination: NMRPagination + ) => FutureData<{ target: NMRFragmentTarget; pagination: NMRPagination }>; + getNMRTarget: (target: BasicNMRFragmentTarget) => FutureData; + saveNMRTarget: (target: NMRFragmentTarget) => void; +} + +export interface NMRPagination { + page: number; + pageSize: number; + count: number; +} diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/repositories/SourcesRepository.ts b/app/assets/javascripts/3dbio_viewer/src/domain/repositories/SourcesRepository.ts new file mode 100644 index 000000000..0ca11544b --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/domain/repositories/SourcesRepository.ts @@ -0,0 +1,6 @@ +import { FutureData } from "../entities/FutureData"; +import { Source } from "../entities/Source"; + +export interface SourcesRepository { + get(): FutureData; +} diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/usecases/GetPartialNMRTargetUseCase.ts b/app/assets/javascripts/3dbio_viewer/src/domain/usecases/GetPartialNMRTargetUseCase.ts new file mode 100644 index 000000000..1481e2b5f --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/domain/usecases/GetPartialNMRTargetUseCase.ts @@ -0,0 +1,10 @@ +import { BasicNMRFragmentTarget } from "../entities/Protein"; +import { NMRRepository, NMRPagination } from "../repositories/NMRRepository"; + +export class GetPartialNMRTargetUseCase { + constructor(private nmrRepository: NMRRepository) {} + + execute(target: BasicNMRFragmentTarget, pagination: NMRPagination) { + return this.nmrRepository.getPartialNMRTarget(target, pagination); + } +} diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/usecases/GetSourcesUseCase.ts b/app/assets/javascripts/3dbio_viewer/src/domain/usecases/GetSourcesUseCase.ts new file mode 100644 index 000000000..865b6fd27 --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/domain/usecases/GetSourcesUseCase.ts @@ -0,0 +1,11 @@ +import { FutureData } from "../entities/FutureData"; +import { Source } from "../entities/Source"; +import { SourcesRepository } from "../repositories/SourcesRepository"; + +export class GetSourcesUseCase { + constructor(private sourcesRepository: SourcesRepository) {} + + execute(): FutureData { + return this.sourcesRepository.get(); + } +} diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/usecases/SaveNMRTargetUseCase.ts b/app/assets/javascripts/3dbio_viewer/src/domain/usecases/SaveNMRTargetUseCase.ts new file mode 100644 index 000000000..894dec770 --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/domain/usecases/SaveNMRTargetUseCase.ts @@ -0,0 +1,12 @@ +import { BasicNMRFragmentTarget } from "../entities/Protein"; +import { NMRRepository } from "../repositories/NMRRepository"; + +export class SaveNMRTargetUseCase { + constructor(private nmrRepository: NMRRepository) {} + + execute(target: BasicNMRFragmentTarget) { + return this.nmrRepository + .getNMRTarget(target) + .map(target => this.nmrRepository.saveNMRTarget(target)); + } +} diff --git a/app/assets/javascripts/3dbio_viewer/src/routes.ts b/app/assets/javascripts/3dbio_viewer/src/routes.ts index cd309a07d..44b99d772 100644 --- a/app/assets/javascripts/3dbio_viewer/src/routes.ts +++ b/app/assets/javascripts/3dbio_viewer/src/routes.ts @@ -6,7 +6,7 @@ const test = process.env.NODE_ENV === "test"; // If empty, use relative requests. export const routes = { bionotes: isDev ? "/3dbionotes" : test ? "https://3dbionotes.cnb.csic.es" : "", - bionotesStaging: isDev ? "/rinchen-dos" : test ? "http://rinchen-dos.cnb.csic.es" : "", + bionotesStaging: isDev ? "/rinchen-dos" : test ? "https://3dbionotes.cnb.csic.es" : "", ebi: isDev ? "/ebi" : "https://www.ebi.ac.uk", uniprot: isDev ? "/uniprot" : "https://rest.uniprot.org", }; diff --git a/app/assets/javascripts/3dbio_viewer/src/utils/future.ts b/app/assets/javascripts/3dbio_viewer/src/utils/future.ts index e2bd117c9..a29a79ed2 100644 --- a/app/assets/javascripts/3dbio_viewer/src/utils/future.ts +++ b/app/assets/javascripts/3dbio_viewer/src/utils/future.ts @@ -60,6 +60,10 @@ export class Future { return new Future(instance); } + static sequential(futures: Array>): Future> { + return Future.parallel(futures, { maxConcurrency: 1 }); + } + static parallel( futures: Array>, options: { maxConcurrency?: number } = {} diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/AppContext.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/AppContext.tsx index 404208169..d26e70070 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/components/AppContext.tsx +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/components/AppContext.tsx @@ -1,30 +1,44 @@ import React from "react"; -import { getCompositionRoot } from "../../compositionRoot"; +import { CompositionRoot, getCompositionRoot } from "../../compositionRoot"; +import { Source } from "../../domain/entities/Source"; -const appContextValue = { - compositionRoot: getCompositionRoot(), +type AppContextState = { + compositionRoot: CompositionRoot; + sources: Source[]; }; -type AppContextValue = typeof appContextValue; +const compositionRoot = getCompositionRoot(); -const AppReactContext = React.createContext(appContextValue); +export const AppReactContext = React.createContext({ + compositionRoot, + sources: [], +}); -export function useAppContext(): AppContextValue { +export function useAppContext(): AppContextState { return React.useContext(AppReactContext); } export const AppContext: React.FC = React.memo(props => { - return ( - - {props.children} - - ); + const [appContext, setAppContext] = React.useState({ + compositionRoot, + sources: [], + }); + + React.useEffect(() => { + compositionRoot.getSources + .execute() + .run(sources => setAppContext({ compositionRoot, sources }), console.error); + }, []); + + React.useEffect(() => { + window.app = appContext; + }, [appContext]); + + return {props.children}; }); declare global { interface Window { - app: AppContextValue; + app: AppContextState; } } - -window.app = appContextValue; diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/idr/IDRViewerBlock.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/idr/IDRViewerBlock.tsx index 1cfe3b31d..844e234ae 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/components/idr/IDRViewerBlock.tsx +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/components/idr/IDRViewerBlock.tsx @@ -202,6 +202,8 @@ const ListItem: React.FC = React.memo(props => { ); }); +export const NonBulletListItem = ListItem; + interface AssayFCProps { assay: Assay; dataSource: { label: string; href: string }; diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/loader-mask/LoaderMask.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/loader-mask/LoaderMask.tsx index 370d2266f..70eb5d33a 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/components/loader-mask/LoaderMask.tsx +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/components/loader-mask/LoaderMask.tsx @@ -1,6 +1,7 @@ import React from "react"; import { Backdrop, CircularProgress, makeStyles } from "@material-ui/core"; import styled from "styled-components"; +import { isDev } from "../../../routes"; interface LoaderProps { open: boolean; diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/nmr/NMRDialog.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/nmr/NMRDialog.tsx new file mode 100644 index 000000000..dc80bec78 --- /dev/null +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/components/nmr/NMRDialog.tsx @@ -0,0 +1,452 @@ +import _ from "lodash"; +import React from "react"; +import styled from "styled-components"; +import { + Button, + CircularProgress, + Dialog, + DialogTitle, + IconButton, + LinearProgress, + Paper, + Portal, + Table, + TableBody, + TableCell, + TableContainer, + TableHead, + TablePagination, + TableRow, + Typography, + makeStyles, +} from "@material-ui/core"; +import { BasicNMRFragmentTarget, NMRFragmentTarget } from "../../../domain/entities/Protein"; +import { Close as CloseIcon, GetApp as GetAppIcon, Stop as StopIcon } from "@material-ui/icons"; +import { useAppContext } from "../AppContext"; +import { useBooleanState } from "../../hooks/use-boolean"; +import { LoaderMask } from "../loader-mask/LoaderMask"; +import { Cancel } from "../../../utils/future"; +import { NMRPagination } from "../../../domain/repositories/NMRRepository"; +import { getSource } from "../../../domain/entities/Source"; +import { NonBulletListItem as ListItem } from "../idr/IDRViewerBlock"; +import i18n from "../../utils/i18n"; + +interface NMRDialogProps { + basicTarget: BasicNMRFragmentTarget; + open: boolean; + closeDialog: () => void; +} + +export const NMRDialog: React.FC = React.memo(props => { + const { basicTarget, open, closeDialog } = props; + const { + getNMR, + target, + saveTarget, + pagination: [pagination, setPagination], + nmrSource, + } = useNMR(basicTarget); + const [isSaving, savingActions] = useBooleanState(); + const [isLoading, loadingActions] = useBooleanState(); + + const classes = useStyles(); + + const nmrMethod = nmrSource?.methods[0]; + + const save = React.useCallback( + () => saveTarget({ show: savingActions.open, hide: savingActions.close }), + [saveTarget, savingActions] + ); + + const title = `${i18n.t("NMR-based fragment screening on")}: ${target?.name ?? ""}`; + + React.useEffect(() => { + getNMR({ show: loadingActions.open, hide: loadingActions.close }); + }, [getNMR, loadingActions]); + + const nmrReference = nmrMethod && ( + + + + + + {nmrMethod.externalLink} + + + + + + ); + + const fragmentsList = target ? ( + + {isLoading && pagination.pageSize >= 25 && } + + +
{isLoading && }
+
+ ) : ( + {i18n.t("Unable to retrieve NMR")} + ); + + return ( + <> + + + {title} + + + + + {nmrReference} + {fragmentsList} + + + + + + ); +}); + +interface ToolbarProps { + pagination: NMRPagination; + setPagination: SetNMRPagination; + save: () => Cancel | undefined; + hideSaving: () => void; + isSaving: boolean; +} + +const Toolbar: React.FC = React.memo(props => { + const { + pagination, + setPagination: { setPage, setPageSize }, + isSaving, + save, + hideSaving, + } = props; + + const { handleChangePage, handleChangeRowsPerPage, onClick, stopSaving } = useToolbar({ + setPage, + setPageSize, + save, + isSaving, + hideSaving, + }); + + const classes = useStyles(); + + return ( +
+ + +
+ ); +}); + +interface ExportButtonProps { + isProcessing: boolean; + onClick: () => void; + stop: () => void; +} + +const ExportButton: React.FC = React.memo(({ isProcessing, onClick, stop }) => { + const classes = useStyles(); + + return ( +
+ + + {isProcessing && ( +
+ + +
+ )} +
+ ); +}); + +interface DialogContentProps { + target: NMRFragmentTarget; + pagination: NMRPagination; +} + +const DialogContent: React.FC = React.memo(({ target, pagination }) => { + const headers = ["Name", "SMILES", "InchiKey", "Formula", "PubChem_ID", "Target", "Result"]; + const Headers = headers.map((h, idx) => ( + + {h} + + )); + + const fragments = React.useMemo(() => _.sortBy(target.fragments, f => !f.binding), [target]); + + return ( + + + + + + {Headers} + + + + {fragments.map((fragment, idx) => { + const { + binding, + ligand: { name: ligandName, smiles, inChI, formula, pubchemId }, + } = fragment; + + return ( + + ); + })} + +
+
+ ); +}); + +interface ItemRowProps extends DialogContentProps { + idx: number; + binding: boolean; + name: string; + smiles: string; + inChI: string; + formula: string; + pubchemId: string; +} + +const ItemRow: React.FC = React.memo(props => { + const { binding, name, smiles, inChI, formula, pubchemId, target, pagination, idx } = props; + + return ( + + {pagination.pageSize * pagination.page + idx + 1} + {name} + {smiles} + {inChI} + {formula} + {pubchemId} + {target.name} + + {binding ? i18n.t("Binding") : i18n.t("Not binding")} + + + ); +}); + +function useNMR(basicTarget: BasicNMRFragmentTarget) { + const [page, setPage] = React.useState(0); + const [pageSize, setPageSize] = React.useState(25); + const [count, setCount] = React.useState(0); + const { compositionRoot, sources } = useAppContext(); + const [target, setTarget] = React.useState(); + + React.useEffect(() => { + setCount(0); + }, [basicTarget]); + + const getNMR = React.useCallback( + (loading: { show: () => void; hide: () => void }) => { + loading.show(); + return compositionRoot.getPartialNMR + .execute(basicTarget, { page, pageSize, count }) + .run( + ({ target, pagination }) => { + setCount(pagination.count); + setTarget(target); + loading.hide(); + }, + err => { + console.error(err); + loading.hide(); + } + ); + }, + [compositionRoot, count, pageSize, page, basicTarget] + ); + + const saveTarget = React.useCallback( + (loading: { show: () => void; hide: () => void }) => { + loading.show(); + return compositionRoot.saveNMR.execute(basicTarget).run( + () => { + loading.hide(); + }, + err => { + console.error(err); + loading.hide(); + } + ); + }, + [compositionRoot, basicTarget] + ); + + return { + getNMR, + target, + saveTarget, + pagination: [ + { page, pageSize, count }, + { setPage, setPageSize, setCount }, + ] as const, + nmrSource: getSource(sources, "NMR"), + }; +} + +function useToolbar(props: { + setPage: React.Dispatch>; + setPageSize: React.Dispatch>; + save: () => Cancel | undefined; + isSaving: boolean; + hideSaving: () => void; +}) { + const { setPage, setPageSize, save, isSaving, hideSaving } = props; + const [saving, setSaving] = React.useState(); + + const handleChangePage = React.useCallback( + (_event: React.MouseEvent | null, newPage: number) => { + setPage(newPage); + }, + [setPage] + ); + + const handleChangeRowsPerPage = React.useCallback( + (event: React.ChangeEvent) => { + setPageSize(parseInt(event.target.value, 10)); + setPage(1); + }, + [setPage, setPageSize] + ); + + const onClick = React.useCallback(() => { + if (isSaving) return; + const cancel = save(); + setSaving(_saving => cancel); + }, [isSaving, save]); + + const stopSaving = React.useCallback(() => { + if (saving) { + saving(); + hideSaving(); + } + }, [saving, hideSaving]); + + return { handleChangePage, handleChangeRowsPerPage, onClick, stopSaving }; +} + +const useStyles = makeStyles({ + toolbar: { + display: "flex", + justifyContent: "space-between", + paddingLeft: "1em", + margin: "0.5em 0 0.25em", + }, + exportButton: { + display: "flex", + alignItems: "center", + color: "#607d8b", + position: "relative", + justifyContent: "center", + }, + exportStopButton: { + cursor: "pointer", + display: "flex", + alignItems: "center", + color: "#009688", + position: "absolute", + justifyContent: "center", + }, + stop: { position: "absolute", fontSize: "14px" }, + bottomProgress: { height: "4px" }, +}); + +interface SetNMRPagination { + setPage: React.Dispatch>; + setPageSize: React.Dispatch>; + setCount: React.Dispatch>; +} + +const StyledHeadTableRow = styled(TableRow)` + background: #fff; + & .MuiTableCell-root { + border-bottom: unset; + } +`; + +const StyledTableRow = styled(StyledHeadTableRow)<{ binding: boolean }>` + background: ${props => (props.binding ? "#dcedc8" : "#ffcdd2")}; + border: ${props => (props.binding ? "1px solid #9ccc65" : "1px solid #ef5350")}; +`; + +const StyledLinearProgress = styled(LinearProgress)` + &.MuiLinearProgress-colorPrimary { + background-color: #c6ece8; + } + & .MuiLinearProgress-barColorPrimary { + background-color: #009688; + } +`; + +const StyledCircularProgress = styled(CircularProgress)` + position: absolute; + &.MuiCircularProgress-colorPrimary { + color: #009688; + } +`; + +const List = styled.ul` + list-style: none; + margin: 1.5rem 2rem 0; + padding: 0; + box-sizing: border-box; +`; + +const Content = styled(Paper)` + margin: 1.5rem 2rem; +`; diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Protvista.helpers.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Protvista.helpers.tsx index 403646c4d..290be9198 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Protvista.helpers.tsx +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Protvista.helpers.tsx @@ -11,7 +11,13 @@ interface AddAction { trackId: string; } -export type ProtvistaAction = AddAction; +interface ShowNMRDialog { + type: "showDialog"; + start: number; + end: number; +} + +export type ProtvistaAction = AddAction | ShowNMRDialog; interface Options { onAction?(action: ProtvistaAction): void; @@ -41,7 +47,11 @@ interface ProtvistaPdbActionEvent { } function isProtvistaPdbActionEvent(ev: any): ev is ProtvistaPdbActionEvent { - return ev.detail && ev.detail.type === "add" && ev.detail.trackId; + return ( + ev.detail && + ((ev.detail.type === "add" && ev.detail.trackId) || + (ev.detail.type === "showDialog" && ev.detail.start && ev.detail.end)) + ); } export function getVisibleBlocks( diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaPdb.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaPdb.tsx index b78c4ff2e..d7d3e616c 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaPdb.tsx +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaPdb.tsx @@ -4,6 +4,7 @@ import { Pdb } from "../../../domain/entities/Pdb"; import { loadPdbView, ProtvistaAction } from "./Protvista.helpers"; import { BlockDef, ProtvistaTrackElement } from "./Protvista.types"; import { getPdbView } from "../../view-models/PdbView"; +import { useAppContext } from "../AppContext"; export interface ProtvistaPdbProps { pdb: Pdb; @@ -15,10 +16,11 @@ export interface ProtvistaPdbProps { export const ProtvistaPdb: React.FC = React.memo(props => { const { pdb, block, showAllTracks, onAction, setVisible } = props; + const { sources } = useAppContext(); const elementRef = React.useRef(null); const pdbView = React.useMemo(() => { - const pdbView = getPdbView(pdb, { block, showAllTracks, chainId: pdb.chainId }); + const pdbView = getPdbView(pdb, { block, showAllTracks, chainId: pdb.chainId, sources }); if (block.id === "mapValidation") { const stats = _.first(pdb.emdbs)?.emv?.stats; //if only structure coverage is selected and there is no stats @@ -26,7 +28,7 @@ export const ProtvistaPdb: React.FC = React.memo(props => { setVisible(false); } return pdbView; - }, [pdb, block, showAllTracks, setVisible]); + }, [pdb, block, showAllTracks, setVisible, sources]); React.useEffect(() => { return loadPdbView(elementRef, pdbView, { onAction }); diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaPdbValidation.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaPdbValidation.tsx index aa2c63131..27d078797 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaPdbValidation.tsx +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaPdbValidation.tsx @@ -124,10 +124,7 @@ const SVGBar: React.FC = React.memo(({ stats }) => { = props => { const { pdb, selection, blocks, pdbInfo, setBlockVisibility, setSelection } = props; + const [nmrTarget, setNMRTarget] = React.useState(); + const [openNMRDialog, { enable: showNMRDialog, disable: closeNMRDialog }] = useBooleanState( + false + ); + const protein = pdb.protein; const setBlockVisible = React.useCallback( @@ -86,6 +94,20 @@ export const ProtvistaViewer: React.FC = props => { [pdb, geneName, geneBankEntry, ligandsAndSmallMoleculesCount, protein] ); + const action = React.useCallback( + (protvistaAction: ProtvistaAction) => { + if (protvistaAction.type === "showDialog" && protein) { + showNMRDialog(); + setNMRTarget({ + start: protvistaAction.start, + end: protvistaAction.end, + uniprotId: protein.id, + }); + } + }, + [protein, setNMRTarget, showNMRDialog] + ); + const renderBlocks = React.useMemo( () => blocks.map((block, idx) => ( @@ -97,21 +119,34 @@ export const ProtvistaViewer: React.FC = props => { selection={selection} setSelection={setSelection} setVisible={setBlockVisible} + protvistaAction={action} /> )), - [namespace, pdb, selection, blocks, setBlockVisible, setSelection] + [namespace, pdb, selection, blocks, setBlockVisible, setSelection, action] ); - return
{renderBlocks}
; + return ( +
+ {renderBlocks} + {nmrTarget && ( + + )} +
+ ); }; interface ProtvistaBlockProps extends Omit { namespace: BlockProps["namespace"]; setVisible: (block: BlockDef) => (visible: boolean) => void; + protvistaAction?: (action: ProtvistaAction) => void; } const ProtvistaBlock: React.FC = React.memo(props => { - const { pdb, selection, setSelection, block, namespace, setVisible } = props; + const { pdb, selection, setSelection, block, namespace, setVisible, protvistaAction } = props; const { compositionRoot } = useAppContext(); const CustomComponent = block.component; @@ -147,7 +182,12 @@ const ProtvistaBlock: React.FC = React.memo(props => { setSelection={setSelection} /> ) : ( - + )} {block.tracks.map((trackDef, idx) => { diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Tooltip.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Tooltip.tsx index fe9c9d78c..e7ddedf5d 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Tooltip.tsx +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Tooltip.tsx @@ -5,28 +5,39 @@ import { Fragment, getFragmentToolsLink } from "../../../domain/entities/Fragmen import { Fragment2, getConflict } from "../../../domain/entities/Fragment2"; import { Pdb } from "../../../domain/entities/Pdb"; import { Subtrack } from "../../../domain/entities/Track"; -import i18n from "../../utils/i18n"; import { renderJoin } from "../../utils/react"; import { Link } from "../Link"; import { Protein } from "../../../domain/entities/Protein"; +import { getSource, Source as SourceEntity } from "../../../domain/entities/Source"; +import i18n from "../../utils/i18n"; +import styled from "styled-components"; interface TooltipProps { pdb: Pdb; subtrack: Subtrack; fragment: FragmentP; + sources: SourceEntity[]; } type FragmentP = Fragment | Fragment2; export const Tooltip: React.FC = React.memo(props => { - const { pdb, subtrack, fragment } = props; + //cannot use sources from AppContext as context is not initalized + const { pdb, subtrack, fragment, sources } = props; const { description, alignmentScore } = fragment; + + //no react.memo as is finally rendered to string + const nmrSource = getSource(sources, "NMR"); const score = alignmentScore ? alignmentScore + " %" : undefined; + const isNMR = subtrack.accession === "nmr"; return ( - + @@ -34,6 +45,9 @@ export const Tooltip: React.FC = React.memo(props => { {pdb.protein && } + {isNMR && nmrSource && ( + + )} ); }); @@ -49,6 +63,39 @@ const styles = { }, }; +const NMR: React.FC<{ start: number; end: number; nmrSource: SourceEntity }> = props => { + const { nmrSource } = props; + const nmrMethod = nmrSource?.methods[0]; + + if (!nmrMethod) return null; + + return ( + <> + + + {nmrMethod => } + + + + {i18n.t("Tools")} + + + {i18n.t("Library of tested ligands")} + + + + + ); +}; + const TooltipTable: React.FC = props => { return {props.children}
; }; @@ -171,3 +218,9 @@ const ReferencesRows: React.FC<{ title?: string; sources: Reference[] }> = props ); }; + +const ButtonLink = styled.button` + margin: 0; + padding: 0; + font-weight: normal; +`; diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/protvista-blocks.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/protvista-blocks.tsx index 137d4314c..6471fc67c 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/protvista-blocks.tsx +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/protvista-blocks.tsx @@ -169,7 +169,7 @@ The local resolution values are between \${poorQualityRegionMin} (percentile 25) For this protein, we found \${ligandsAndSmallMoleculesCount} different ligands or small molecules.`), help: "", - tracks: [tracks.structureCoverage, tracks.ligands], + tracks: [tracks.structureCoverage, tracks.nmr], profiles: [profiles.drugDesign, profiles.biomedicine], isSubtitle: true, }, diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/hooks/use-boolean.ts b/app/assets/javascripts/3dbio_viewer/src/webapp/hooks/use-boolean.ts index 280e7e531..efd04b7b2 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/hooks/use-boolean.ts +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/hooks/use-boolean.ts @@ -14,7 +14,7 @@ interface UseBooleanActions { } export function useBooleanState(initialValue?: boolean): UseBooleanReturn { - const [value, setValue] = React.useState(initialValue || false); + const [value, setValue] = React.useState(initialValue ?? false); const actions = React.useMemo(() => { return { diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/pages/app/App.css b/app/assets/javascripts/3dbio_viewer/src/webapp/pages/app/App.css index a2bc9fa96..3302ed17b 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/pages/app/App.css +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/pages/app/App.css @@ -65,11 +65,6 @@ header { .contents { margin-bottom: 10px; } - -.MuiPaper-root { - background-color: inherit !important; -} - .MuiDialogContent-root { background-color: #fff; } diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/view-models/PdbView.ts b/app/assets/javascripts/3dbio_viewer/src/webapp/view-models/PdbView.ts index 701f0299a..622c775e1 100644 --- a/app/assets/javascripts/3dbio_viewer/src/webapp/view-models/PdbView.ts +++ b/app/assets/javascripts/3dbio_viewer/src/webapp/view-models/PdbView.ts @@ -11,6 +11,7 @@ import { BlockDef } from "../components/protvista/Protvista.types"; import { Tooltip } from "../components/protvista/Tooltip"; import { trackDefinitions } from "../../domain/definitions/tracks"; import { getBlockTracks } from "../components/protvista/Protvista.helpers"; +import { Source } from "../../domain/entities/Source"; // https://github.com/ebi-webcomponents/nightingale/tree/master/packages/protvista-track @@ -73,14 +74,14 @@ export interface FragmentView { export function getPdbView( pdb: Pdb, - options: { block: BlockDef; showAllTracks?: boolean; chainId?: string } + options: { block: BlockDef; showAllTracks?: boolean; chainId?: string; sources: Source[] } ): PdbView { - const { block, showAllTracks = false, chainId } = options; + const { block, showAllTracks = false, chainId, sources } = options; const data = showAllTracks ? pdb.tracks : getBlockTracks(pdb.tracks, block); const tracks = _(data) .map((pdbTrack): TrackView | undefined => { - const subtracks = getSubtracks(pdb, pdbTrack); + const subtracks = getSubtracks(pdb, pdbTrack, sources); if (_.isEmpty(subtracks)) return undefined; return { @@ -124,13 +125,13 @@ function getVariants(pdb: Pdb): VariantsView | undefined { }; } -function getSubtracks(pdb: Pdb, track: Track): TrackView["data"] { +function getSubtracks(pdb: Pdb, track: Track, sources: Source[]): TrackView["data"] { return _.flatMap(track.subtracks, subtrack => { - return hasFragments(subtrack) ? [getSubtrack(pdb, subtrack)] : []; + return hasFragments(subtrack) ? [getSubtrack(pdb, subtrack, sources)] : []; }); } -function getSubtrack(pdb: Pdb, subtrack: Subtrack): SubtrackView { +function getSubtrack(pdb: Pdb, subtrack: Subtrack, sources: Source[]): SubtrackView { const label = subtrack.subtype ? `[${subtrack.subtype.name}] ${subtrack.label}` : subtrack.label; @@ -150,7 +151,7 @@ function getSubtrack(pdb: Pdb, subtrack: Subtrack): SubtrackView { ...fragment, color: fragment.color || "black", tooltipContent: renderToString( - React.createElement(Tooltip, { pdb, subtrack, fragment }) + React.createElement(Tooltip, { pdb, subtrack, fragment, sources }) ), })), })), diff --git a/app/assets/javascripts/3dbio_viewer/yarn.lock b/app/assets/javascripts/3dbio_viewer/yarn.lock index 58efae7c1..c0b29c4e4 100644 --- a/app/assets/javascripts/3dbio_viewer/yarn.lock +++ b/app/assets/javascripts/3dbio_viewer/yarn.lock @@ -15,10 +15,10 @@ lodash "^4.17.21" molstar "3.15.0" -"@3dbionotes/protvista-pdb@2.0.1-est-2": - version "2.0.1-est-2" - resolved "https://registry.yarnpkg.com/@3dbionotes/protvista-pdb/-/protvista-pdb-2.0.1-est-2.tgz#96560a0d82e00739cb16463f4b0ccc1d83779484" - integrity sha512-ZwxvPIyA1Mx+HlJOyUWfaDIrDOzLw8+jUhwPCRoEanMKrtzUTN3oSxd/fP/Kup25b78uTxHFtFQuzSE9CcNjDw== +"@3dbionotes/protvista-pdb@2.0.1-est-2-beta.1": + version "2.0.1-est-2-beta.1" + resolved "https://registry.yarnpkg.com/@3dbionotes/protvista-pdb/-/protvista-pdb-2.0.1-est-2-beta.1.tgz#9db59040a702a4b9bd5b4283e4d6ae1d63cd26ad" + integrity sha512-EuW6xY0ZlhKhUqievJPSmBqXPeE+LHK8oGku78yE5RGgCePaHYnBff0X1PL/lvhRBU968bxiZls2z1HOyKU8mQ== dependencies: lodash-es "^4.17.11" protvista-filter "2.0.0" @@ -2340,6 +2340,11 @@ "@types/qs" "*" "@types/serve-static" "*" +"@types/file-saver@^2.0.7": + version "2.0.7" + resolved "https://registry.yarnpkg.com/@types/file-saver/-/file-saver-2.0.7.tgz#8dbb2f24bdc7486c54aa854eb414940bbd056f7d" + integrity sha512-dNKVfHd/jk0SkR/exKGj2ggkB45MAkzvWCaqLUUgkyjITkGNzH8H+yUwr+BLJUBjZOe9w8X3wgmXhZDRg1ED6A== + "@types/geojson@*": version "7946.0.8" resolved "https://registry.yarnpkg.com/@types/geojson/-/geojson-7946.0.8.tgz#30744afdb385e2945e22f3b033f897f76b1f12ca" @@ -2454,6 +2459,11 @@ dependencies: "@types/unist" "*" +"@types/mime-types@^2.1.4": + version "2.1.4" + resolved "https://registry.yarnpkg.com/@types/mime-types/-/mime-types-2.1.4.tgz#93a1933e24fed4fb9e4adc5963a63efcbb3317a2" + integrity sha512-lfU4b34HOri+kAY5UheuFMWPDOI+OPceBSHZKp69gEyTL/mmJ4cnU6Y/rlme3UL3GyOn6Y42hyIEw0/q8sWx5w== + "@types/mime@*": version "2.0.3" resolved "https://registry.npmjs.org/@types/mime/-/mime-2.0.3.tgz#c893b73721db73699943bfc3653b1deb7faa4a3a" @@ -6427,6 +6437,11 @@ file-loader@6.1.1: loader-utils "^2.0.0" schema-utils "^3.0.0" +file-saver@^2.0.5: + version "2.0.5" + resolved "https://registry.yarnpkg.com/file-saver/-/file-saver-2.0.5.tgz#d61cfe2ce059f414d899e9dd6d4107ee25670c38" + integrity sha512-P9bmyZ3h/PRG+Nzga+rbdI4OEpNDzAVyy74uVO9ATgzLK6VtAsYybF/+TOCvrc0MO793d6+42lLyZTw7/ArVzA== + file-selector@^0.2.2: version "0.2.4" resolved "https://registry.yarnpkg.com/file-selector/-/file-selector-0.2.4.tgz#7b98286f9dbb9925f420130ea5ed0a69238d4d80" diff --git a/app/assets/javascripts/covid19/.env b/app/assets/javascripts/covid19/.env index 7b935ece4..bf4aedca0 100644 --- a/app/assets/javascripts/covid19/.env +++ b/app/assets/javascripts/covid19/.env @@ -1,3 +1,4 @@ BROWSER=false PORT=3002 SKIP_PREFLIGHT_CHECK=true +REACT_APP_BWS=https://3dbionotes.cnb.csic.es diff --git a/app/assets/javascripts/covid19/README.md b/app/assets/javascripts/covid19/README.md index a142e62c5..bf80c0505 100644 --- a/app/assets/javascripts/covid19/README.md +++ b/app/assets/javascripts/covid19/README.md @@ -20,6 +20,12 @@ Linting: $ yarn lint ``` +Backend (you can use `localhost:8080` for development if you are deploying the backend on your local machine): + +``` +REACT_APP_BWS=https://3dbionotes.cnb.csic.es +``` + ## Tests Run unit tests: diff --git a/app/assets/javascripts/covid19/i18n/en.pot b/app/assets/javascripts/covid19/i18n/en.pot index 30a080b9c..d1a73d29d 100644 --- a/app/assets/javascripts/covid19/i18n/en.pot +++ b/app/assets/javascripts/covid19/i18n/en.pot @@ -5,8 +5,8 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=(n != 1)\n" -"POT-Creation-Date: 2024-02-08T11:48:47.351Z\n" -"PO-Revision-Date: 2024-02-08T11:48:47.351Z\n" +"POT-Creation-Date: 2024-05-06T09:35:53.618Z\n" +"PO-Revision-Date: 2024-05-06T09:35:53.618Z\n" msgid "No ontologies found." msgstr "" @@ -17,6 +17,12 @@ msgstr "" msgid "No organisms found." msgstr "" +msgid "NMR Error: no target found" +msgstr "" + +msgid "NMR Unexpected Error: no start / no end on fragments. Unable to get target." +msgstr "" + msgid "Error from API: No ligands found." msgstr "" @@ -44,6 +50,9 @@ msgstr "" msgid "IDR" msgstr "" +msgid "CV19-NMR-C" +msgstr "" + msgid "COVID-19 Structural Hub" msgstr "" @@ -110,6 +119,15 @@ msgstr "" msgid "No {{name}} found" msgstr "" +msgid "Page" +msgstr "" + +msgid "of {{pageCount}}" +msgstr "" + +msgid "Go to page" +msgstr "" + msgid "Ligand IDR" msgstr "" @@ -134,6 +152,21 @@ msgstr "" msgid "Ontology" msgstr "" +msgid "NMR-based fragment screening on" +msgstr "" + +msgid "Export all fragments" +msgstr "" + +msgid "Ligand interaction" +msgstr "" + +msgid "Binding" +msgstr "" + +msgid "Not binding" +msgstr "" + msgid "Search protein/organism/PDB ID/EMDB ID/UniProt ID" msgstr "" @@ -207,12 +240,27 @@ msgid "" " to check the whole list." msgstr "" +msgid "Cancel request" +msgstr "" + +msgid "Loading request..." +msgstr "" + msgid "Examples" msgstr "" msgid "View more" msgstr "" +msgid "C19-NMR" +msgstr "" + +msgid "Loading NMR..." +msgstr "" + +msgid "Loading IDR..." +msgstr "" + msgid "Sample" msgstr "" @@ -297,5 +345,8 @@ msgstr "" msgid "No {{field}} found" msgstr "" +msgid "Request has been cancelled" +msgstr "" + msgid " and {{overflow}} more..." msgstr "" diff --git a/app/assets/javascripts/covid19/package.json b/app/assets/javascripts/covid19/package.json index becd54fcc..291bde7fd 100644 --- a/app/assets/javascripts/covid19/package.json +++ b/app/assets/javascripts/covid19/package.json @@ -5,6 +5,7 @@ "homepage": ".", "dependencies": { "@dhis2/d2-i18n": "1.0.6", + "@eyeseetea/d2-ui-components": "^2.8.0", "@material-ui/core": "4.12.4", "@material-ui/data-grid": "^4.0.0-alpha.31", "@material-ui/icons": "4.11.2", @@ -96,4 +97,4 @@ "typescript": "4.3.5", "wait-on": "5.2.1" } -} \ No newline at end of file +} diff --git a/app/assets/javascripts/covid19/src/compositionRoot.ts b/app/assets/javascripts/covid19/src/compositionRoot.ts index e35b30d65..2a9139e79 100644 --- a/app/assets/javascripts/covid19/src/compositionRoot.ts +++ b/app/assets/javascripts/covid19/src/compositionRoot.ts @@ -1,33 +1,32 @@ -import { Covid19InfoFromJsonRepository } from "./data/repositories/Covid19InfoFromJsonRepository"; import { BrowserDataGridRepository } from "./data/repositories/BrowserDataGridRepository"; import { ExportStructuresUseCase } from "./domain/usecases/ExportStructuresUseCase"; import { GetCovid19InfoUseCase } from "./domain/usecases/GetCovid19InfoUseCase"; import { GetAutoSuggestionsUseCase } from "./domain/usecases/GetAutoSuggestionsUseCase"; -import { SearchCovid19InfoUseCase } from "./domain/usecases/SearchCovid19InfoUseCase"; -import { AddDynamicInfoToCovid19InfoUseCase } from "./domain/usecases/AddDynamicInfoToCovid19InfoUseCase"; -import { LocalStorageCacheRepository } from "./data/repositories/LocalStorageCacheRepository"; import { LigandsApiRepository } from "./data/repositories/LigandsApiRepository"; import { GetLigandImageDataResourcesUseCase } from "./domain/usecases/GetLigandImageDataResourcesUseCase"; import { BionotesOntologyRepository } from "./data/repositories/BioOntologyRepository"; import { BionotesOrganismRepository } from "./data/repositories/BionotesOrganismRepository"; +import { Covid19InfoApiRepository } from "./data/repositories/Covid19InfoApiRepository"; +import { EntitiesApiRepository } from "./data/repositories/EntitiesApiRepository"; +import { GetPartialNMRTargetUseCase } from "./domain/usecases/GetPartialNMRTargetUseCase"; +import { SaveNMRTargetUseCase } from "./domain/usecases/SaveNMRTargetUseCase"; +import { GetSourcesUseCase } from "./domain/usecases/GetSourcesUseCase"; +import { SourcesApiRepository } from "./data/repositories/SourcesApiRepository"; export function getCompositionRoot() { - const covid19InfoRepository = new Covid19InfoFromJsonRepository(); + const sourcesRepository = new SourcesApiRepository(); + const covid19InfoApiRepository = new Covid19InfoApiRepository(); const dataGridRepository = new BrowserDataGridRepository(); - const cacheRepository = new LocalStorageCacheRepository(); const ligandsRepository = new LigandsApiRepository(); const ontologyRepository = new BionotesOntologyRepository(); const organismRepository = new BionotesOrganismRepository(); + const entitiesRepository = new EntitiesApiRepository(); return { - getCovid19Info: new GetCovid19InfoUseCase(covid19InfoRepository), - getAutoSuggestions: new GetAutoSuggestionsUseCase(covid19InfoRepository), - searchCovid19Info: new SearchCovid19InfoUseCase(covid19InfoRepository), + getSources: new GetSourcesUseCase(sourcesRepository), + getCovid19Info: new GetCovid19InfoUseCase(covid19InfoApiRepository), + getAutoSuggestions: new GetAutoSuggestionsUseCase(covid19InfoApiRepository), exportStructures: new ExportStructuresUseCase(dataGridRepository), - addDynamicInfo: new AddDynamicInfoToCovid19InfoUseCase( - covid19InfoRepository, - cacheRepository - ), ligands: { getIDR: new GetLigandImageDataResourcesUseCase( ligandsRepository, @@ -35,6 +34,10 @@ export function getCompositionRoot() { organismRepository ), }, + entities: { + getPartialNMR: new GetPartialNMRTargetUseCase(entitiesRepository), + saveNMR: new SaveNMRTargetUseCase(entitiesRepository), + }, }; } diff --git a/app/assets/javascripts/covid19/src/data/Covid19Data.types.ts b/app/assets/javascripts/covid19/src/data/Covid19Data.types.ts index 45eac5eba..0c1f459a9 100644 --- a/app/assets/javascripts/covid19/src/data/Covid19Data.types.ts +++ b/app/assets/javascripts/covid19/src/data/Covid19Data.types.ts @@ -22,6 +22,9 @@ export interface Entity { isAntibody: boolean; isNanobody: boolean; isSybody: boolean; + seq_align_begin: number | undefined; + seq_align_end: number | undefined; + xRef: { xDB: string; xDB_code: string }[] | undefined; } export interface Ligand { diff --git a/app/assets/javascripts/covid19/src/data/LigandToImageData.ts b/app/assets/javascripts/covid19/src/data/LigandToImageData.ts index 566072924..b376b9cc0 100644 --- a/app/assets/javascripts/covid19/src/data/LigandToImageData.ts +++ b/app/assets/javascripts/covid19/src/data/LigandToImageData.ts @@ -4,9 +4,9 @@ import { Codec, exactly, GetType, + nullable, nullType, number, - oneOf, optional, string, } from "purify-ts"; @@ -22,18 +22,14 @@ import { } from "../domain/entities/LigandImageData"; import { Ontology, OntologyTerm as BioOntologyTerm } from "../domain/entities/Ontology"; -function maybeNull(type: Codec) { - return oneOf([type, nullType]); -} - const additionalAnalysisC = Codec.interface({ name: string, relation: exactly("'<'", "'>'", "'='"), value: number, description: string, - units: maybeNull(string), - pvalue: maybeNull(number), - dataComment: maybeNull(string), + units: nullable(string), + pvalue: nullable(number), + dataComment: nullable(string), }); const wellC = Codec.interface({ @@ -45,7 +41,7 @@ const wellC = Codec.interface({ cellLine: string, controlType: optional(string), qualityControl: string, - micromolarConcentration: maybeNull(number), + micromolarConcentration: nullable(number), percentageInhibition: number, hitOver75Activity: string, numberCells: number, @@ -121,18 +117,22 @@ const imageDataC = Codec.interface({ assays: array(assayC), }); -export const pdbLigandC = Codec.interface({ +export const commonLigand = { IUPACInChIkey: string, - dbId: string, - pubChemCompoundId: string, name: string, formula: string, formula_weight: number, imageLink: string, externalLink: string, + pubChemCompoundId: string, IUPACInChI: string, isomericSMILES: string, canonicalSMILES: string, +}; + +export const pdbLigandC = Codec.interface({ + ...commonLigand, + dbId: string, imageData: optional(array(imageDataC)), //it shouldn't be an array... }); @@ -140,8 +140,8 @@ export const pdbLigandsC = array(pdbLigandC); export const pdbEntryResponseC = Codec.interface({ count: number, - next: maybeNull(string), - previous: maybeNull(string), + next: nullable(string), + previous: nullable(string), results: pdbLigandsC, }); diff --git a/app/assets/javascripts/covid19/src/data/LocalStorageProvider.ts b/app/assets/javascripts/covid19/src/data/LocalStorageProvider.ts new file mode 100644 index 000000000..8424f638f --- /dev/null +++ b/app/assets/javascripts/covid19/src/data/LocalStorageProvider.ts @@ -0,0 +1,26 @@ +import { StorageProvider } from "../domain/usecases/common/StorageProvider"; + +export class LocalStorageProvider implements StorageProvider { + private getFromLocalStorage(key: string): T | undefined { + const value = localStorage.getItem(key); + return value === null ? undefined : (JSON.parse(value) as T); + } + + private set(key: string, value: T): void { + const json = JSON.stringify(value); + localStorage.setItem(key, json); + } + + get(options: { key: string; getter: () => T }): T { + const { key, getter } = options; + const valueFromCache = this.getFromLocalStorage(key); + + if (valueFromCache !== undefined) { + return valueFromCache; + } else { + const value = getter(); + this.set(key, value); + return value; + } + } +} diff --git a/app/assets/javascripts/covid19/src/data/NMRScreening.ts b/app/assets/javascripts/covid19/src/data/NMRScreening.ts new file mode 100644 index 000000000..91600a730 --- /dev/null +++ b/app/assets/javascripts/covid19/src/data/NMRScreening.ts @@ -0,0 +1,28 @@ +import _ from "lodash"; +import { Codec, GetType, nullType, number, oneOf, string } from "purify-ts"; +import { commonLigand, pdbLigandC } from "./LigandToImageData"; + +const featureTypeCodec = Codec.interface({ + dataSource: string, + name: string, // binding | not binding + description: string, + externalLink: string, +}); + +export const nmrFragmentCodec = Codec.interface({ + name: string, + description: string, + externalLink: string, + pdbentry: nullType, + uniprotentry: string, + ligandentity: oneOf([Codec.interface(commonLigand), pdbLigandC]), + details: Codec.interface({ + type: string, // binding | notbinding + entity: string, // NMR Target + }), + start: number, + end: number, + featureType: featureTypeCodec, +}); + +export type NMRScreeningFragment = GetType; diff --git a/app/assets/javascripts/covid19/src/data/Ontologies.ts b/app/assets/javascripts/covid19/src/data/Ontologies.ts index 31f0e1ddb..cda3f0126 100644 --- a/app/assets/javascripts/covid19/src/data/Ontologies.ts +++ b/app/assets/javascripts/covid19/src/data/Ontologies.ts @@ -1,14 +1,10 @@ -import { array, Codec, GetType, nullType, number, oneOf, string } from "purify-ts"; - -function maybeNull(type: Codec) { - return oneOf([type, nullType]); -} +import { array, Codec, GetType, nullable, number, string } from "purify-ts"; function getOntologiesResponse(codec: Codec) { return Codec.interface({ count: number, - next: maybeNull(string), - previous: maybeNull(string), + next: nullable(string), + previous: nullable(string), results: codec, }); } diff --git a/app/assets/javascripts/covid19/src/data/Organisms.ts b/app/assets/javascripts/covid19/src/data/Organisms.ts index f71d93e18..8e8a9877d 100644 --- a/app/assets/javascripts/covid19/src/data/Organisms.ts +++ b/app/assets/javascripts/covid19/src/data/Organisms.ts @@ -1,16 +1,11 @@ -import _ from "lodash"; -import { array, Codec, GetType, nullType, number, oneOf, string } from "purify-ts"; +import { array, Codec, GetType, nullable, number, string } from "purify-ts"; import { Organism } from "../domain/entities/LigandImageData"; -function maybeNull(type: Codec) { - return oneOf([type, nullType]); -} - function getOrganismsResponse(codec: Codec) { return Codec.interface({ count: number, - next: maybeNull(string), - previous: maybeNull(string), + next: nullable(string), + previous: nullable(string), results: codec, }); } diff --git a/app/assets/javascripts/covid19/src/data/codec-utils.ts b/app/assets/javascripts/covid19/src/data/codec-utils.ts new file mode 100644 index 000000000..0f3309491 --- /dev/null +++ b/app/assets/javascripts/covid19/src/data/codec-utils.ts @@ -0,0 +1,21 @@ +import { Codec, array, nullable, number, string } from "purify-ts"; + +export function paginationCodec(type: Codec): Codec> { + return Codec.interface({ + count: number, + next: nullable(string), + previous: nullable(string), + results: array(type), + }); +} + +export function getResults(pagination?: Pagination) { + return pagination?.results ?? []; +} + +export type Pagination = { + count: number; + next: string | null; + previous: string | null; + results: K[]; +}; diff --git a/app/assets/javascripts/covid19/src/data/covid19-data.ts b/app/assets/javascripts/covid19/src/data/covid19-data.ts index 94771b16d..3e1d7fc41 100644 --- a/app/assets/javascripts/covid19/src/data/covid19-data.ts +++ b/app/assets/javascripts/covid19/src/data/covid19-data.ts @@ -12,7 +12,7 @@ export const data: Covid19Data = { { ncbi_taxonomy_id: "10090", scientific_name: "Mus musculus", - common_name: "house mouse", + common_name: "", externalLink: "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090", }, { @@ -23,7 +23,7 @@ export const data: Covid19Data = { }, { ncbi_taxonomy_id: "10665", - scientific_name: "Enterobacteria phage T4", + scientific_name: "Tequatrovirus T4", common_name: "", externalLink: "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10665", }, @@ -54,7 +54,7 @@ export const data: Covid19Data = { { ncbi_taxonomy_id: "30538", scientific_name: "Vicugna pacos", - common_name: "", + common_name: "alpaca", externalLink: "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=30538", }, { @@ -93,6 +93,12 @@ export const data: Covid19Data = { common_name: "", externalLink: "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=452646", }, + { + ncbi_taxonomy_id: "4932", + scientific_name: "Saccharomyces cerevisiae", + common_name: "baker's yeast", + externalLink: "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4932", + }, { ncbi_taxonomy_id: "562", scientific_name: "Escherichia coli", @@ -162,7 +168,7 @@ export const data: Covid19Data = { { ncbi_taxonomy_id: "9685", scientific_name: "Felis catus", - common_name: "domestic cat", + common_name: "Cat", externalLink: "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9685", }, { @@ -234,7 +240,7 @@ export const data: Covid19Data = { { ncbi_taxonomy_id: "9986", scientific_name: "Oryctolagus cuniculus", - common_name: "rabbit", + common_name: "", externalLink: "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9986", }, ], @@ -303,6 +309,30 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ORHBXUUXSCNDEV-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/5281426", }, + { + IUPACInChIkey: "QBWBVQMSMXVSSF-NJBJSMFESA-N", + dbId: "0AX", + pubChemCompoundId: "168654837", + name: + "N-[(2S)-3-cyclohexyl-1-oxidanylidene-1-[[(2S,3R)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide", + details: + "N-[(2S)-3-cyclohexyl-1-oxidanylidene-1-[[(2S,3R)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QBWBVQMSMXVSSF-NJBJSMFESA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168654837", + }, + { + IUPACInChIkey: "FLHCDUBGBDAQOK-PETUGJSASA-N", + dbId: "0BO", + pubChemCompoundId: "168654838", + name: + "N-[(2S)-3-cyclohexyl-1-[[(2S,3R)-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-benzofuran-2-carboxamide", + details: + "N-[(2S)-3-cyclohexyl-1-[[(2S,3R)-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-benzofuran-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FLHCDUBGBDAQOK-PETUGJSASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168654838", + }, { IUPACInChIkey: "JXGIYKRRPGCLFV-JOCHJYFZSA-N", dbId: "0EN", @@ -2578,6 +2608,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RYHBNJHYFVUHQT-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/31275", }, + { + IUPACInChIkey: "POTVAILTNPOQJH-UHFFFAOYSA-N", + dbId: "DJU", + pubChemCompoundId: "73814", + name: "N,N-dimethyl-1-(5-phenylmethoxy-1H-indol-3-yl)methanamine", + details: "N,N-dimethyl-1-(5-phenylmethoxy-1H-indol-3-yl)methanamine", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/POTVAILTNPOQJH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/73814", + }, { IUPACInChIkey: "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", dbId: "DMS", @@ -4310,16 +4350,6 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JMYSPFGUBNENSE-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/2777223", }, - { - IUPACInChIkey: "WFEGFRJBAYCOHP-UHFFFAOYSA-N", - dbId: "K34", - pubChemCompoundId: "57116692", - name: "5-(1,3-thiazol-2-yl)-1H-1,2,4-triazole", - details: "5-(1,3-thiazol-2-yl)-1H-1,2,4-triazole", - imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WFEGFRJBAYCOHP-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/57116692", - }, { IUPACInChIkey: "BSPZFJDYQHDZNR-BOSXTWCSSA-N", dbId: "K36", @@ -4386,6 +4416,99 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LBLGMVCPRZTJIF-SFHVURJKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168477802", }, + { + IUPACInChIkey: "VNWMUCGFGSYBMK-OAHLLOKOSA-N", + dbId: "KFU", + pubChemCompoundId: "156906799", + name: "(3S)-5-chloro-N-(isoquinolin-4-yl)-2,3-dihydro-1-benzofuran-3-carboxamide", + details: "(3S)-5-chloro-N-(isoquinolin-4-yl)-2,3-dihydro-1-benzofuran-3-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VNWMUCGFGSYBMK-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906799", + }, + { + IUPACInChIkey: "YAYDSAMHSQCKIM-OAQYLSRUSA-N", + dbId: "KG9", + pubChemCompoundId: "156906151", + name: + "(4S)-6-chloro-2-[(1-cyanocyclopropyl)methanesulfonyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[(1-cyanocyclopropyl)methanesulfonyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YAYDSAMHSQCKIM-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906151", + }, + { + IUPACInChIkey: "OZRCAPIRQWCXDS-UHFFFAOYSA-N", + dbId: "KJI", + pubChemCompoundId: "154851708", + name: "N-(4-methylpyridin-3-yl)-N~2~-(quinolin-4-yl)glycinamide", + details: "N-(4-methylpyridin-3-yl)-N~2~-(quinolin-4-yl)glycinamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OZRCAPIRQWCXDS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154851708", + }, + { + IUPACInChIkey: "SAMABBIQJZLRPK-UHFFFAOYSA-N", + dbId: "KJO", + pubChemCompoundId: "154875870", + name: "N-phenyl-2-(pyridin-3-yl)prop-2-enamide", + details: "N-phenyl-2-(pyridin-3-yl)prop-2-enamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SAMABBIQJZLRPK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154875870", + }, + { + IUPACInChIkey: "QNNCYWWAACHETJ-UHFFFAOYSA-N", + dbId: "KL6", + pubChemCompoundId: "169408165", + name: "1-{2-[(methanesulfonyl)amino]ethyl}-1,2,3,4-tetrahydroquinoline-7-sulfonamide", + details: + "1-{2-[(methanesulfonyl)amino]ethyl}-1,2,3,4-tetrahydroquinoline-7-sulfonamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QNNCYWWAACHETJ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408165", + }, + { + IUPACInChIkey: "OUPPHPJHMDQSCE-SFHVURJKSA-N", + dbId: "KLR", + pubChemCompoundId: "169408166", + name: "(2S)-N-tert-butyl-2-[4-(2-cyanoethyl)anilino]-2-(pyridin-3-yl)acetamide", + details: "(2S)-N-tert-butyl-2-[4-(2-cyanoethyl)anilino]-2-(pyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OUPPHPJHMDQSCE-SFHVURJKSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408166", + }, + { + IUPACInChIkey: "AYUDXVQMLKGODN-UHFFFAOYSA-N", + dbId: "KM6", + pubChemCompoundId: "11600777", + name: "2-(4-chlorophenyl)-1,3,4-oxadiazole", + details: "2-(4-chlorophenyl)-1,3,4-oxadiazole", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AYUDXVQMLKGODN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/11600777", + }, + { + IUPACInChIkey: "FZEKPYMSMRNNKF-UHFFFAOYSA-N", + dbId: "KMF", + pubChemCompoundId: "169452747", + name: "N-[2-(4-acetylpiperazin-1-yl)ethyl]naphthalene-1-carboxamide", + details: "N-[2-(4-acetylpiperazin-1-yl)ethyl]naphthalene-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FZEKPYMSMRNNKF-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452747", + }, + { + IUPACInChIkey: "CZSFWPWYLTWYHF-UHFFFAOYSA-N", + dbId: "KMX", + pubChemCompoundId: "169452748", + name: "1-{4-[(2-benzyl-1,3-thiazol-5-yl)methyl]piperazin-1-yl}ethan-1-one", + details: "1-{4-[(2-benzyl-1,3-thiazol-5-yl)methyl]piperazin-1-yl}ethan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CZSFWPWYLTWYHF-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452748", + }, { IUPACInChIkey: "KHZWIIFEFQBNKL-UHFFFAOYSA-N", dbId: "KNL", @@ -4396,6 +4519,172 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KHZWIIFEFQBNKL-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/11332", }, + { + IUPACInChIkey: "UITKLCSYIUGNOE-LURJTMIESA-N", + dbId: "KNU", + pubChemCompoundId: "169452749", + name: "N-[(1S)-1-(3-chloro-5-fluorophenyl)ethyl]acetamide", + details: "N-[(1S)-1-(3-chloro-5-fluorophenyl)ethyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UITKLCSYIUGNOE-LURJTMIESA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452749", + }, + { + IUPACInChIkey: "NFHVZMZTKNOYHY-UHFFFAOYSA-N", + dbId: "KO9", + pubChemCompoundId: "154851698", + name: "N-(5-cyanopyridin-3-yl)-2-(pyridin-3-yl)acetamide", + details: "N-(5-cyanopyridin-3-yl)-2-(pyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NFHVZMZTKNOYHY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154851698", + }, + { + IUPACInChIkey: "JXVSAHMJMLDNGG-UHFFFAOYSA-N", + dbId: "KOI", + pubChemCompoundId: "95212045", + name: "2-(3-chlorophenyl)-N-(pyridin-3-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(pyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JXVSAHMJMLDNGG-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/95212045", + }, + { + IUPACInChIkey: "GCADPMUYKNHGSM-UHFFFAOYSA-N", + dbId: "KP0", + pubChemCompoundId: "156907267", + name: "N-(3-chlorophenyl)-N-(2-cyclohexylethyl)-N'-(pyridin-3-yl)urea", + details: "N-(3-chlorophenyl)-N-(2-cyclohexylethyl)-N'-(pyridin-3-yl)urea", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GCADPMUYKNHGSM-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907267", + }, + { + IUPACInChIkey: "MLWZGJVGRRIOOY-UHFFFAOYSA-N", + dbId: "KQ3", + pubChemCompoundId: "156907266", + name: "N-(3-chlorophenyl)-N-[2-(morpholin-4-yl)ethyl]-N'-(pyridin-3-yl)urea", + details: "N-(3-chlorophenyl)-N-[2-(morpholin-4-yl)ethyl]-N'-(pyridin-3-yl)urea", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MLWZGJVGRRIOOY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907266", + }, + { + IUPACInChIkey: "XYFCSWHALYQBPC-UHFFFAOYSA-N", + dbId: "KQL", + pubChemCompoundId: "169408170", + name: "N-(4-methylpyridin-3-yl)-2-[3-(trifluoromethyl)phenyl]acetamide", + details: "N-(4-methylpyridin-3-yl)-2-[3-(trifluoromethyl)phenyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XYFCSWHALYQBPC-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408170", + }, + { + IUPACInChIkey: "ADHDKMXDJWXBNY-UHFFFAOYSA-N", + dbId: "KQX", + pubChemCompoundId: "169408171", + name: "2-(4-methylphenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(4-methylphenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ADHDKMXDJWXBNY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408171", + }, + { + IUPACInChIkey: "DFWHOCVEAQNIBM-UHFFFAOYSA-N", + dbId: "KS0", + pubChemCompoundId: "19323503", + name: "1-{4-[(4-fluorophenyl)methyl]piperazin-1-yl}propan-1-one", + details: "1-{4-[(4-fluorophenyl)methyl]piperazin-1-yl}propan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DFWHOCVEAQNIBM-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/19323503", + }, + { + IUPACInChIkey: "NQWZHKWPOKKPNU-KRWDZBQOSA-N", + dbId: "KSI", + pubChemCompoundId: "169452750", + name: "1-[(3S)-4-[(3-chlorophenyl)methyl]-3-(2-methylpropyl)piperazin-1-yl]ethan-1-one", + details: + "1-[(3S)-4-[(3-chlorophenyl)methyl]-3-(2-methylpropyl)piperazin-1-yl]ethan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NQWZHKWPOKKPNU-KRWDZBQOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452750", + }, + { + IUPACInChIkey: "MAYMKKDCBJTHBQ-UHFFFAOYSA-N", + dbId: "KSX", + pubChemCompoundId: "154875993", + name: "2-(5-cyanopyridin-3-yl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(5-cyanopyridin-3-yl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MAYMKKDCBJTHBQ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154875993", + }, + { + IUPACInChIkey: "BBXRTGNKDKIMPV-INIZCTEOSA-N", + dbId: "KT9", + pubChemCompoundId: "169408174", + name: "N-(3-methyl-5-{[(2S)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyrimidin-5-yl)acetamide", + details: + "N-(3-methyl-5-{[(2S)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyrimidin-5-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BBXRTGNKDKIMPV-INIZCTEOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408174", + }, + { + IUPACInChIkey: "MMSFMHOFPDOWCH-LLVKDONJSA-N", + dbId: "KU6", + pubChemCompoundId: "156907138", + name: + "(4R)-6-chloro-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MMSFMHOFPDOWCH-LLVKDONJSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907138", + }, + { + IUPACInChIkey: "AIEXTLCJBMNDNF-MRXNPFEDSA-N", + dbId: "KUU", + pubChemCompoundId: "169408175", + name: "(2R)-2-(3-chlorophenyl)-3-methyl-N-(4-methylpyridin-3-yl)butanamide", + details: "(2R)-2-(3-chlorophenyl)-3-methyl-N-(4-methylpyridin-3-yl)butanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AIEXTLCJBMNDNF-MRXNPFEDSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408175", + }, + { + IUPACInChIkey: "AATSBPIJUYIMKX-ZDUSSCGKSA-N", + dbId: "KVF", + pubChemCompoundId: "169408176", + name: "(2S)-2-(3-chlorophenyl)-N-(5-methylpyridazin-4-yl)butanamide", + details: "(2S)-2-(3-chlorophenyl)-N-(5-methylpyridazin-4-yl)butanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AATSBPIJUYIMKX-ZDUSSCGKSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408176", + }, + { + IUPACInChIkey: "XEOITIZTKXMLOT-UHFFFAOYSA-N", + dbId: "KVO", + pubChemCompoundId: "167888283", + name: "2-(3-chlorophenyl)-N-(2,4-dimethylpyridin-3-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(2,4-dimethylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XEOITIZTKXMLOT-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/167888283", + }, + { + IUPACInChIkey: "BWTWLKMAKBVNDU-GFCCVEGCSA-N", + dbId: "KVX", + pubChemCompoundId: "156907197", + name: + "(3S)-5-chloro-N-[4-(hydroxymethyl)pyridin-3-yl]-2,3-dihydro-1-benzofuran-3-carboxamide", + details: + "(3S)-5-chloro-N-[4-(hydroxymethyl)pyridin-3-yl]-2,3-dihydro-1-benzofuran-3-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BWTWLKMAKBVNDU-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907197", + }, { IUPACInChIkey: "ILUKGDRLISPDRN-WGQQHEPDSA-N", dbId: "KW6", @@ -4408,6 +4697,88 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ILUKGDRLISPDRN-WGQQHEPDSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168300959", }, + { + IUPACInChIkey: "KKIJAAYVRSUCNW-UHFFFAOYSA-N", + dbId: "KW9", + pubChemCompoundId: "154861447", + name: "7-fluoro-N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + details: + "7-fluoro-N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KKIJAAYVRSUCNW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154861447", + }, + { + IUPACInChIkey: "OCMQJJQEZJQFRH-INIZCTEOSA-N", + dbId: "KWR", + pubChemCompoundId: "169408177", + name: "N-(3-{[(2S)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyridin-3-yl)acetamide", + details: "N-(3-{[(2S)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OCMQJJQEZJQFRH-INIZCTEOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408177", + }, + { + IUPACInChIkey: "LMUJWKIRCRWFKF-GFCCVEGCSA-N", + dbId: "KX9", + pubChemCompoundId: "169408178", + name: "(2R)-2-(3-chlorophenyl)-N-[(4M)-4-(1H-pyrazol-1-yl)pyridin-3-yl]propanamide", + details: "(2R)-2-(3-chlorophenyl)-N-[(4M)-4-(1H-pyrazol-1-yl)pyridin-3-yl]propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LMUJWKIRCRWFKF-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408178", + }, + { + IUPACInChIkey: "JOMCPDPKDFHNEK-UHFFFAOYSA-N", + dbId: "KXF", + pubChemCompoundId: "63327372", + name: "2-(3-hydroxyphenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(3-hydroxyphenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JOMCPDPKDFHNEK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/63327372", + }, + { + IUPACInChIkey: "SFHHIQYDZORTHQ-HNNXBMFYSA-N", + dbId: "KXR", + pubChemCompoundId: "169408179", + name: "N-(3-fluoro-5-{[(2S)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyrimidin-5-yl)acetamide", + details: + "N-(3-fluoro-5-{[(2S)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyrimidin-5-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SFHHIQYDZORTHQ-HNNXBMFYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408179", + }, + { + IUPACInChIkey: "AIYYCYBWGZIFKY-UHFFFAOYSA-N", + dbId: "KY0", + pubChemCompoundId: "156907219", + name: "1-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)cyclopropane-1-carboxamide", + details: "1-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)cyclopropane-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AIYYCYBWGZIFKY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907219", + }, + { + IUPACInChIkey: "XRWOUNDNLXZKFZ-HNNXBMFYSA-N", + dbId: "KYC", + pubChemCompoundId: "169408180", + name: "(2S)-2-(3-chlorophenyl)-2-(dimethylamino)-N-(4-methylpyridin-3-yl)acetamide", + details: "(2S)-2-(3-chlorophenyl)-2-(dimethylamino)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XRWOUNDNLXZKFZ-HNNXBMFYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408180", + }, + { + IUPACInChIkey: "IIKFZOGWCHXLNB-UHFFFAOYSA-N", + dbId: "KYU", + pubChemCompoundId: "167807948", + name: "2-(3-chlorophenyl)-2,2-difluoro-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(3-chlorophenyl)-2,2-difluoro-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IIKFZOGWCHXLNB-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/167807948", + }, { IUPACInChIkey: "RICRAVHJCLFPFF-UHFFFAOYSA-N", dbId: "KZ0", @@ -4418,6 +4789,37 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RICRAVHJCLFPFF-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/778089", }, + { + IUPACInChIkey: "FTMBCXQGAOJUAX-UHFFFAOYSA-N", + dbId: "KZC", + pubChemCompoundId: "154861204", + name: "N-(2-anilinoethyl)-2-oxo-1,2-dihydroquinoline-4-carboxamide", + details: "N-(2-anilinoethyl)-2-oxo-1,2-dihydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FTMBCXQGAOJUAX-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154861204", + }, + { + IUPACInChIkey: "MLLQAKCWQMHQOK-UHFFFAOYSA-N", + dbId: "KZX", + pubChemCompoundId: "154859403", + name: "2-(3-fluorophenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(3-fluorophenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MLLQAKCWQMHQOK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154859403", + }, + { + IUPACInChIkey: "BIHUQYISOBUTJB-UHFFFAOYSA-N", + dbId: "L1F", + pubChemCompoundId: "154857678", + name: "N-[2-(2-methoxyphenoxy)ethyl]-N-methyl-2-oxo-1,2-dihydroquinoline-4-carboxamide", + details: + "N-[2-(2-methoxyphenoxy)ethyl]-N-methyl-2-oxo-1,2-dihydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BIHUQYISOBUTJB-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154857678", + }, { IUPACInChIkey: "SEOHEWZQAGEAGZ-SHYZEUOFSA-N", dbId: "L2B", @@ -4428,6 +4830,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SEOHEWZQAGEAGZ-SHYZEUOFSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/16220805", }, + { + IUPACInChIkey: "AMGHFKIRDXLNJU-HNNXBMFYSA-N", + dbId: "L2I", + pubChemCompoundId: "169408181", + name: "(2S)-4-(methylamino)-2-phenyl-N-(pyridin-3-yl)butanamide", + details: "(2S)-4-(methylamino)-2-phenyl-N-(pyridin-3-yl)butanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AMGHFKIRDXLNJU-HNNXBMFYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408181", + }, { IUPACInChIkey: "OZOFJVFWGZHBHV-UHFFFAOYSA-N", dbId: "L30", @@ -4438,6 +4850,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OZOFJVFWGZHBHV-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/532824", }, + { + IUPACInChIkey: "QOWQEKIGADCHLL-UHFFFAOYSA-N", + dbId: "L3I", + pubChemCompoundId: "154861288", + name: "2-(3-chlorophenyl)-2-methyl-N-(4-methylpyridin-3-yl)propanamide", + details: "2-(3-chlorophenyl)-2-methyl-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QOWQEKIGADCHLL-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154861288", + }, { IUPACInChIkey: "LCSLEHAEHBSCSA-UHFFFAOYSA-N", dbId: "L46", @@ -4448,6 +4870,150 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LCSLEHAEHBSCSA-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/47265390", }, + { + IUPACInChIkey: "FNCISWRYQRGLKF-LLVKDONJSA-N", + dbId: "L4N", + pubChemCompoundId: "169408185", + name: "(5R)-N-(4-methylpyridin-3-yl)spiro[2.4]heptane-5-carboxamide", + details: "(5R)-N-(4-methylpyridin-3-yl)spiro[2.4]heptane-5-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FNCISWRYQRGLKF-LLVKDONJSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408185", + }, + { + IUPACInChIkey: "PPQIRWKGFHIKDH-NSHDSACASA-N", + dbId: "L4U", + pubChemCompoundId: "169408184", + name: "(3S)-3,4-dimethyl-N-(4-methylpyridin-3-yl)pentanamide", + details: "(3S)-3,4-dimethyl-N-(4-methylpyridin-3-yl)pentanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PPQIRWKGFHIKDH-NSHDSACASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408184", + }, + { + IUPACInChIkey: "SRXLGHBNKKQZHE-SNVBAGLBSA-N", + dbId: "L5I", + pubChemCompoundId: "169408183", + name: "(2R)-3-cyclopropyl-2-methyl-N-(4-methylpyridin-3-yl)propanamide", + details: "(2R)-3-cyclopropyl-2-methyl-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SRXLGHBNKKQZHE-SNVBAGLBSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408183", + }, + { + IUPACInChIkey: "YHLCUCKEOZVUDL-UHFFFAOYSA-N", + dbId: "L6D", + pubChemCompoundId: "154858286", + name: "N-(1H-benzimidazol-1-yl)-2-(3-chlorophenyl)acetamide", + details: "N-(1H-benzimidazol-1-yl)-2-(3-chlorophenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YHLCUCKEOZVUDL-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154858286", + }, + { + IUPACInChIkey: "QJMYJFPUHDEEBX-OAHLLOKOSA-N", + dbId: "L6R", + pubChemCompoundId: "169408182", + name: "(2R)-2-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)pentanamide", + details: "(2R)-2-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)pentanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QJMYJFPUHDEEBX-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408182", + }, + { + IUPACInChIkey: "ZVPGUVBZPWGJPX-RISCZKNCSA-N", + dbId: "L7F", + pubChemCompoundId: "169408186", + name: "2-[(1S,5R)-bicyclo[3.1.0]hexan-1-yl]-N-(4-methylpyridin-3-yl)acetamide", + details: "2-[(1S,5R)-bicyclo[3.1.0]hexan-1-yl]-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZVPGUVBZPWGJPX-RISCZKNCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408186", + }, + { + IUPACInChIkey: "BLCPNJMZJGFGAP-UHFFFAOYSA-N", + dbId: "L7Q", + pubChemCompoundId: "154859404", + name: "3-methyl-N-(4-methylpyridin-3-yl)-3-phenylbutanamide", + details: "3-methyl-N-(4-methylpyridin-3-yl)-3-phenylbutanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BLCPNJMZJGFGAP-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154859404", + }, + { + IUPACInChIkey: "SHUFUJKRBBPZHJ-ZDUSSCGKSA-N", + dbId: "L7V", + pubChemCompoundId: "97012525", + name: + "1-[(2S)-2-(5-cyclopropyl-1,2,4-oxadiazol-3-yl)pyrrolidin-1-yl]-2-(pyridin-3-yl)ethan-1-one", + details: + "1-[(2S)-2-(5-cyclopropyl-1,2,4-oxadiazol-3-yl)pyrrolidin-1-yl]-2-(pyridin-3-yl)ethan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SHUFUJKRBBPZHJ-ZDUSSCGKSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/97012525", + }, + { + IUPACInChIkey: "HMBNRINOSXPSCN-UHFFFAOYSA-N", + dbId: "L83", + pubChemCompoundId: "154875997", + name: "N-(2-amino-4-methylpyridin-3-yl)-2-(3-chlorophenyl)acetamide", + details: "N-(2-amino-4-methylpyridin-3-yl)-2-(3-chlorophenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HMBNRINOSXPSCN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154875997", + }, + { + IUPACInChIkey: "KKPILUQDBWPVTM-UHFFFAOYSA-N", + dbId: "L8F", + pubChemCompoundId: "154706032", + name: "N-(2-{7-[(4-acetylpiperazin-1-yl)methyl]-1H-indol-3-yl}ethyl)acetamide", + details: "N-(2-{7-[(4-acetylpiperazin-1-yl)methyl]-1H-indol-3-yl}ethyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KKPILUQDBWPVTM-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154706032", + }, + { + IUPACInChIkey: "MQSDDXXCNVJVGH-GOSISDBHSA-N", + dbId: "L8O", + pubChemCompoundId: "169452751", + name: "1-[(4R)-4-(3-methylphenyl)-3,4-dihydroisoquinolin-2(1H)-yl]ethan-1-one", + details: "1-[(4R)-4-(3-methylphenyl)-3,4-dihydroisoquinolin-2(1H)-yl]ethan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MQSDDXXCNVJVGH-GOSISDBHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452751", + }, + { + IUPACInChIkey: "LZQQUMOUOYPMFQ-GFCCVEGCSA-N", + dbId: "L93", + pubChemCompoundId: "169408189", + name: + "6-fluoro-N-[(2R)-2-(2-methoxyphenoxy)propyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + details: + "6-fluoro-N-[(2R)-2-(2-methoxyphenoxy)propyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LZQQUMOUOYPMFQ-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408189", + }, + { + IUPACInChIkey: "GSEMEGPVJJVGNC-GFCCVEGCSA-N", + dbId: "L9F", + pubChemCompoundId: "169408190", + name: "(3P,5R)-3-(3-chlorophenyl)-5-(pyridin-3-yl)imidazolidine-2,4-dione", + details: "(3P,5R)-3-(3-chlorophenyl)-5-(pyridin-3-yl)imidazolidine-2,4-dione", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GSEMEGPVJJVGNC-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408190", + }, + { + IUPACInChIkey: "XFQCOLJIUXXMKV-LLVKDONJSA-N", + dbId: "L9O", + pubChemCompoundId: "169408191", + name: "(1S)-N-(4-methylpyridin-3-yl)spiro[3.3]heptane-1-carboxamide", + details: "(1S)-N-(4-methylpyridin-3-yl)spiro[3.3]heptane-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XFQCOLJIUXXMKV-LLVKDONJSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408191", + }, { IUPACInChIkey: "GUWSLQUAAYEZAF-UHFFFAOYSA-L", dbId: "LAC", @@ -4458,6 +5024,56 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GUWSLQUAAYEZAF-UHFFFAOYSA-L/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/9317", }, + { + IUPACInChIkey: "SPZNGMCOZXKTMM-UHFFFAOYSA-N", + dbId: "LB0", + pubChemCompoundId: "154866117", + name: "(1r,3r)-3-cyclopropyl-N-(4-methylpyridin-3-yl)cyclobutane-1-carboxamide", + details: "(1r,3r)-3-cyclopropyl-N-(4-methylpyridin-3-yl)cyclobutane-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SPZNGMCOZXKTMM-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154866117", + }, + { + IUPACInChIkey: "MUVSGYUDBWMCJG-UHFFFAOYSA-N", + dbId: "LBC", + pubChemCompoundId: "154862362", + name: "2-(3-iodophenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(3-iodophenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MUVSGYUDBWMCJG-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154862362", + }, + { + IUPACInChIkey: "PTTAFUMPUWHBTC-UHFFFAOYSA-N", + dbId: "LBO", + pubChemCompoundId: "154864737", + name: "2-(3-cyclopropylphenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(3-cyclopropylphenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PTTAFUMPUWHBTC-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154864737", + }, + { + IUPACInChIkey: "WEHZCBNACMTKKE-YOGCLGLASA-N", + dbId: "LCU", + pubChemCompoundId: "169408192", + name: "2-[(1R,3s,5S)-bicyclo[3.1.0]hexan-3-yl]-N-(4-methylpyridin-3-yl)acetamide", + details: "2-[(1R,3s,5S)-bicyclo[3.1.0]hexan-3-yl]-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WEHZCBNACMTKKE-YOGCLGLASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408192", + }, + { + IUPACInChIkey: "QOFPSTBMBIOUPW-UHFFFAOYSA-N", + dbId: "LDX", + pubChemCompoundId: "154859412", + name: "3-(2-fluorophenyl)-N-(4-methylpyridin-3-yl)propanamide", + details: "3-(2-fluorophenyl)-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QOFPSTBMBIOUPW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154859412", + }, { IUPACInChIkey: "ROHFNLRQFUQHCH-YFKPBYRVSA-N", dbId: "LEU", @@ -4468,6 +5084,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ROHFNLRQFUQHCH-YFKPBYRVSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/6106", }, + { + IUPACInChIkey: "SHDRXRMTUQTXFE-UHFFFAOYSA-N", + dbId: "LF3", + pubChemCompoundId: "154859410", + name: + "2-(6-chloro-3-oxo-2,3-dihydro-4H-1,4-benzoxazin-4-yl)-N-(4-methylpyridin-3-yl)acetamide", + details: + "2-(6-chloro-3-oxo-2,3-dihydro-4H-1,4-benzoxazin-4-yl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SHDRXRMTUQTXFE-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154859410", + }, { IUPACInChIkey: "QUKZXHGECCPEIZ-JGVFFNPUSA-N", dbId: "LF6", @@ -4500,16 +5128,6 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VCOQVAJFXPHUAM-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/793024", }, - { - IUPACInChIkey: "HOQHKYACTYMRFK-UHFFFAOYSA-N", - dbId: "LHR", - pubChemCompoundId: "4198553", - name: "N-(1H-indazol-6-yl)acetamide", - details: "N-(1H-indazol-6-yl)acetamide", - imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HOQHKYACTYMRFK-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/4198553", - }, { IUPACInChIkey: "HBBGRARXTFLTSG-UHFFFAOYSA-N", dbId: "LI", @@ -4520,6 +5138,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HBBGRARXTFLTSG-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/28486", }, + { + IUPACInChIkey: "UPGQLXSOIHDKRZ-QYJAPNMZSA-N", + dbId: "LJ0", + pubChemCompoundId: "169408194", + name: "(1R,6S,7r)-N-(4-methylpyridin-3-yl)bicyclo[4.1.0]heptane-7-carboxamide", + details: "(1R,6S,7r)-N-(4-methylpyridin-3-yl)bicyclo[4.1.0]heptane-7-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UPGQLXSOIHDKRZ-QYJAPNMZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408194", + }, { IUPACInChIkey: "NIHQHFJWDDQIMY-SSDOTTSWSA-N", dbId: "LJ6", @@ -4550,6 +5178,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZDAUOJUKQPYKAC-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/53501411", }, + { + IUPACInChIkey: "UDNOYHYGEXMWIJ-GFCCVEGCSA-N", + dbId: "LJO", + pubChemCompoundId: "169408193", + name: "(3R)-3-cyano-N-(4-methylpyridin-3-yl)oxolane-3-carboxamide", + details: "(3R)-3-cyano-N-(4-methylpyridin-3-yl)oxolane-3-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UDNOYHYGEXMWIJ-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408193", + }, { IUPACInChIkey: "PFWYRMPHHJKJBB-UHFFFAOYSA-N", dbId: "LJR", @@ -4570,6 +5208,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LMUYJJAKMZKBHS-SECBINFHSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/93848778", }, + { + IUPACInChIkey: "XFTYNEPZRSHDOA-UHFFFAOYSA-N", + dbId: "LKI", + pubChemCompoundId: "154864173", + name: "3-chloro-N-(4-methylpyridin-3-yl)benzene-1-sulfonamide", + details: "3-chloro-N-(4-methylpyridin-3-yl)benzene-1-sulfonamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XFTYNEPZRSHDOA-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154864173", + }, { IUPACInChIkey: "WBIQOAOWXPGYEU-UHFFFAOYSA-N", dbId: "LKL", @@ -4580,6 +5228,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WBIQOAOWXPGYEU-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/79727358", }, + { + IUPACInChIkey: "SOEDEYVDCDYMMH-UHFFFAOYSA-N", + dbId: "LKR", + pubChemCompoundId: "5281692", + name: "3,7-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one", + details: "3,7-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SOEDEYVDCDYMMH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/5281692", + }, { IUPACInChIkey: "HSWJYBWHEHPWSP-UHFFFAOYSA-N", dbId: "LKU", @@ -4590,6 +5248,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HSWJYBWHEHPWSP-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/837703", }, + { + IUPACInChIkey: "IADLNEMEFCQDCX-UHFFFAOYSA-N", + dbId: "LKX", + pubChemCompoundId: "154860168", + name: "2-(3-chlorophenyl)-N-(5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IADLNEMEFCQDCX-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154860168", + }, { IUPACInChIkey: "XDODAVQVIOWLPT-UHFFFAOYSA-N", dbId: "LL0", @@ -4610,6 +5278,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MMWXPDDADHYFFS-LURJTMIESA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/8042141", }, + { + IUPACInChIkey: "SATVLGDJXZFYJA-ZDUSSCGKSA-N", + dbId: "LM0", + pubChemCompoundId: "169452752", + name: "(3S)-N',2-diacetyl-1,2,3,4-tetrahydroisoquinoline-3-carbohydrazide", + details: "(3S)-N',2-diacetyl-1,2,3,4-tetrahydroisoquinoline-3-carbohydrazide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SATVLGDJXZFYJA-ZDUSSCGKSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452752", + }, { IUPACInChIkey: "IPBXAQNEXLMXRW-UHFFFAOYSA-N", dbId: "LM6", @@ -4640,6 +5318,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NPBRDFPBRHOBAK-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/43558273", }, + { + IUPACInChIkey: "NGQXLOHCACFSJS-UHFFFAOYSA-N", + dbId: "LO0", + pubChemCompoundId: "169452753", + name: "N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-2,3-dihydropyridine-4-carboxamide", + details: "N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-2,3-dihydropyridine-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NGQXLOHCACFSJS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452753", + }, { IUPACInChIkey: "KVTKFHLTYQIGCM-KNVOCYPGSA-N", dbId: "LO6", @@ -4670,6 +5358,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GIIIJZOPGUFGBF-UHFFFAOYSA-O/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/6952762", }, + { + IUPACInChIkey: "YPZKHKYPLKRQED-UHFFFAOYSA-N", + dbId: "LQ0", + pubChemCompoundId: "154859408", + name: "2-(6-chloro-1H-indol-1-yl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(6-chloro-1H-indol-1-yl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YPZKHKYPLKRQED-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154859408", + }, { IUPACInChIkey: "LTVXNUWMTTYHRL-UHFFFAOYSA-N", dbId: "LQ3", @@ -4714,6 +5412,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GFKMUMPBDKROCT-OCAPTIKFSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/129349253", }, + { + IUPACInChIkey: "HZRMBUYOMGCVMU-GOSISDBHSA-N", + dbId: "LQU", + pubChemCompoundId: "169452754", + name: "3-[(4R)-2-acetyl-1,2,3,4-tetrahydroisoquinolin-4-yl]benzonitrile", + details: "3-[(4R)-2-acetyl-1,2,3,4-tetrahydroisoquinolin-4-yl]benzonitrile", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HZRMBUYOMGCVMU-GOSISDBHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452754", + }, { IUPACInChIkey: "BFRXGCPOQMOBHK-VIFPVBQESA-N", dbId: "LQV", @@ -4734,6 +5442,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NNJVILVZKWQKPM-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/3676", }, + { + IUPACInChIkey: "OVXVQSQKNSMPOY-CYBMUJFWSA-N", + dbId: "LR0", + pubChemCompoundId: "169408195", + name: + "(7R)-N-(4-acetamidopyridin-3-yl)-4-fluorobicyclo[4.2.0]octa-1,3,5-triene-7-carboxamide", + details: + "(7R)-N-(4-acetamidopyridin-3-yl)-4-fluorobicyclo[4.2.0]octa-1,3,5-triene-7-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OVXVQSQKNSMPOY-CYBMUJFWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408195", + }, { IUPACInChIkey: "URNKFNQWYLXELN-UHFFFAOYSA-N", dbId: "LR9", @@ -4744,6 +5464,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/URNKFNQWYLXELN-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/43262925", }, + { + IUPACInChIkey: "OCRRKPZGCOGESB-UHFFFAOYSA-N", + dbId: "LRC", + pubChemCompoundId: "156907218", + name: "2-(5-chloropyridin-3-yl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(5-chloropyridin-3-yl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OCRRKPZGCOGESB-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907218", + }, { IUPACInChIkey: "BCFQGXBWVPWHCV-UHFFFAOYSA-N", dbId: "LRF", @@ -4777,11 +5507,53 @@ export const data: Covid19Data = { externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/288839", }, { - IUPACInChIkey: "OWETVOGOOABRTJ-UHFFFAOYSA-N", - dbId: "LUY", - pubChemCompoundId: "923827", - name: "~{N}-(2-phenylethyl)-1~{H}-benzimidazol-2-amine", - details: "~{N}-(2-phenylethyl)-1~{H}-benzimidazol-2-amine", + IUPACInChIkey: "FTEMSYPIGWJMTH-UHFFFAOYSA-N", + dbId: "LS0", + pubChemCompoundId: "154876166", + name: "2-(6-fluoro-1H-indol-1-yl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(6-fluoro-1H-indol-1-yl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FTEMSYPIGWJMTH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154876166", + }, + { + IUPACInChIkey: "OWPHHWQTUZCDRN-QGZVFWFLSA-N", + dbId: "LSF", + pubChemCompoundId: "169408199", + name: "N-(4-methylpyridin-3-yl)-2-(3-{[(2R)-4-oxoazetidin-2-yl]oxy}phenyl)acetamide", + details: "N-(4-methylpyridin-3-yl)-2-(3-{[(2R)-4-oxoazetidin-2-yl]oxy}phenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OWPHHWQTUZCDRN-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408199", + }, + { + IUPACInChIkey: "NYGOHBKHNOCJCL-UHFFFAOYSA-N", + dbId: "LT9", + pubChemCompoundId: "169408200", + name: "1-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)-3-oxocyclobutane-1-carboxamide", + details: "1-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)-3-oxocyclobutane-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NYGOHBKHNOCJCL-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408200", + }, + { + IUPACInChIkey: "JCZDGTYSQGAPDN-QGZVFWFLSA-N", + dbId: "LUC", + pubChemCompoundId: "169408201", + name: + "2-(3-chloro-5-{[(2R)-4-oxoazetidin-2-yl]oxy}phenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: + "2-(3-chloro-5-{[(2R)-4-oxoazetidin-2-yl]oxy}phenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JCZDGTYSQGAPDN-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408201", + }, + { + IUPACInChIkey: "OWETVOGOOABRTJ-UHFFFAOYSA-N", + dbId: "LUY", + pubChemCompoundId: "923827", + name: "~{N}-(2-phenylethyl)-1~{H}-benzimidazol-2-amine", + details: "~{N}-(2-phenylethyl)-1~{H}-benzimidazol-2-amine", imageLink: "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OWETVOGOOABRTJ-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/923827", @@ -4798,6 +5570,26 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UFZXDNQNUPUWBP-MJGOQNOKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/167530386", }, + { + IUPACInChIkey: "QJWPFRCAJGJSOH-UHFFFAOYSA-N", + dbId: "LV9", + pubChemCompoundId: "154864657", + name: "N-(4-benzyloxan-4-yl)-N'-(pyridin-3-yl)urea", + details: "N-(4-benzyloxan-4-yl)-N'-(pyridin-3-yl)urea", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QJWPFRCAJGJSOH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154864657", + }, + { + IUPACInChIkey: "BEZLDJLMZNYTJV-UHFFFAOYSA-N", + dbId: "LVM", + pubChemCompoundId: "169408202", + name: "N-(4-methylpyridin-3-yl)-2-(spiro[2.3]hexan-5-yl)acetamide", + details: "N-(4-methylpyridin-3-yl)-2-(spiro[2.3]hexan-5-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BEZLDJLMZNYTJV-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408202", + }, { IUPACInChIkey: "PYEYIJGOSSTTFY-XCJLJZCSSA-N", dbId: "LVX", @@ -4820,6 +5612,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CNUDBTRUORMMPA-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/7364", }, + { + IUPACInChIkey: "JFDDFGLNZWNJTK-UHFFFAOYSA-N", + dbId: "LW6", + pubChemCompoundId: "333703", + name: "1H-indole-4-carbaldehyde", + details: "1H-indole-4-carbaldehyde", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JFDDFGLNZWNJTK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/333703", + }, { IUPACInChIkey: "FSZYBIFIACXSAG-JTQLQIEISA-N", dbId: "LWA", @@ -4830,6 +5632,28 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FSZYBIFIACXSAG-JTQLQIEISA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/1086839", }, + { + IUPACInChIkey: "RMLYDSUPMGBCJP-UHFFFAOYSA-N", + dbId: "LWO", + pubChemCompoundId: "56973493", + name: + "2-(1H-benzotriazol-1-yl)-N-[4-(methylamino)phenyl]-N-[(thiophen-3-yl)methyl]acetamide", + details: + "2-(1H-benzotriazol-1-yl)-N-[4-(methylamino)phenyl]-N-[(thiophen-3-yl)methyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RMLYDSUPMGBCJP-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/56973493", + }, + { + IUPACInChIkey: "UNUUEHGQHLOCFZ-UHFFFAOYSA-N", + dbId: "LXF", + pubChemCompoundId: "169423456", + name: "N-{4-[(2-phenylethyl)sulfamoyl]-1,3-benzothiazol-2-yl}acetamide", + details: "N-{4-[(2-phenylethyl)sulfamoyl]-1,3-benzothiazol-2-yl}acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UNUUEHGQHLOCFZ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169423456", + }, { IUPACInChIkey: "BAXOFTOLAUCFNW-UHFFFAOYSA-N", dbId: "LZ1", @@ -4840,6 +5664,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BAXOFTOLAUCFNW-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/9221", }, + { + IUPACInChIkey: "FZUTWGQMCFORPQ-OAHLLOKOSA-N", + dbId: "LZX", + pubChemCompoundId: "169408207", + name: "(2R)-4-[(methanesulfonyl)amino]-2-phenyl-N-(pyridin-3-yl)butanamide", + details: "(2R)-4-[(methanesulfonyl)amino]-2-phenyl-N-(pyridin-3-yl)butanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FZUTWGQMCFORPQ-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408207", + }, { IUPACInChIkey: "WXWJUKLQMQAVFB-UYYZUGKPSA-N", dbId: "M0C", @@ -4852,6 +5686,144 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WXWJUKLQMQAVFB-UYYZUGKPSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168477804", }, + { + IUPACInChIkey: "NJXUEBRIEJJDBY-INIZCTEOSA-N", + dbId: "M0G", + pubChemCompoundId: "169408206", + name: "(2S)-2-(3-chlorophenyl)-2-hydroxy-N-(4-methylpyridin-3-yl)butanamide", + details: "(2S)-2-(3-chlorophenyl)-2-hydroxy-N-(4-methylpyridin-3-yl)butanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NJXUEBRIEJJDBY-INIZCTEOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408206", + }, + { + IUPACInChIkey: "UEXLZKRRYKGPRD-UHFFFAOYSA-N", + dbId: "M0X", + pubChemCompoundId: "156907149", + name: + "2-(1H-benzotriazol-1-yl)-N-[4-(dimethylamino)phenyl]-N-[(thiophen-3-yl)methyl]acetamide", + details: + "2-(1H-benzotriazol-1-yl)-N-[4-(dimethylamino)phenyl]-N-[(thiophen-3-yl)methyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UEXLZKRRYKGPRD-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907149", + }, + { + IUPACInChIkey: "HRBNXNLHEPAYDR-RDJZCZTQSA-N", + dbId: "M26", + pubChemCompoundId: "169408205", + name: + "N-[(1R)-1-(3-bromophenyl)-2-methoxyethyl]-2-[(3S)-5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl]acetamide", + details: + "N-[(1R)-1-(3-bromophenyl)-2-methoxyethyl]-2-[(3S)-5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HRBNXNLHEPAYDR-RDJZCZTQSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408205", + }, + { + IUPACInChIkey: "YBRJTZIFZNLYKE-CQSZACIVSA-N", + dbId: "M2X", + pubChemCompoundId: "169408204", + name: "(2R)-2-amino-2-(5-bromo-2-methoxyphenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "(2R)-2-amino-2-(5-bromo-2-methoxyphenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YBRJTZIFZNLYKE-CQSZACIVSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408204", + }, + { + IUPACInChIkey: "SXIRQVINYJTTGB-ZDUSSCGKSA-N", + dbId: "M4L", + pubChemCompoundId: "169408203", + name: "(2S)-2-(3-bromophenyl)-2-hydroxy-N-(4-methoxypyridin-3-yl)acetamide", + details: "(2S)-2-(3-bromophenyl)-2-hydroxy-N-(4-methoxypyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SXIRQVINYJTTGB-ZDUSSCGKSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408203", + }, + { + IUPACInChIkey: "VUGOQWLHGHMVIW-UHFFFAOYSA-N", + dbId: "M50", + pubChemCompoundId: "154862921", + name: "2-(3-chlorophenyl)-N-(5-methylpyridazin-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(5-methylpyridazin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VUGOQWLHGHMVIW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154862921", + }, + { + IUPACInChIkey: "VKQLRXLEZSWDDW-UHFFFAOYSA-N", + dbId: "M5I", + pubChemCompoundId: "154875989", + name: "N-(3-chlorophenyl)-2-(4-methylpyridin-3-yl)acetamide", + details: "N-(3-chlorophenyl)-2-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VKQLRXLEZSWDDW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154875989", + }, + { + IUPACInChIkey: "KJMQFACDQCJBET-ZETCQYMHSA-N", + dbId: "M5X", + pubChemCompoundId: "169452756", + name: "(3S)-3-hydroxy-2-oxo-2,3-dihydro-1H-indole-5-sulfonamide", + details: "(3S)-3-hydroxy-2-oxo-2,3-dihydro-1H-indole-5-sulfonamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KJMQFACDQCJBET-ZETCQYMHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452756", + }, + { + IUPACInChIkey: "QGLBBAUVPATXPV-UHFFFAOYSA-N", + dbId: "M6I", + pubChemCompoundId: "898797", + name: "N-(3-chlorophenyl)-N'-(pyridin-3-yl)urea", + details: "N-(3-chlorophenyl)-N'-(pyridin-3-yl)urea", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QGLBBAUVPATXPV-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/898797", + }, + { + IUPACInChIkey: "WFXWGHHTPVLTRG-UHFFFAOYSA-N", + dbId: "M6U", + pubChemCompoundId: "138023908", + name: "N-(4-ethylpyridin-3-yl)-2-[6-(trifluoromethyl)pyridin-2-yl]acetamide", + details: "N-(4-ethylpyridin-3-yl)-2-[6-(trifluoromethyl)pyridin-2-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WFXWGHHTPVLTRG-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/138023908", + }, + { + IUPACInChIkey: "BMYRQBMWNFDONV-UHFFFAOYSA-N", + dbId: "M7X", + pubChemCompoundId: "110727314", + name: "2-(3-chlorophenyl)-N-(5-methylpyridin-3-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(5-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BMYRQBMWNFDONV-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/110727314", + }, + { + IUPACInChIkey: "XLONNNGKPLHXDC-GFCCVEGCSA-N", + dbId: "M93", + pubChemCompoundId: "169408210", + name: + "(4R)-6-chloro-N-[4-(hydroxymethyl)pyridin-3-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-[4-(hydroxymethyl)pyridin-3-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XLONNNGKPLHXDC-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408210", + }, + { + IUPACInChIkey: "MMSFMHOFPDOWCH-NSHDSACASA-N", + dbId: "M9U", + pubChemCompoundId: "156907139", + name: + "(4S)-6-chloro-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MMSFMHOFPDOWCH-NSHDSACASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907139", + }, { IUPACInChIkey: "WQZGKKKJIJFFOK-QTVWNMPRSA-N", dbId: "MAN", @@ -4872,6 +5844,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SXGZJKUKBWWHRA-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/78165", }, + { + IUPACInChIkey: "SEFKQYGCOOMXHK-SNVBAGLBSA-N", + dbId: "MF0", + pubChemCompoundId: "169408209", + name: "(2R)-2-(5-chloropyridin-3-yl)-N-(4-methylpyridin-3-yl)propanamide", + details: "(2R)-2-(5-chloropyridin-3-yl)-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SEFKQYGCOOMXHK-SNVBAGLBSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408209", + }, { IUPACInChIkey: "JLVVSXFLKOJNIY-UHFFFAOYSA-N", dbId: "MG", @@ -4913,6 +5895,26 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UDFJXRJYAZANFF-VBHAUSMQSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/137796783", }, + { + IUPACInChIkey: "YSMRCXUJRFLNNU-UHFFFAOYSA-N", + dbId: "MJR", + pubChemCompoundId: "154858274", + name: "2-(3-chlorophenyl)-N-(3-methyl-1H-pyrazol-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(3-methyl-1H-pyrazol-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YSMRCXUJRFLNNU-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154858274", + }, + { + IUPACInChIkey: "KTTFDHLIVPVQIE-UHFFFAOYSA-N", + dbId: "MKI", + pubChemCompoundId: "154861803", + name: "2-(3-chlorophenyl)-N-methyl-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(3-chlorophenyl)-N-methyl-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KTTFDHLIVPVQIE-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154861803", + }, { IUPACInChIkey: "OFOBLEOULBTSOW-UHFFFAOYSA-N", dbId: "MLA", @@ -4993,6 +5995,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DVLFYONBTKHTER-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/70807", }, + { + IUPACInChIkey: "KMBBZQXTAKMYIS-GFCCVEGCSA-N", + dbId: "MQ3", + pubChemCompoundId: "169408212", + name: "(2R)-2-cyclohexyl-N-(4-methylpyridin-3-yl)propanamide", + details: "(2R)-2-cyclohexyl-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KMBBZQXTAKMYIS-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408212", + }, { IUPACInChIkey: "WUUGFSXJNOTRMR-IOSLPCCCSA-N", dbId: "MTA", @@ -5003,6 +6015,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WUUGFSXJNOTRMR-IOSLPCCCSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/439176", }, + { + IUPACInChIkey: "BMUGFKLSYMKHTP-GFCCVEGCSA-N", + dbId: "MU3", + pubChemCompoundId: "169408213", + name: + "(4R)-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BMUGFKLSYMKHTP-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408213", + }, { IUPACInChIkey: "ZLIBICFPKPWGIZ-UHFFFAOYSA-N", dbId: "MUK", @@ -5013,6 +6037,51 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZLIBICFPKPWGIZ-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/91650", }, + { + IUPACInChIkey: "SMTCZNNYBUKPMF-UHFFFAOYSA-N", + dbId: "MVR", + pubChemCompoundId: "156907171", + name: + "N-[(1-methyl-1H-pyrazol-3-yl)methyl]-2-(pyridin-3-yl)-N-[4-(pyridin-2-yl)phenyl]acetamide", + details: + "N-[(1-methyl-1H-pyrazol-3-yl)methyl]-2-(pyridin-3-yl)-N-[4-(pyridin-2-yl)phenyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SMTCZNNYBUKPMF-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907171", + }, + { + IUPACInChIkey: "UWYNTVRTJWFJEK-LLVKDONJSA-N", + dbId: "MVX", + pubChemCompoundId: "169408214", + name: + "(3S)-5-chloro-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-2,3-dihydro-1-benzofuran-3-carboxamide", + details: + "(3S)-5-chloro-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-2,3-dihydro-1-benzofuran-3-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UWYNTVRTJWFJEK-LLVKDONJSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408214", + }, + { + IUPACInChIkey: "CLECANRFNXEJLT-MRVPVSSYSA-N", + dbId: "MWN", + pubChemCompoundId: "169452757", + name: "methyl (3R)-5-bromo-3-hydroxy-2-oxo-2,3-dihydro-1H-indole-7-carboxylate", + details: "methyl (3R)-5-bromo-3-hydroxy-2-oxo-2,3-dihydro-1H-indole-7-carboxylate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CLECANRFNXEJLT-MRVPVSSYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452757", + }, + { + IUPACInChIkey: "BWTXNZHOZOMCDB-OAHLLOKOSA-N", + dbId: "MX9", + pubChemCompoundId: "169452758", + name: "(3-methylphenyl)methyl (3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indole-7-carboxylate", + details: + "(3-methylphenyl)methyl (3R)-3-hydroxy-2-oxo-2,3-dihydro-1H-indole-7-carboxylate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BWTXNZHOZOMCDB-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452758", + }, { IUPACInChIkey: "YMWUJEATGCHHMB-UHFFFAOYSA-N", dbId: "MYC", @@ -5033,6 +6102,28 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/COCNDHOPIHDTHK-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/18986", }, + { + IUPACInChIkey: "LYOFEJVGYOXWIE-SNVBAGLBSA-N", + dbId: "MZF", + pubChemCompoundId: "169452759", + name: + "(3R)-5-bromo-3-hydroxy-1-[(1,2,4-oxadiazol-3-yl)methyl]-1,3-dihydro-2H-indol-2-one", + details: + "(3R)-5-bromo-3-hydroxy-1-[(1,2,4-oxadiazol-3-yl)methyl]-1,3-dihydro-2H-indol-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LYOFEJVGYOXWIE-SNVBAGLBSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452759", + }, + { + IUPACInChIkey: "ISYVWNKBJIDJSU-SECBINFHSA-N", + dbId: "N00", + pubChemCompoundId: "169408218", + name: "(2R)-2-(6-chloro-1-methyl-9H-carbazol-2-yl)propanoic acid", + details: "(2R)-2-(6-chloro-1-methyl-9H-carbazol-2-yl)propanoic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ISYVWNKBJIDJSU-SECBINFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408218", + }, { IUPACInChIkey: "OHWHQNCVWRVQFT-UHFFFAOYSA-N", dbId: "N0E", @@ -5043,6 +6134,118 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OHWHQNCVWRVQFT-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/836055", }, + { + IUPACInChIkey: "ASXLXOCGCKXODB-QGZVFWFLSA-N", + dbId: "N0F", + pubChemCompoundId: "169408219", + name: + "(3R)-3-(4-hydroxypiperidin-1-yl)-N-(4-methylpyridin-3-yl)-3-(thiophen-3-yl)propanamide", + details: + "(3R)-3-(4-hydroxypiperidin-1-yl)-N-(4-methylpyridin-3-yl)-3-(thiophen-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ASXLXOCGCKXODB-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408219", + }, + { + IUPACInChIkey: "MRZHVMLGHCTVMT-CQSZACIVSA-N", + dbId: "N0O", + pubChemCompoundId: "169408220", + name: + "(3S)-5-chloro-N-(4-phenyl-4H-1,2,4-triazol-3-yl)-2,3-dihydro-1-benzofuran-3-carboxamide", + details: + "(3S)-5-chloro-N-(4-phenyl-4H-1,2,4-triazol-3-yl)-2,3-dihydro-1-benzofuran-3-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MRZHVMLGHCTVMT-CQSZACIVSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408220", + }, + { + IUPACInChIkey: "UPRDTUXXNWJLMA-MRXNPFEDSA-N", + dbId: "N0X", + pubChemCompoundId: "169408221", + name: + "(4R)-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-4-methyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-N-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)-4-methyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UPRDTUXXNWJLMA-MRXNPFEDSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408221", + }, + { + IUPACInChIkey: "QMCANAKFKPPQKX-KRWDZBQOSA-N", + dbId: "N1U", + pubChemCompoundId: "169452760", + name: + "(3S)-5-bromo-1-[(3,4-dimethoxyphenyl)methyl]-3-hydroxy-7-methyl-1,3-dihydro-2H-indol-2-one", + details: + "(3S)-5-bromo-1-[(3,4-dimethoxyphenyl)methyl]-3-hydroxy-7-methyl-1,3-dihydro-2H-indol-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QMCANAKFKPPQKX-KRWDZBQOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452760", + }, + { + IUPACInChIkey: "DDTMARFKTVIEHP-INIZCTEOSA-N", + dbId: "N2X", + pubChemCompoundId: "169452761", + name: "(3S)-5-bromo-1-[(2-ethoxyphenyl)methyl]-3-hydroxy-1,3-dihydro-2H-indol-2-one", + details: "(3S)-5-bromo-1-[(2-ethoxyphenyl)methyl]-3-hydroxy-1,3-dihydro-2H-indol-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DDTMARFKTVIEHP-INIZCTEOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452761", + }, + { + IUPACInChIkey: "WXCJKPMYIYFEDR-UHFFFAOYSA-N", + dbId: "N3I", + pubChemCompoundId: "154876006", + name: "2-(3-chloro-5-methoxyphenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(3-chloro-5-methoxyphenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WXCJKPMYIYFEDR-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154876006", + }, + { + IUPACInChIkey: "HLMOMNRZAYBAJZ-UHFFFAOYSA-N", + dbId: "N3R", + pubChemCompoundId: "167765427", + name: "5-fluoro-N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + details: + "5-fluoro-N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HLMOMNRZAYBAJZ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/167765427", + }, + { + IUPACInChIkey: "NXFNSWGPJUOQPY-UHFFFAOYSA-N", + dbId: "N43", + pubChemCompoundId: "166316691", + name: + "5-methoxy-N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + details: + "5-methoxy-N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NXFNSWGPJUOQPY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/166316691", + }, + { + IUPACInChIkey: "FVKXXNFROYGAEF-UHFFFAOYSA-N", + dbId: "N4L", + pubChemCompoundId: "154876065", + name: "N-[2-(2-methoxyphenoxy)ethyl]-5-methyl-2-oxo-1,2-dihydroquinoline-4-carboxamide", + details: + "N-[2-(2-methoxyphenoxy)ethyl]-5-methyl-2-oxo-1,2-dihydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FVKXXNFROYGAEF-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154876065", + }, + { + IUPACInChIkey: "YFDTZFVQPPSTPK-UHFFFAOYSA-N", + dbId: "N5L", + pubChemCompoundId: "154875846", + name: "N-(5-amino-4-methylpyridin-3-yl)-2-(3-chlorophenyl)acetamide", + details: "N-(5-amino-4-methylpyridin-3-yl)-2-(3-chlorophenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YFDTZFVQPPSTPK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154875846", + }, { IUPACInChIkey: "SOKKEQHRVRNCKI-VERUCKTNSA-N", dbId: "N63", @@ -5055,6 +6258,56 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SOKKEQHRVRNCKI-VERUCKTNSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163321822", }, + { + IUPACInChIkey: "YRFAWMIACMUIGK-JTQLQIEISA-N", + dbId: "N6F", + pubChemCompoundId: "169408224", + name: "(2S)-N-(4-acetamidopyridin-3-yl)-2-(3-chlorophenyl)propanamide", + details: "(2S)-N-(4-acetamidopyridin-3-yl)-2-(3-chlorophenyl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YRFAWMIACMUIGK-JTQLQIEISA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408224", + }, + { + IUPACInChIkey: "MDGSUONMRGWOAQ-UHFFFAOYSA-N", + dbId: "N6X", + pubChemCompoundId: "156907268", + name: "N-(5-amino-4-methylpyridin-3-yl)-2-(3-cyanophenyl)acetamide", + details: "N-(5-amino-4-methylpyridin-3-yl)-2-(3-cyanophenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MDGSUONMRGWOAQ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907268", + }, + { + IUPACInChIkey: "TYFFVSFZMUBUOV-DTWKUNHWSA-N", + dbId: "N7L", + pubChemCompoundId: "154876031", + name: "(1R,2R)-2-(fluoromethyl)-N-(4-methylpyridin-3-yl)cyclopropane-1-carboxamide", + details: "(1R,2R)-2-(fluoromethyl)-N-(4-methylpyridin-3-yl)cyclopropane-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TYFFVSFZMUBUOV-DTWKUNHWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154876031", + }, + { + IUPACInChIkey: "UDMVRKGFUBDAMY-UHFFFAOYSA-N", + dbId: "N8X", + pubChemCompoundId: "154865835", + name: "2-(3,5-dimethylphenyl)-N-(4-methyl-4H-1,2,4-triazol-3-yl)acetamide", + details: "2-(3,5-dimethylphenyl)-N-(4-methyl-4H-1,2,4-triazol-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UDMVRKGFUBDAMY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154865835", + }, + { + IUPACInChIkey: "IICDEQKQIDLVOQ-UHFFFAOYSA-N", + dbId: "N9I", + pubChemCompoundId: "154865604", + name: "2-(4-methylpyridin-3-yl)-N-(1,2,3,4-tetrahydroisoquinolin-8-yl)acetamide", + details: "2-(4-methylpyridin-3-yl)-N-(1,2,3,4-tetrahydroisoquinolin-8-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IICDEQKQIDLVOQ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154865604", + }, { IUPACInChIkey: "FKNQFGJONOIPTF-UHFFFAOYSA-N", dbId: "NA", @@ -5075,6 +6328,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OVRNDRQMDRJTHS-FMDGEEDCSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/24139", }, + { + IUPACInChIkey: "ONQQLMKVMVPYKH-UHFFFAOYSA-N", + dbId: "NB0", + pubChemCompoundId: "6459955", + name: "4-[4-(2-fluorophenyl)piperazine-1-carbonyl]quinolin-2(1H)-one", + details: "4-[4-(2-fluorophenyl)piperazine-1-carbonyl]quinolin-2(1H)-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ONQQLMKVMVPYKH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/6459955", + }, { IUPACInChIkey: "RXHKWDZUWDFTBO-QXMOZHRRSA-N", dbId: "NB2", @@ -5087,6 +6350,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RXHKWDZUWDFTBO-QXMOZHRRSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/162677692", }, + { + IUPACInChIkey: "ZTLMWKAKNVXEJW-UHFFFAOYSA-N", + dbId: "NB6", + pubChemCompoundId: "154859409", + name: "2-(3-bromophenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(3-bromophenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZTLMWKAKNVXEJW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154859409", + }, { IUPACInChIkey: "NVORCMBCUHQRDL-UHFFFAOYSA-N", dbId: "NC3", @@ -5117,6 +6390,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NTUQAPWIPIIWLT-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/85598", }, + { + IUPACInChIkey: "CYQCEAJKJVOFMS-UHFFFAOYSA-N", + dbId: "NEL", + pubChemCompoundId: "156907146", + name: "2-(3-chlorophenyl)-N-(1H-indazol-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(1H-indazol-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CYQCEAJKJVOFMS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907146", + }, { IUPACInChIkey: "GHAZCVNUKKZTLG-UHFFFAOYSA-N", dbId: "NEN", @@ -5127,6 +6410,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GHAZCVNUKKZTLG-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/16842", }, + { + IUPACInChIkey: "PZYJRCQIDAUQHX-NSHDSACASA-N", + dbId: "NGX", + pubChemCompoundId: "169408225", + name: "(2S)-1-(3-chlorophenyl)-3-(1H-1,2,4-triazol-1-yl)propan-2-ol", + details: "(2S)-1-(3-chlorophenyl)-3-(1H-1,2,4-triazol-1-yl)propan-2-ol", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PZYJRCQIDAUQHX-NSHDSACASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408225", + }, { IUPACInChIkey: "MNIGYIKCFSPQRJ-UHFFFAOYSA-N", dbId: "NHE", @@ -5147,6 +6440,56 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VEQPNABPJHWNSG-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/934", }, + { + IUPACInChIkey: "RBRNVPIASJICKN-UHFFFAOYSA-N", + dbId: "NIJ", + pubChemCompoundId: "156907209", + name: "3-(3-fluorophenyl)-N-(4-methylpyridin-3-yl)propanamide", + details: "3-(3-fluorophenyl)-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RBRNVPIASJICKN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907209", + }, + { + IUPACInChIkey: "KNBSSRRKRQQGOO-UHFFFAOYSA-N", + dbId: "NJE", + pubChemCompoundId: "156907211", + name: "N-(4-methylpyridin-3-yl)-2-(piperidin-1-yl)acetamide", + details: "N-(4-methylpyridin-3-yl)-2-(piperidin-1-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KNBSSRRKRQQGOO-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907211", + }, + { + IUPACInChIkey: "KVBRDRRWOWILOL-UHFFFAOYSA-N", + dbId: "NJU", + pubChemCompoundId: "154872712", + name: "2-(3-chlorophenyl)-N-(5,6,7,8-tetrahydroisoquinolin-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(5,6,7,8-tetrahydroisoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KVBRDRRWOWILOL-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154872712", + }, + { + IUPACInChIkey: "HSYVELSOLBWEKK-UHFFFAOYSA-N", + dbId: "NKU", + pubChemCompoundId: "51189284", + name: "2-(1H-benzotriazol-1-yl)-N-[(3-chlorophenyl)methyl]-N-methylacetamide", + details: "2-(1H-benzotriazol-1-yl)-N-[(3-chlorophenyl)methyl]-N-methylacetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HSYVELSOLBWEKK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/51189284", + }, + { + IUPACInChIkey: "GRCPKASYWFJZEJ-UHFFFAOYSA-N", + dbId: "NM0", + pubChemCompoundId: "154872926", + name: "2-(3-chlorophenyl)-N-[(4R)-imidazo[1,2-a]pyridin-3-yl]acetamide", + details: "2-(3-chlorophenyl)-N-[(4R)-imidazo[1,2-a]pyridin-3-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GRCPKASYWFJZEJ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154872926", + }, { IUPACInChIkey: "VVKVBQDZJLGAFG-UHFFFAOYSA-N", dbId: "NMI", @@ -5179,6 +6522,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KOBHCUDVWOTEKO-VKHMYHEASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/446124", }, + { + IUPACInChIkey: "CLLYBOMGFSNDSO-UHFFFAOYSA-N", + dbId: "NO0", + pubChemCompoundId: "154872925", + name: "2-(3-ethynylphenyl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(3-ethynylphenyl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CLLYBOMGFSNDSO-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154872925", + }, { IUPACInChIkey: "NHNBFGGVMKEFGY-UHFFFAOYSA-N", dbId: "NO3", @@ -5199,6 +6552,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GHRYSOFWKRRLMI-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/76313", }, + { + IUPACInChIkey: "DVAZCJFDVZFHLG-UHFFFAOYSA-N", + dbId: "NOI", + pubChemCompoundId: "156907107", + name: "2-(3-chlorophenyl)-N-(1-methyl-1H-imidazol-5-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(1-methyl-1H-imidazol-5-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DVAZCJFDVZFHLG-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907107", + }, { IUPACInChIkey: "YIWYOEOSWRXENJ-FFXRMZKPSA-N", dbId: "NOL", @@ -5211,6 +6574,59 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YIWYOEOSWRXENJ-FFXRMZKPSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/11844232", }, + { + IUPACInChIkey: "NCRWUWJGTHEGCI-UHFFFAOYSA-N", + dbId: "NQ3", + pubChemCompoundId: "169408226", + name: + "(1M,3P)-1-(3-chlorophenyl)-3-(4-methylpyridin-3-yl)-1,3-dihydro-2H-imidazol-2-one", + details: + "(1M,3P)-1-(3-chlorophenyl)-3-(4-methylpyridin-3-yl)-1,3-dihydro-2H-imidazol-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NCRWUWJGTHEGCI-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408226", + }, + { + IUPACInChIkey: "ZNGNXXLXHHJCCJ-UHFFFAOYSA-N", + dbId: "NQO", + pubChemCompoundId: "154875995", + name: "2-(3-chlorophenyl)-N-(4-methylpyridazin-3-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(4-methylpyridazin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZNGNXXLXHHJCCJ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154875995", + }, + { + IUPACInChIkey: "LOFUGDOYUSJHEA-CQSZACIVSA-N", + dbId: "NRC", + pubChemCompoundId: "169408227", + name: "methyl (2R)-2-(3-chlorophenyl)-3-[(4-methylpyridin-3-yl)amino]-3-oxopropanoate", + details: + "methyl (2R)-2-(3-chlorophenyl)-3-[(4-methylpyridin-3-yl)amino]-3-oxopropanoate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LOFUGDOYUSJHEA-CQSZACIVSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408227", + }, + { + IUPACInChIkey: "SDPLNJUUYIUIPZ-UHFFFAOYSA-N", + dbId: "NRX", + pubChemCompoundId: "156907121", + name: "2-(3-chlorophenyl)-N-[(4S)-imidazo[1,5-a]pyridin-1-yl]acetamide", + details: "2-(3-chlorophenyl)-N-[(4S)-imidazo[1,5-a]pyridin-1-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SDPLNJUUYIUIPZ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907121", + }, + { + IUPACInChIkey: "QRUNNMAOPKEFMJ-OAHLLOKOSA-N", + dbId: "NSR", + pubChemCompoundId: "154878592", + name: "(4R)-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: "(4R)-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QRUNNMAOPKEFMJ-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154878592", + }, { IUPACInChIkey: "DRDAOZOONYPMPX-UHFFFAOYSA-N", dbId: "NT9", @@ -5231,6 +6647,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QPJKHSFVBDONPD-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/79838750", }, + { + IUPACInChIkey: "VQNYZMIKTVJRNS-UHFFFAOYSA-N", + dbId: "NU0", + pubChemCompoundId: "154873548", + name: "2-(3-chlorophenyl)-N-(2,6-naphthyridin-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(2,6-naphthyridin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VQNYZMIKTVJRNS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873548", + }, { IUPACInChIkey: "UVTFDTBDFQZRHD-UHFFFAOYSA-N", dbId: "NUA", @@ -5241,6 +6667,26 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UVTFDTBDFQZRHD-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/51114235", }, + { + IUPACInChIkey: "XFUDGCDECOIROA-UHFFFAOYSA-N", + dbId: "NUR", + pubChemCompoundId: "154873551", + name: "2-(3-chlorophenyl)-N-(isoquinolin-4-yl)-N-methylacetamide", + details: "2-(3-chlorophenyl)-N-(isoquinolin-4-yl)-N-methylacetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XFUDGCDECOIROA-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873551", + }, + { + IUPACInChIkey: "VSOZJTYJJHNDPD-UHFFFAOYSA-N", + dbId: "NV9", + pubChemCompoundId: "154862192", + name: "2-(3-chlorophenyl)-N-(4-phenylpyridin-3-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(4-phenylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VSOZJTYJJHNDPD-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154862192", + }, { IUPACInChIkey: "OMPJBNCRMGITSC-UHFFFAOYSA-N", dbId: "NVD", @@ -5251,6 +6697,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OMPJBNCRMGITSC-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/7187", }, + { + IUPACInChIkey: "ATNZGZHLHMEMFV-UHFFFAOYSA-N", + dbId: "NVO", + pubChemCompoundId: "154873539", + name: "2-(3-chlorophenyl)-N-(phthalazin-1-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(phthalazin-1-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ATNZGZHLHMEMFV-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873539", + }, { IUPACInChIkey: "BVSIAYQIMUUCRW-UHFFFAOYSA-N", dbId: "NVU", @@ -5261,6 +6717,26 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BVSIAYQIMUUCRW-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/301729", }, + { + IUPACInChIkey: "CQMIDRCPLJZCFD-UHFFFAOYSA-N", + dbId: "NW0", + pubChemCompoundId: "154859407", + name: "3-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)propanamide", + details: "3-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CQMIDRCPLJZCFD-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154859407", + }, + { + IUPACInChIkey: "AFQAFSYTYCJOEN-UHFFFAOYSA-N", + dbId: "NWI", + pubChemCompoundId: "154873537", + name: "2-(3-chlorophenyl)-N-(1,6-naphthyridin-8-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(1,6-naphthyridin-8-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AFQAFSYTYCJOEN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873537", + }, { IUPACInChIkey: "DFVPCNAMNAPBCX-LTGWCKQJSA-N", dbId: "NWX", @@ -5284,8 +6760,18 @@ export const data: Covid19Data = { externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/588246", }, { - IUPACInChIkey: "ZUNGTEUNVMHDIX-UHFFFAOYSA-N", - dbId: "NXS", + IUPACInChIkey: "SDKQWVALTYIIDW-UHFFFAOYSA-N", + dbId: "NX9", + pubChemCompoundId: "62504273", + name: "2-(3-chlorophenyl)-N-(1H-pyrazol-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(1H-pyrazol-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SDKQWVALTYIIDW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/62504273", + }, + { + IUPACInChIkey: "ZUNGTEUNVMHDIX-UHFFFAOYSA-N", + dbId: "NXS", pubChemCompoundId: "2776521", name: "[1-(pyrimidin-2-yl)piperidin-4-yl]methanol", details: "[1-(pyrimidin-2-yl)piperidin-4-yl]methanol", @@ -5303,6 +6789,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SRFLDWOWAGQZAD-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/16226828", }, + { + IUPACInChIkey: "BYGPKLOEYHRCEP-UHFFFAOYSA-N", + dbId: "NYR", + pubChemCompoundId: "167861653", + name: "N-(3-chlorophenyl)-2-(3-methyl-1H-pyrazol-4-yl)acetamide", + details: "N-(3-chlorophenyl)-2-(3-methyl-1H-pyrazol-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BYGPKLOEYHRCEP-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/167861653", + }, { IUPACInChIkey: "DEJLCHRMKBBNPV-UHFFFAOYSA-N", dbId: "NYV", @@ -5353,6 +6849,36 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VSYPROQBASLXDK-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/772233", }, + { + IUPACInChIkey: "SIFMSWJDYLFFPS-UHFFFAOYSA-N", + dbId: "NZK", + pubChemCompoundId: "156907079", + name: "2-(4-acetylpiperazin-1-yl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(4-acetylpiperazin-1-yl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SIFMSWJDYLFFPS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907079", + }, + { + IUPACInChIkey: "ITQMQTJYJVFFAW-UHFFFAOYSA-N", + dbId: "O0C", + pubChemCompoundId: "154873538", + name: "2-(3-chlorophenyl)-N-(2,7-naphthyridin-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(2,7-naphthyridin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ITQMQTJYJVFFAW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873538", + }, + { + IUPACInChIkey: "TVYREULMZIPGLM-UHFFFAOYSA-N", + dbId: "O0R", + pubChemCompoundId: "154873536", + name: "2-(3-chlorophenyl)-N-(4-cyclopropylpyridin-3-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(4-cyclopropylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TVYREULMZIPGLM-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873536", + }, { IUPACInChIkey: "DXVKZDBYLFVMFB-UHFFFAOYSA-N", dbId: "O0S", @@ -5363,6 +6889,36 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DXVKZDBYLFVMFB-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/1487531", }, + { + IUPACInChIkey: "ACBAQCKSRSEYGV-UHFFFAOYSA-N", + dbId: "O0X", + pubChemCompoundId: "156907106", + name: "2-(3-chlorophenyl)-N-(1,7-naphthyridin-5-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(1,7-naphthyridin-5-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ACBAQCKSRSEYGV-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907106", + }, + { + IUPACInChIkey: "YUJIYWCEKJSKBQ-CYBMUJFWSA-N", + dbId: "O1I", + pubChemCompoundId: "169408228", + name: "(2S)-2-(3-chlorophenyl)-3-hydroxy-N-(4-methylpyridin-3-yl)propanamide", + details: "(2S)-2-(3-chlorophenyl)-3-hydroxy-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YUJIYWCEKJSKBQ-CYBMUJFWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408228", + }, + { + IUPACInChIkey: "XVSORZZOZIKMAO-ZETCQYMHSA-N", + dbId: "O1X", + pubChemCompoundId: "156907187", + name: "(2S)-2-(difluoromethoxy)-N-(4-methylpyridin-3-yl)propanamide", + details: "(2S)-2-(difluoromethoxy)-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XVSORZZOZIKMAO-ZETCQYMHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907187", + }, { IUPACInChIkey: "OKVUYVXDTGOYRU-UHFFFAOYSA-N", dbId: "O2A", @@ -5383,6 +6939,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/URRZFISTFWQMHO-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/45830775", }, + { + IUPACInChIkey: "BNLQGZVZNCOJKF-UHFFFAOYSA-N", + dbId: "O2R", + pubChemCompoundId: "154875988", + name: "2-(2-butoxy-5-chlorophenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(2-butoxy-5-chlorophenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BNLQGZVZNCOJKF-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154875988", + }, { IUPACInChIkey: "SXZSRGKJZKOZRP-UHFFFAOYSA-N", dbId: "O3G", @@ -5393,6 +6959,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SXZSRGKJZKOZRP-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/784761", }, + { + IUPACInChIkey: "KWOZOQHUQWBGBH-UHFFFAOYSA-N", + dbId: "O3I", + pubChemCompoundId: "154873529", + name: + "2-[(1M)-5-chloro-2',3'-difluoro-4'-methyl[1,1'-biphenyl]-3-yl]-N-(4-methylpyridin-3-yl)acetamide", + details: + "2-[(1M)-5-chloro-2',3'-difluoro-4'-methyl[1,1'-biphenyl]-3-yl]-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KWOZOQHUQWBGBH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873529", + }, { IUPACInChIkey: "UMTNBAIWJVAAGI-UHFFFAOYSA-N", dbId: "O3R", @@ -5403,6 +6981,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UMTNBAIWJVAAGI-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/9104855", }, + { + IUPACInChIkey: "NZKPFLQQMFCJHQ-UHFFFAOYSA-N", + dbId: "O3U", + pubChemCompoundId: "169452762", + name: + "N-[(1R)-1,5-dicyano-4-(methylsulfanyl)-3-azaspiro[5.5]undeca-2,4-dien-2-yl]acetamide", + details: + "N-[(1R)-1,5-dicyano-4-(methylsulfanyl)-3-azaspiro[5.5]undeca-2,4-dien-2-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NZKPFLQQMFCJHQ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452762", + }, { IUPACInChIkey: "UQVBMSYLQWGFOX-UHFFFAOYSA-N", dbId: "O46", @@ -5423,6 +7013,28 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VADYKWPOUVEKIU-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/145886223", }, + { + IUPACInChIkey: "ZRVUXGAJUNHVRN-UHFFFAOYSA-N", + dbId: "O4L", + pubChemCompoundId: "169452763", + name: + "N-(3-acetyl-2,5-dimethyl-1H-pyrrol-1-yl)-4-oxo-3,4-dihydrophthalazine-1-carboxamide", + details: + "N-(3-acetyl-2,5-dimethyl-1H-pyrrol-1-yl)-4-oxo-3,4-dihydrophthalazine-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZRVUXGAJUNHVRN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452763", + }, + { + IUPACInChIkey: "NSDJNMWFQYNAQU-UHFFFAOYSA-N", + dbId: "O5C", + pubChemCompoundId: "11837274", + name: "1-[(4S)-3-(4-fluorobenzoyl)-2-methylindolizin-1-yl]ethan-1-one", + details: "1-[(4S)-3-(4-fluorobenzoyl)-2-methylindolizin-1-yl]ethan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NSDJNMWFQYNAQU-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/11837274", + }, { IUPACInChIkey: "CTPLSMAVLSTZPJ-QFIPXVFZSA-N", dbId: "O5F", @@ -5471,6 +7083,71 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FRACPXUHUTXLCX-BELIEFIBSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/146018708", }, + { + IUPACInChIkey: "NKHDYQSOEVSMNT-UHFFFAOYSA-N", + dbId: "O87", + pubChemCompoundId: "2449860", + name: "4-{4-[3-(trifluoromethyl)phenyl]piperazine-1-carbonyl}quinolin-2(1H)-one", + details: "4-{4-[3-(trifluoromethyl)phenyl]piperazine-1-carbonyl}quinolin-2(1H)-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NKHDYQSOEVSMNT-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/2449860", + }, + { + IUPACInChIkey: "NGODSAZXSLLARZ-APPDUMDISA-N", + dbId: "O8L", + pubChemCompoundId: "169408232", + name: + "(2S)-2-(3-chloro-5-{[(2R)-4-oxoazetidin-2-yl]oxy}phenyl)-N-(4-methylpyridin-3-yl)propanamide", + details: + "(2S)-2-(3-chloro-5-{[(2R)-4-oxoazetidin-2-yl]oxy}phenyl)-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NGODSAZXSLLARZ-APPDUMDISA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408232", + }, + { + IUPACInChIkey: "ZJXCDXGMXIYGBJ-UHFFFAOYSA-N", + dbId: "O9O", + pubChemCompoundId: "154873059", + name: "N-{3-chloro-5-[(6-methoxypyridin-2-yl)oxy]phenyl}-2-(isoquinolin-4-yl)acetamide", + details: + "N-{3-chloro-5-[(6-methoxypyridin-2-yl)oxy]phenyl}-2-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZJXCDXGMXIYGBJ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873059", + }, + { + IUPACInChIkey: "XVSORZZOZIKMAO-SSDOTTSWSA-N", + dbId: "O9X", + pubChemCompoundId: "156907051", + name: "(2R)-2-(difluoromethoxy)-N-(4-methylpyridin-3-yl)propanamide", + details: "(2R)-2-(difluoromethoxy)-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XVSORZZOZIKMAO-SSDOTTSWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907051", + }, + { + IUPACInChIkey: "ISRHBBIYTNRSMM-UHFFFAOYSA-N", + dbId: "OAO", + pubChemCompoundId: "156907061", + name: + "2-{3-chloro-5-[(3-methyl-1,2,4-oxadiazol-5-yl)methoxy]phenyl}-N-(4-methylpyridin-3-yl)acetamide", + details: + "2-{3-chloro-5-[(3-methyl-1,2,4-oxadiazol-5-yl)methoxy]phenyl}-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ISRHBBIYTNRSMM-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907061", + }, + { + IUPACInChIkey: "NXBRVTFHRPPFLN-UHFFFAOYSA-N", + dbId: "OBO", + pubChemCompoundId: "154873547", + name: "2-(3-chlorophenyl)-N-(1H-imidazo[4,5-c]pyridin-7-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(1H-imidazo[4,5-c]pyridin-7-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NXBRVTFHRPPFLN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873547", + }, { IUPACInChIkey: "WWZKQHOCKIZLMA-UHFFFAOYSA-N", dbId: "OCA", @@ -5481,6 +7158,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WWZKQHOCKIZLMA-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/379", }, + { + IUPACInChIkey: "NLTIJDKXVUTASZ-UHFFFAOYSA-N", + dbId: "OCI", + pubChemCompoundId: "156907137", + name: "2-(3-chloro-5-sulfamamidophenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(3-chloro-5-sulfamamidophenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NLTIJDKXVUTASZ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907137", + }, { IUPACInChIkey: "TVMXDCGIABBOFY-UHFFFAOYSA-N", dbId: "OCT", @@ -5491,6 +7178,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TVMXDCGIABBOFY-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/356", }, + { + IUPACInChIkey: "NIAFAWJPFVWDCR-UHFFFAOYSA-N", + dbId: "OD7", + pubChemCompoundId: "156907161", + name: + "2-(6-methoxy-1H-benzotriazol-1-yl)-N-[4-(piperidin-4-yl)phenyl]-N-[(pyridin-2-yl)methyl]acetamide", + details: + "2-(6-methoxy-1H-benzotriazol-1-yl)-N-[4-(piperidin-4-yl)phenyl]-N-[(pyridin-2-yl)methyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NIAFAWJPFVWDCR-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907161", + }, { IUPACInChIkey: "RWELMBQGCLVKOE-ZJOCIWLNSA-N", dbId: "ODN", @@ -5503,6 +7202,28 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RWELMBQGCLVKOE-ZJOCIWLNSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/137349831", }, + { + IUPACInChIkey: "SXRYZSBUMPNSOT-WMZOPIPTSA-N", + dbId: "ODX", + pubChemCompoundId: "169408233", + name: + "2-(3-chloro-5-{[(1S,2S)-2-hydroxycyclopentyl]amino}phenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: + "2-(3-chloro-5-{[(1S,2S)-2-hydroxycyclopentyl]amino}phenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SXRYZSBUMPNSOT-WMZOPIPTSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408233", + }, + { + IUPACInChIkey: "OYXJREXTFZDGLT-UHFFFAOYSA-N", + dbId: "OE6", + pubChemCompoundId: "156907053", + name: "N-(1H-benzotriazol-1-yl)-2-(3-chlorophenyl)acetamide", + details: "N-(1H-benzotriazol-1-yl)-2-(3-chlorophenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OYXJREXTFZDGLT-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907053", + }, { IUPACInChIkey: "XNIOWJUQPMKCIJ-UHFFFAOYSA-N", dbId: "OEI", @@ -5513,6 +7234,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XNIOWJUQPMKCIJ-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/4348", }, + { + IUPACInChIkey: "NWMNITATBGAXEW-UHFFFAOYSA-N", + dbId: "OEO", + pubChemCompoundId: "154878601", + name: + "N-[4-(dimethylamino)phenyl]-2-(isoquinolin-4-yl)-N-[(thiophen-3-yl)methyl]acetamide", + details: + "N-[4-(dimethylamino)phenyl]-2-(isoquinolin-4-yl)-N-[(thiophen-3-yl)methyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NWMNITATBGAXEW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154878601", + }, { IUPACInChIkey: "YHQACXKNKUPSSA-UHFFFAOYSA-N", dbId: "OF6", @@ -5535,6 +7268,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QXLYQUMSFSBBGE-ZLNRFVROSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168451669", }, + { + IUPACInChIkey: "NAUKDTRKBNSCDS-UHFFFAOYSA-N", + dbId: "OFX", + pubChemCompoundId: "154878585", + name: + "2-(1H-benzotriazol-1-yl)-N-[4-(dimethylamino)phenyl]-N-[(1H-pyrazol-5-yl)methyl]acetamide", + details: + "2-(1H-benzotriazol-1-yl)-N-[4-(dimethylamino)phenyl]-N-[(1H-pyrazol-5-yl)methyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NAUKDTRKBNSCDS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154878585", + }, { IUPACInChIkey: "PINPOEWMCLFRRB-ZCFIWIBFSA-N", dbId: "OG3", @@ -5545,6 +7290,48 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PINPOEWMCLFRRB-ZCFIWIBFSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/1715226", }, + { + IUPACInChIkey: "VEPQAUCCEYXBOH-UHFFFAOYSA-N", + dbId: "OGF", + pubChemCompoundId: "156907038", + name: + "2-(1H-benzotriazol-1-yl)-N-[4-(methylcarbamamido)phenyl]-N-[(thiophen-3-yl)methyl]acetamide", + details: + "2-(1H-benzotriazol-1-yl)-N-[4-(methylcarbamamido)phenyl]-N-[(thiophen-3-yl)methyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VEPQAUCCEYXBOH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907038", + }, + { + IUPACInChIkey: "CEVTZHLIFCWJPO-UHFFFAOYSA-N", + dbId: "OGO", + pubChemCompoundId: "167883978", + name: "4-[3-(2-methoxyphenoxy)azetidine-1-carbonyl]quinolin-2(1H)-one", + details: "4-[3-(2-methoxyphenoxy)azetidine-1-carbonyl]quinolin-2(1H)-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CEVTZHLIFCWJPO-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/167883978", + }, + { + IUPACInChIkey: "PICHRHZICCXQLR-UHFFFAOYSA-N", + dbId: "OGV", + pubChemCompoundId: "156906982", + name: "2-(3-chlorophenyl)-N-[(4S)-[1,2,4]triazolo[4,3-a]pyridin-3-yl]acetamide", + details: "2-(3-chlorophenyl)-N-[(4S)-[1,2,4]triazolo[4,3-a]pyridin-3-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PICHRHZICCXQLR-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906982", + }, + { + IUPACInChIkey: "XDVRTJWPDGZLAS-UHFFFAOYSA-N", + dbId: "OHC", + pubChemCompoundId: "154873541", + name: "2-[3-(acetamidomethyl)-5-chlorophenyl]-N-(4-methylpyridin-3-yl)acetamide", + details: "2-[3-(acetamidomethyl)-5-chlorophenyl]-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XDVRTJWPDGZLAS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154873541", + }, { IUPACInChIkey: "CCVYRRGZDBSHFU-UHFFFAOYSA-N", dbId: "OHP", @@ -5555,6 +7342,132 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CCVYRRGZDBSHFU-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/11970", }, + { + IUPACInChIkey: "KJMNRTLNVIILOB-GFCCVEGCSA-N", + dbId: "OI4", + pubChemCompoundId: "155971407", + name: + "(4R)-6-chloro-N-(4-methylpyridin-3-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(4-methylpyridin-3-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KJMNRTLNVIILOB-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155971407", + }, + { + IUPACInChIkey: "WBAYRCXMIZFJCT-UHFFFAOYSA-N", + dbId: "OIE", + pubChemCompoundId: "156907034", + name: "2-(4-chloropyridin-2-yl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(4-chloropyridin-2-yl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WBAYRCXMIZFJCT-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907034", + }, + { + IUPACInChIkey: "UIQBSVLMOPGDAQ-UHFFFAOYSA-N", + dbId: "OIK", + pubChemCompoundId: "156907025", + name: "(isoquinolin-4-yl)(4-phenylpiperazin-1-yl)methanone", + details: "(isoquinolin-4-yl)(4-phenylpiperazin-1-yl)methanone", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UIQBSVLMOPGDAQ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907025", + }, + { + IUPACInChIkey: "SWRAJWUUCVFLBR-UHFFFAOYSA-N", + dbId: "OIX", + pubChemCompoundId: "156907022", + name: "N-[2-(2-methoxyphenoxy)ethyl]isoquinoline-4-carboxamide", + details: "N-[2-(2-methoxyphenoxy)ethyl]isoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SWRAJWUUCVFLBR-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907022", + }, + { + IUPACInChIkey: "BSHOYSAYHBYYEY-UHFFFAOYSA-N", + dbId: "OJ9", + pubChemCompoundId: "169408234", + name: "2-(5-chloro-1-benzofuran-7-yl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(5-chloro-1-benzofuran-7-yl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BSHOYSAYHBYYEY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408234", + }, + { + IUPACInChIkey: "CZIBGCQCFNYACK-UHFFFAOYSA-N", + dbId: "OJO", + pubChemCompoundId: "146140258", + name: "1-{4-[(3-chloro-5-hydroxyphenyl)methyl]piperazin-1-yl}ethan-1-one", + details: "1-{4-[(3-chloro-5-hydroxyphenyl)methyl]piperazin-1-yl}ethan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CZIBGCQCFNYACK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/146140258", + }, + { + IUPACInChIkey: "KZHJLIYVOMIHCX-BENRWUELSA-N", + dbId: "OK9", + pubChemCompoundId: "169452764", + name: + "N-{(1Z)-1-[5-(morpholin-4-yl)thiophen-2-yl]-3-oxoprop-1-en-2-yl}thiophene-2-carboxamide", + details: + "N-{(1Z)-1-[5-(morpholin-4-yl)thiophen-2-yl]-3-oxoprop-1-en-2-yl}thiophene-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KZHJLIYVOMIHCX-BENRWUELSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452764", + }, + { + IUPACInChIkey: "NJHYHXQHRGWKMO-UHFFFAOYSA-N", + dbId: "OKW", + pubChemCompoundId: "156906980", + name: "2-(3-chlorophenyl)-N-(6,7-dihydro-5H-cyclopenta[c]pyridin-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(6,7-dihydro-5H-cyclopenta[c]pyridin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NJHYHXQHRGWKMO-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906980", + }, + { + IUPACInChIkey: "MDMQYMUHXMGVBC-LLVKDONJSA-N", + dbId: "OLX", + pubChemCompoundId: "169452765", + name: "[(3R)-5-ethyl-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid", + details: "[(3R)-5-ethyl-3-hydroxy-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MDMQYMUHXMGVBC-LLVKDONJSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452765", + }, + { + IUPACInChIkey: "DFIJRDVINKLDBU-UHFFFAOYSA-N", + dbId: "ONU", + pubChemCompoundId: "166319509", + name: "4-[3-(2-methoxyanilino)azetidine-1-carbonyl]quinolin-2(1H)-one", + details: "4-[3-(2-methoxyanilino)azetidine-1-carbonyl]quinolin-2(1H)-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DFIJRDVINKLDBU-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/166319509", + }, + { + IUPACInChIkey: "SGXOKACJPFKOBB-CWTRNNRKSA-N", + dbId: "OO6", + pubChemCompoundId: "155971390", + name: + "(3S,4R)-6-chloro-N-(isoquinolin-4-yl)-3-methyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(3S,4R)-6-chloro-N-(isoquinolin-4-yl)-3-methyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SGXOKACJPFKOBB-CWTRNNRKSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155971390", + }, + { + IUPACInChIkey: "ZNXPLNWUFWZUFS-UHFFFAOYSA-N", + dbId: "OOL", + pubChemCompoundId: "169452766", + name: "(E)-1-(4,6-dimethoxypyrimidin-2-yl)methanimine", + details: "(E)-1-(4,6-dimethoxypyrimidin-2-yl)methanimine", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZNXPLNWUFWZUFS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452766", + }, { IUPACInChIkey: "BUMHFBGBXFTGJZ-UHFFFAOYSA-N", dbId: "OPU", @@ -5568,143 +7481,461 @@ export const data: Covid19Data = { externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/119557", }, { - IUPACInChIkey: "TWWPGJPLBPBRGX-FHULIHMCSA-N", - dbId: "OW1", - pubChemCompoundId: "166625067", - name: "Nirmatrelvir (reacted form)", - details: "Nirmatrelvir (reacted form)", + IUPACInChIkey: "BZTBYCRNDCQTCD-UHFFFAOYSA-N", + dbId: "OQF", + pubChemCompoundId: "156907065", + name: + "2-(1H-benzotriazol-1-yl)-N-[4-(dimethylamino)phenyl]-N-[(1,3-thiazol-4-yl)methyl]acetamide", + details: + "2-(1H-benzotriazol-1-yl)-N-[4-(dimethylamino)phenyl]-N-[(1,3-thiazol-4-yl)methyl]acetamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TWWPGJPLBPBRGX-FHULIHMCSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/166625067", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BZTBYCRNDCQTCD-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907065", }, { - IUPACInChIkey: "RRQYJINTUHWNHW-UHFFFAOYSA-N", - dbId: "P4G", - pubChemCompoundId: "8179", - name: "1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE", - details: "1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE", + IUPACInChIkey: "TUZBEGQKTWHIIP-OAHLLOKOSA-N", + dbId: "OQL", + pubChemCompoundId: "156906807", + name: "(4R)-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: "(4R)-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RRQYJINTUHWNHW-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/8179", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TUZBEGQKTWHIIP-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906807", }, { - IUPACInChIkey: "VADPVOZBGIXSAG-UHFFFAOYSA-N", - dbId: "P5X", - pubChemCompoundId: "168475482", + IUPACInChIkey: "RVLKWCGLMRBJIF-UHFFFAOYSA-N", + dbId: "OQX", + pubChemCompoundId: "156906975", name: - "N-[(4-chlorothiophen-2-yl)methyl]-N-[4-(dimethylamino)phenyl]-2-(isoquinolin-4-yl)acetamide", + "2-(1H-benzotriazol-1-yl)-N-[(3-chlorophenyl)methyl]-N-(4-methoxyphenyl)acetamide", details: - "N-[(4-chlorothiophen-2-yl)methyl]-N-[4-(dimethylamino)phenyl]-2-(isoquinolin-4-yl)acetamide", + "2-(1H-benzotriazol-1-yl)-N-[(3-chlorophenyl)methyl]-N-(4-methoxyphenyl)acetamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VADPVOZBGIXSAG-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168475482", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RVLKWCGLMRBJIF-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906975", }, { - IUPACInChIkey: "IIRDTKBZINWQAW-UHFFFAOYSA-N", - dbId: "P6G", - pubChemCompoundId: "17472", - name: "HEXAETHYLENE GLYCOL", - details: "HEXAETHYLENE GLYCOL", + IUPACInChIkey: "KFDIFJWRZNKQEO-UHFFFAOYSA-N", + dbId: "ORR", + pubChemCompoundId: "156906960", + name: "1-(5-amino-3,4-dihydro-1,7-naphthyridin-1(2H)-yl)-2-(3-chlorophenyl)ethan-1-one", + details: + "1-(5-amino-3,4-dihydro-1,7-naphthyridin-1(2H)-yl)-2-(3-chlorophenyl)ethan-1-one", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IIRDTKBZINWQAW-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/17472", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KFDIFJWRZNKQEO-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906960", }, { - IUPACInChIkey: "GANIBVZSZGNMNB-QMMMGPOBSA-N", - dbId: "P6N", - pubChemCompoundId: "7058063", - name: "(2~{S})-2-methyl-3,4-dihydro-2~{H}-naphthalen-1-one", - details: "(2~{S})-2-methyl-3,4-dihydro-2~{H}-naphthalen-1-one", + IUPACInChIkey: "CPQDCUNLQZNEBN-HXUWFJFHSA-N", + dbId: "OSI", + pubChemCompoundId: "156907049", + name: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-4-methyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-4-methyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GANIBVZSZGNMNB-QMMMGPOBSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/7058063", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CPQDCUNLQZNEBN-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907049", }, { - IUPACInChIkey: "VAAIHZIVXKAKRN-UHFFFAOYSA-N", - dbId: "P6R", - pubChemCompoundId: "168475484", + IUPACInChIkey: "UELOTNVORDVOMK-UHFFFAOYSA-N", + dbId: "OT6", + pubChemCompoundId: "156907091", name: - "N-(4-tert-butylphenyl)-N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)acetamide", + "2-{3-chloro-5-[(2-cyano-2-methylpropyl)amino]phenyl}-N-(4-methylpyridin-3-yl)acetamide", details: - "N-(4-tert-butylphenyl)-N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)acetamide", + "2-{3-chloro-5-[(2-cyano-2-methylpropyl)amino]phenyl}-N-(4-methylpyridin-3-yl)acetamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VAAIHZIVXKAKRN-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168475484", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UELOTNVORDVOMK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907091", }, { - IUPACInChIkey: "CKKMMWWEOWLHCZ-UHFFFAOYSA-N", - dbId: "P7L", - pubChemCompoundId: "168475485", + IUPACInChIkey: "ROXLXWPALVCDCD-CABCVRRESA-N", + dbId: "OTV", + pubChemCompoundId: "169408240", name: - "N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)-N-(4-methoxyphenyl)acetamide", + "2-(3-chloro-5-{[(1S,2R)-2-(trifluoromethyl)cyclopropyl]amino}phenyl)-N-(4-methylpyridin-3-yl)acetamide", details: - "N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)-N-(4-methoxyphenyl)acetamide", + "2-(3-chloro-5-{[(1S,2R)-2-(trifluoromethyl)cyclopropyl]amino}phenyl)-N-(4-methylpyridin-3-yl)acetamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CKKMMWWEOWLHCZ-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168475485", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ROXLXWPALVCDCD-CABCVRRESA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408240", }, { - IUPACInChIkey: "DLNUNWNLBKOMMX-PGIRCJHISA-O", - dbId: "P8C", - pubChemCompoundId: "163410438", + IUPACInChIkey: "FZPIZTYHLRGZPR-UHFFFAOYSA-N", + dbId: "OU3", + pubChemCompoundId: "169447977", name: - "[(1~{S},2~{R})-2-[4,4-bis(fluoranyl)cyclohexyl]cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + "3-(4-fluoranyl-3-methyl-phenyl)-2-(2-methylpropyl)-5,6,7-tris(oxidanyl)quinazolin-4-one", details: - "[(1~{S},2~{R})-2-[4,4-bis(fluoranyl)cyclohexyl]cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + "3-(4-fluoranyl-3-methyl-phenyl)-2-(2-methylpropyl)-5,6,7-tris(oxidanyl)quinazolin-4-one", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DLNUNWNLBKOMMX-PGIRCJHISA-O/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163410438", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FZPIZTYHLRGZPR-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169447977", }, { - IUPACInChIkey: "VKRZPHPWNNQDHJ-HUWCRECTSA-O", - dbId: "P8L", - pubChemCompoundId: "163410439", + IUPACInChIkey: "AWGPPDHJJBIGAJ-UHFFFAOYSA-N", + dbId: "OUF", + pubChemCompoundId: "20910270", name: - "[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + "N-[(furan-2-yl)methyl]-N'-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)-N-{3-[(propan-2-yl)oxy]propyl}urea", details: - "[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + "N-[(furan-2-yl)methyl]-N'-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)-N-{3-[(propan-2-yl)oxy]propyl}urea", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VKRZPHPWNNQDHJ-HUWCRECTSA-O/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163410439", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AWGPPDHJJBIGAJ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/20910270", }, { - IUPACInChIkey: "VKRZPHPWNNQDHJ-MWOXCZGJSA-O", - dbId: "P8U", - pubChemCompoundId: "163410440", + IUPACInChIkey: "KOZCSUYCMLWBNN-UHFFFAOYSA-N", + dbId: "OV4", + pubChemCompoundId: "156907082", + name: "2-(1H-benzotriazol-1-yl)-N-benzyl-N-[4-(dimethylamino)phenyl]acetamide", + details: "2-(1H-benzotriazol-1-yl)-N-benzyl-N-[4-(dimethylamino)phenyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KOZCSUYCMLWBNN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907082", + }, + { + IUPACInChIkey: "DJHGLSHYLFLFFG-UHFFFAOYSA-N", + dbId: "OVF", + pubChemCompoundId: "156907083", name: - "[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + "2-(1H-benzotriazol-1-yl)-N-[(3-chlorophenyl)methyl]-N-[4-(dimethylamino)phenyl]acetamide", details: - "[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + "2-(1H-benzotriazol-1-yl)-N-[(3-chlorophenyl)methyl]-N-[4-(dimethylamino)phenyl]acetamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VKRZPHPWNNQDHJ-MWOXCZGJSA-O/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163410440", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DJHGLSHYLFLFFG-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907083", }, { - IUPACInChIkey: "LVNGJLRDBYCPGB-LDLOPFEMSA-O", - dbId: "PEE", - pubChemCompoundId: "5289131", - name: "1,2-dioleoyl-sn-glycero-3-phosphoethanolamine", - details: "1,2-dioleoyl-sn-glycero-3-phosphoethanolamine", + IUPACInChIkey: "OMBIOAUKLYASJI-UHFFFAOYSA-N", + dbId: "OVX", + pubChemCompoundId: "156906897", + name: "1-(3-chlorophenyl)-4-(isoquinoline-4-carbonyl)piperazin-2-one", + details: "1-(3-chlorophenyl)-4-(isoquinoline-4-carbonyl)piperazin-2-one", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LVNGJLRDBYCPGB-LDLOPFEMSA-O/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/5289131", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OMBIOAUKLYASJI-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906897", }, { - IUPACInChIkey: "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - dbId: "PEG", - pubChemCompoundId: "8117", - name: "DI(HYDROXYETHYL)ETHER", - details: "DI(HYDROXYETHYL)ETHER", + IUPACInChIkey: "TWWPGJPLBPBRGX-FHULIHMCSA-N", + dbId: "OW1", + pubChemCompoundId: "166625067", + name: "Nirmatrelvir (reacted form)", + details: "Nirmatrelvir (reacted form)", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MTHSVFCYNBDYFN-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/8117", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TWWPGJPLBPBRGX-FHULIHMCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/166625067", }, { - IUPACInChIkey: "RIERSGULWXEJKL-UHFFFAOYSA-N", - dbId: "PF0", - pubChemCompoundId: "252023", - name: "3-hydroxy-2-methylbenzoic acid", - details: "3-hydroxy-2-methylbenzoic acid", + IUPACInChIkey: "WATOKUBUEBNRTN-SFHVURJKSA-N", + dbId: "OWC", + pubChemCompoundId: "169408241", + name: "(3S)-3-(3-chlorophenyl)-1-(isoquinolin-4-yl)piperidin-2-one", + details: "(3S)-3-(3-chlorophenyl)-1-(isoquinolin-4-yl)piperidin-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WATOKUBUEBNRTN-SFHVURJKSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408241", + }, + { + IUPACInChIkey: "CVTLEGSZWVPMPP-UHFFFAOYSA-N", + dbId: "OWX", + pubChemCompoundId: "156907036", + name: "2-(3-chlorophenyl)-N-(1,2,3,4-tetrahydro-1,7-naphthyridin-5-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(1,2,3,4-tetrahydro-1,7-naphthyridin-5-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CVTLEGSZWVPMPP-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907036", + }, + { + IUPACInChIkey: "KCXBRLJFVUQUIR-CQSZACIVSA-N", + dbId: "OYF", + pubChemCompoundId: "156906882", + name: + "(4R)-6-chloro-N-(2,7-naphthyridin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(2,7-naphthyridin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KCXBRLJFVUQUIR-CQSZACIVSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906882", + }, + { + IUPACInChIkey: "COUGPWQMAYMVGH-UHFFFAOYSA-N", + dbId: "OYX", + pubChemCompoundId: "156906978", + name: "N-(2-cyclohexylethyl)-2-(isoquinolin-4-yl)-N-[(thiophen-2-yl)methyl]acetamide", + details: + "N-(2-cyclohexylethyl)-2-(isoquinolin-4-yl)-N-[(thiophen-2-yl)methyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/COUGPWQMAYMVGH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906978", + }, + { + IUPACInChIkey: "CWUQSFBFZRKOOX-KOUJMVCDSA-N", + dbId: "OZ6", + pubChemCompoundId: "162685361", + name: + "(1R,2S,5S)-3-[(2S)-2-(tert-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-N-[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + details: + "(1R,2S,5S)-3-[(2S)-2-(tert-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-N-[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CWUQSFBFZRKOOX-KOUJMVCDSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/162685361", + }, + { + IUPACInChIkey: "RIKAUFAETQRQJH-LUKYLMHMSA-N", + dbId: "OZB", + pubChemCompoundId: "168719760", + name: + "(8S)-N-[(1S)-1-cyano-2-[(3S)-2-oxidanylidenepyrrolidin-3-yl]ethyl]-7-[(2S)-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide", + details: + "(8S)-N-[(1S)-1-cyano-2-[(3S)-2-oxidanylidenepyrrolidin-3-yl]ethyl]-7-[(2S)-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RIKAUFAETQRQJH-LUKYLMHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168719760", + }, + { + IUPACInChIkey: "SHKWJYBWRXZSMY-SFHVURJKSA-N", + dbId: "OZC", + pubChemCompoundId: "169408242", + name: "(3S)-3-(4-chlorophenyl)-1-(isoquinolin-4-yl)piperidin-2-one", + details: "(3S)-3-(4-chlorophenyl)-1-(isoquinolin-4-yl)piperidin-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SHKWJYBWRXZSMY-SFHVURJKSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408242", + }, + { + IUPACInChIkey: "BLRKRWSWARPDLL-XLAORIBOSA-N", + dbId: "OZL", + pubChemCompoundId: "168719761", + name: + "(8~{S})-7-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide", + details: + "(8~{S})-7-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BLRKRWSWARPDLL-XLAORIBOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168719761", + }, + { + IUPACInChIkey: "YZQKBSHQXMHNSJ-UHFFFAOYSA-N", + dbId: "OZX", + pubChemCompoundId: "156907037", + name: "2-(6-chloropyridin-2-yl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(6-chloropyridin-2-yl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YZQKBSHQXMHNSJ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907037", + }, + { + IUPACInChIkey: "BJJZCSKOWCBJFK-UHFFFAOYSA-N", + dbId: "P0X", + pubChemCompoundId: "70744107", + name: "4-[4-(3-chlorophenyl)-3-oxopiperazine-1-carbonyl]quinolin-2(1H)-one", + details: "4-[4-(3-chlorophenyl)-3-oxopiperazine-1-carbonyl]quinolin-2(1H)-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BJJZCSKOWCBJFK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/70744107", + }, + { + IUPACInChIkey: "LDVBEXIDVVQUFA-GHMZBOCLSA-N", + dbId: "P3L", + pubChemCompoundId: "169408243", + name: + "(4R)-6-chloro-N-[(4R)-2-oxopiperidin-4-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-[(4R)-2-oxopiperidin-4-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LDVBEXIDVVQUFA-GHMZBOCLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408243", + }, + { + IUPACInChIkey: "RRQYJINTUHWNHW-UHFFFAOYSA-N", + dbId: "P4G", + pubChemCompoundId: "8179", + name: "1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE", + details: "1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RRQYJINTUHWNHW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/8179", + }, + { + IUPACInChIkey: "FSSOHAWMSBZQQQ-FQEVSTJZSA-N", + dbId: "P4R", + pubChemCompoundId: "156906961", + name: + "(1'M,4S)-6-chloro-1'-(isoquinolin-4-yl)-2,3-dihydrospiro[[1]benzopyran-4,4'-imidazolidine]-2',5'-dione", + details: + "(1'M,4S)-6-chloro-1'-(isoquinolin-4-yl)-2,3-dihydrospiro[[1]benzopyran-4,4'-imidazolidine]-2',5'-dione", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FSSOHAWMSBZQQQ-FQEVSTJZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906961", + }, + { + IUPACInChIkey: "VADPVOZBGIXSAG-UHFFFAOYSA-N", + dbId: "P5X", + pubChemCompoundId: "168475482", + name: + "N-[(4-chlorothiophen-2-yl)methyl]-N-[4-(dimethylamino)phenyl]-2-(isoquinolin-4-yl)acetamide", + details: + "N-[(4-chlorothiophen-2-yl)methyl]-N-[4-(dimethylamino)phenyl]-2-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VADPVOZBGIXSAG-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168475482", + }, + { + IUPACInChIkey: "IIRDTKBZINWQAW-UHFFFAOYSA-N", + dbId: "P6G", + pubChemCompoundId: "17472", + name: "HEXAETHYLENE GLYCOL", + details: "HEXAETHYLENE GLYCOL", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IIRDTKBZINWQAW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/17472", + }, + { + IUPACInChIkey: "CEQRNFLEHMXIOS-UHFFFAOYSA-N", + dbId: "P6I", + pubChemCompoundId: "168475483", + name: + "N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)-N-[4-(methylsulfanyl)phenyl]acetamide", + details: + "N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)-N-[4-(methylsulfanyl)phenyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CEQRNFLEHMXIOS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168475483", + }, + { + IUPACInChIkey: "GANIBVZSZGNMNB-QMMMGPOBSA-N", + dbId: "P6N", + pubChemCompoundId: "7058063", + name: "(2~{S})-2-methyl-3,4-dihydro-2~{H}-naphthalen-1-one", + details: "(2~{S})-2-methyl-3,4-dihydro-2~{H}-naphthalen-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GANIBVZSZGNMNB-QMMMGPOBSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/7058063", + }, + { + IUPACInChIkey: "WTGNNXIIBVYQGH-IBGZPJMESA-N", + dbId: "P6O", + pubChemCompoundId: "169408244", + name: + "(4S)-6-chloro-4-hydroxy-N-(isoquinolin-4-yl)-2-oxo-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: + "(4S)-6-chloro-4-hydroxy-N-(isoquinolin-4-yl)-2-oxo-1,2,3,4-tetrahydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WTGNNXIIBVYQGH-IBGZPJMESA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408244", + }, + { + IUPACInChIkey: "VAAIHZIVXKAKRN-UHFFFAOYSA-N", + dbId: "P6R", + pubChemCompoundId: "168475484", + name: + "N-(4-tert-butylphenyl)-N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)acetamide", + details: + "N-(4-tert-butylphenyl)-N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VAAIHZIVXKAKRN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168475484", + }, + { + IUPACInChIkey: "CKKMMWWEOWLHCZ-UHFFFAOYSA-N", + dbId: "P7L", + pubChemCompoundId: "168475485", + name: + "N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)-N-(4-methoxyphenyl)acetamide", + details: + "N-[(4-chlorothiophen-2-yl)methyl]-2-(isoquinolin-4-yl)-N-(4-methoxyphenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CKKMMWWEOWLHCZ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168475485", + }, + { + IUPACInChIkey: "YNHUBGVMTXFOMC-SNVBAGLBSA-N", + dbId: "P7R", + pubChemCompoundId: "169408245", + name: + "(4R)-6-chloro-N-(1-methyl-2-oxo-2,3-dihydro-1H-imidazo[4,5-c]pyridin-7-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(1-methyl-2-oxo-2,3-dihydro-1H-imidazo[4,5-c]pyridin-7-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YNHUBGVMTXFOMC-SNVBAGLBSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408245", + }, + { + IUPACInChIkey: "DLNUNWNLBKOMMX-PGIRCJHISA-O", + dbId: "P8C", + pubChemCompoundId: "163410438", + name: + "[(1~{S},2~{R})-2-[4,4-bis(fluoranyl)cyclohexyl]cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + details: + "[(1~{S},2~{R})-2-[4,4-bis(fluoranyl)cyclohexyl]cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DLNUNWNLBKOMMX-PGIRCJHISA-O/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163410438", + }, + { + IUPACInChIkey: "VKRZPHPWNNQDHJ-HUWCRECTSA-O", + dbId: "P8L", + pubChemCompoundId: "163410439", + name: + "[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + details: + "[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VKRZPHPWNNQDHJ-HUWCRECTSA-O/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163410439", + }, + { + IUPACInChIkey: "VKRZPHPWNNQDHJ-MWOXCZGJSA-O", + dbId: "P8U", + pubChemCompoundId: "163410440", + name: + "[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + details: + "[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VKRZPHPWNNQDHJ-MWOXCZGJSA-O/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163410440", + }, + { + IUPACInChIkey: "MLMSDXNATONIOS-CYBMUJFWSA-N", + dbId: "P9O", + pubChemCompoundId: "169408246", + name: + "(4R)-6-chloro-N-(5,6,7,8-tetrahydro-2,6-naphthyridin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(5,6,7,8-tetrahydro-2,6-naphthyridin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MLMSDXNATONIOS-CYBMUJFWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408246", + }, + { + IUPACInChIkey: "LVNGJLRDBYCPGB-LDLOPFEMSA-O", + dbId: "PEE", + pubChemCompoundId: "5289131", + name: "1,2-dioleoyl-sn-glycero-3-phosphoethanolamine", + details: "1,2-dioleoyl-sn-glycero-3-phosphoethanolamine", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LVNGJLRDBYCPGB-LDLOPFEMSA-O/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/5289131", + }, + { + IUPACInChIkey: "MTHSVFCYNBDYFN-UHFFFAOYSA-N", + dbId: "PEG", + pubChemCompoundId: "8117", + name: "DI(HYDROXYETHYL)ETHER", + details: "DI(HYDROXYETHYL)ETHER", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MTHSVFCYNBDYFN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/8117", + }, + { + IUPACInChIkey: "RIERSGULWXEJKL-UHFFFAOYSA-N", + dbId: "PF0", + pubChemCompoundId: "252023", + name: "3-hydroxy-2-methylbenzoic acid", + details: "3-hydroxy-2-methylbenzoic acid", imageLink: "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RIERSGULWXEJKL-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/252023", @@ -5779,6 +8010,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XHLKOHSAWQPOFO-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/69590", }, + { + IUPACInChIkey: "FRAUGLSYTUOOAF-FQEVSTJZSA-N", + dbId: "PJ6", + pubChemCompoundId: "156906260", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FRAUGLSYTUOOAF-FQEVSTJZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906260", + }, { IUPACInChIkey: "DLNUNWNLBKOMMX-WUOGMODZSA-O", dbId: "PJR", @@ -5791,6 +8034,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DLNUNWNLBKOMMX-WUOGMODZSA-O/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163410442", }, + { + IUPACInChIkey: "NIZLDWOVHDTVKM-MRXNPFEDSA-N", + dbId: "PJX", + pubChemCompoundId: "156906648", + name: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-1-methyl-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-1-methyl-1,2,3,4-tetrahydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NIZLDWOVHDTVKM-MRXNPFEDSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906648", + }, { IUPACInChIkey: "PXJRMCHXJXWNJG-UHFFFAOYSA-N", dbId: "PK4", @@ -5811,6 +8066,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VOHCMATXIKWIKC-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/146027054", }, + { + IUPACInChIkey: "BKYVVDKZFPPWFC-LLVKDONJSA-N", + dbId: "PKW", + pubChemCompoundId: "169408247", + name: + "(4R)-6-chloro-N-(1-methyl-1H-imidazo[4,5-c]pyridin-7-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(1-methyl-1H-imidazo[4,5-c]pyridin-7-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BKYVVDKZFPPWFC-LLVKDONJSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408247", + }, { IUPACInChIkey: "NBIIXXVUZAFLBC-UHFFFAOYSA-K", dbId: "PO4", @@ -5828,112 +8095,702 @@ export const data: Covid19Data = { name: "N-PROPANOL", details: "N-PROPANOL", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BDERNNFJNOPAEC-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/1031", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BDERNNFJNOPAEC-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/1031", + }, + { + IUPACInChIkey: "XPPKVPWEQAFLFU-UHFFFAOYSA-L", + dbId: "POP", + pubChemCompoundId: "4995", + name: "PYROPHOSPHATE 2-", + details: "PYROPHOSPHATE 2-", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XPPKVPWEQAFLFU-UHFFFAOYSA-L/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/4995", + }, + { + IUPACInChIkey: "ILSGMAUMNXSNQB-FQEVSTJZSA-N", + dbId: "PQ6", + pubChemCompoundId: "156906816", + name: + "(4R)-4-(aminomethyl)-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-4-(aminomethyl)-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ILSGMAUMNXSNQB-FQEVSTJZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906816", + }, + { + IUPACInChIkey: "LQBRGTAIBBFUJJ-ZQDZILKHSA-N", + dbId: "PQL", + pubChemCompoundId: "168476146", + name: + "(8~{S})-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-7-[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide", + details: + "(8~{S})-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-7-[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LQBRGTAIBBFUJJ-ZQDZILKHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168476146", + }, + { + IUPACInChIkey: "WDVSHHCDHLJJJR-UHFFFAOYSA-N", + dbId: "PRL", + pubChemCompoundId: "7099", + name: "PROFLAVIN", + details: "PROFLAVIN", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WDVSHHCDHLJJJR-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/7099", + }, + { + IUPACInChIkey: "HRSANNODOVBCST-UHFFFAOYSA-N", + dbId: "PRO", + pubChemCompoundId: "4930", + name: "PROLINE", + details: "PROLINE", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HRSANNODOVBCST-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/4930", + }, + { + IUPACInChIkey: "OYAZCEPXBNBUAT-QGZVFWFLSA-N", + dbId: "PUU", + pubChemCompoundId: "156906645", + name: + "(4R)-1-acetyl-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: + "(4R)-1-acetyl-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OYAZCEPXBNBUAT-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906645", + }, + { + IUPACInChIkey: "QSGGZCHNCXCCMN-UHFFFAOYSA-N", + dbId: "PVR", + pubChemCompoundId: "156906796", + name: "2-(4-acetylpiperazin-1-yl)-N-(4-cyclopropylpyridin-3-yl)acetamide", + details: "2-(4-acetylpiperazin-1-yl)-N-(4-cyclopropylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QSGGZCHNCXCCMN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906796", + }, + { + IUPACInChIkey: "CDHBUYQLNJHVQW-OAHLLOKOSA-O", + dbId: "PWR", + pubChemCompoundId: "169452768", + name: + "(4~{R})-6-chloranyl-~{N}-(2-oxidanylisoquinolin-4-yl)-3,4-dihydro-2~{H}-chromene-4-carboxamide", + details: + "(4~{R})-6-chloranyl-~{N}-(2-oxidanylisoquinolin-4-yl)-3,4-dihydro-2~{H}-chromene-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CDHBUYQLNJHVQW-OAHLLOKOSA-O/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452768", + }, + { + IUPACInChIkey: "UXKNAXNFIYFMIB-UHFFFAOYSA-N", + dbId: "PYD", + pubChemCompoundId: "445779", + name: "2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE", + details: "2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UXKNAXNFIYFMIB-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/445779", + }, + { + IUPACInChIkey: "ILSGMAUMNXSNQB-HXUWFJFHSA-N", + dbId: "PZ6", + pubChemCompoundId: "156906699", + name: + "(4S)-4-(aminomethyl)-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-4-(aminomethyl)-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ILSGMAUMNXSNQB-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906699", + }, + { + IUPACInChIkey: "ODIAOSOAUUATBH-QGZVFWFLSA-N", + dbId: "Q0I", + pubChemCompoundId: "169452769", + name: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-N-propanoyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-N-propanoyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ODIAOSOAUUATBH-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452769", + }, + { + IUPACInChIkey: "BZNRCHXVMKBNNF-UHFFFAOYSA-N", + dbId: "Q1C", + pubChemCompoundId: "156906798", + name: "2-(4-methylpiperidin-1-yl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(4-methylpiperidin-1-yl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BZNRCHXVMKBNNF-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906798", + }, + { + IUPACInChIkey: "RPTKBNCKDMLWOT-UHFFFAOYSA-N", + dbId: "Q1U", + pubChemCompoundId: "154872713", + name: "2-(3-chlorophenyl)-N-(6-methoxyisoquinolin-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(6-methoxyisoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RPTKBNCKDMLWOT-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154872713", + }, + { + IUPACInChIkey: "SXMQMOJIKMECGG-UHFFFAOYSA-N", + dbId: "Q2G", + pubChemCompoundId: "146125036", + name: "N-(3-chlorophenyl)-N'-(4-methylpyridin-3-yl)urea", + details: "N-(3-chlorophenyl)-N'-(4-methylpyridin-3-yl)urea", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SXMQMOJIKMECGG-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/146125036", + }, + { + IUPACInChIkey: "IOKPKVSTRDCKNE-UHFFFAOYSA-N", + dbId: "Q2U", + pubChemCompoundId: "2558401", + name: "N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + details: "N-[2-(2-methoxyphenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IOKPKVSTRDCKNE-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/2558401", + }, + { + IUPACInChIkey: "QZIZMNNUMXCPSV-GFCCVEGCSA-N", + dbId: "Q36", + pubChemCompoundId: "169408249", + name: "(2R)-2-(3-cyanophenyl)-N-(4-methylpyridin-3-yl)propanamide", + details: "(2R)-2-(3-cyanophenyl)-N-(4-methylpyridin-3-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QZIZMNNUMXCPSV-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408249", + }, + { + IUPACInChIkey: "DJXNJVFEFSWHLY-UHFFFAOYSA-N", + dbId: "Q3C", + pubChemCompoundId: "80971", + name: "quinoline-3-carboxylic acid", + details: "quinoline-3-carboxylic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DJXNJVFEFSWHLY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/80971", + }, + { + IUPACInChIkey: "NNDMILIBNSMJII-UHFFFAOYSA-N", + dbId: "Q3U", + pubChemCompoundId: "154851701", + name: "N-(5-aminopyridin-3-yl)-N'-(3-chlorophenyl)urea", + details: "N-(5-aminopyridin-3-yl)-N'-(3-chlorophenyl)urea", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NNDMILIBNSMJII-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154851701", + }, + { + IUPACInChIkey: "PYUPQBFSNMZSNT-AWEZNQCLSA-N", + dbId: "Q45", + pubChemCompoundId: "169408250", + name: + "2-[(2S)-2-{2-[(methanesulfonyl)amino]ethyl}piperidin-1-yl]-N-(pyridin-3-yl)acetamide", + details: + "2-[(2S)-2-{2-[(methanesulfonyl)amino]ethyl}piperidin-1-yl]-N-(pyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PYUPQBFSNMZSNT-AWEZNQCLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408250", + }, + { + IUPACInChIkey: "YIAJPHRNXAQOJC-KBPBESRZSA-N", + dbId: "Q4F", + pubChemCompoundId: "169452770", + name: + "1-{(1S,4S)-5-[(3-chlorophenyl)methyl]-2,5-diazabicyclo[2.2.1]heptan-2-yl}ethan-1-one", + details: + "1-{(1S,4S)-5-[(3-chlorophenyl)methyl]-2,5-diazabicyclo[2.2.1]heptan-2-yl}ethan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YIAJPHRNXAQOJC-KBPBESRZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452770", + }, + { + IUPACInChIkey: "SLABCQCJIBADKR-UHFFFAOYSA-N", + dbId: "Q4R", + pubChemCompoundId: "154851709", + name: "N~2~-methyl-N-(4-methylpyridin-3-yl)-N~2~-(quinoline-8-sulfonyl)glycinamide", + details: "N~2~-methyl-N-(4-methylpyridin-3-yl)-N~2~-(quinoline-8-sulfonyl)glycinamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SLABCQCJIBADKR-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154851709", + }, + { + IUPACInChIkey: "KLDKNBLMZUYYLD-CIEVZJJWSA-N", + dbId: "Q56", + pubChemCompoundId: "163321826", + name: + "N~2~-{[(naphthalen-2-yl)methoxy]carbonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide", + details: + "N~2~-{[(naphthalen-2-yl)methoxy]carbonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KLDKNBLMZUYYLD-CIEVZJJWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163321826", + }, + { + IUPACInChIkey: "YFRDXIQIPSQACH-UHFFFAOYSA-N", + dbId: "Q5C", + pubChemCompoundId: "154851704", + name: "N-(4-methylpyridin-3-yl)-N~2~-[(pyridin-3-yl)acetyl]glycinamide", + details: "N-(4-methylpyridin-3-yl)-N~2~-[(pyridin-3-yl)acetyl]glycinamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YFRDXIQIPSQACH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154851704", + }, + { + IUPACInChIkey: "BPPBVZDPZTYCEJ-SFHVURJKSA-N", + dbId: "Q5K", + pubChemCompoundId: "169408252", + name: + "(2S)-N-{2-[(4-fluorobenzene-1-sulfonyl)amino]phenyl}-2-hydroxy-2-(pyridin-3-yl)acetamide", + details: + "(2S)-N-{2-[(4-fluorobenzene-1-sulfonyl)amino]phenyl}-2-hydroxy-2-(pyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BPPBVZDPZTYCEJ-SFHVURJKSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408252", + }, + { + IUPACInChIkey: "NZVVEMCRCLJDCU-UHFFFAOYSA-N", + dbId: "Q5R", + pubChemCompoundId: "2083510", + name: "4-(4-phenylpiperazine-1-carbonyl)quinolin-2(1H)-one", + details: "4-(4-phenylpiperazine-1-carbonyl)quinolin-2(1H)-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NZVVEMCRCLJDCU-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/2083510", + }, + { + IUPACInChIkey: "MVIBTDJAVWEOEZ-UHFFFAOYSA-N", + dbId: "Q60", + pubChemCompoundId: "146132136", + name: + "N'-[(1-methyl-1H-1,2,3-triazol-4-yl)methyl]-N-(2-phenylethyl)-N-[(pyridin-3-yl)methyl]urea", + details: + "N'-[(1-methyl-1H-1,2,3-triazol-4-yl)methyl]-N-(2-phenylethyl)-N-[(pyridin-3-yl)methyl]urea", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MVIBTDJAVWEOEZ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/146132136", + }, + { + IUPACInChIkey: "IHPBIPNWENCKAM-JTQLQIEISA-N", + dbId: "Q69", + pubChemCompoundId: "169452771", + name: "N-[(1R)-1-(3-chlorophenyl)-2-hydroxyethyl]acetamide", + details: "N-[(1R)-1-(3-chlorophenyl)-2-hydroxyethyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IHPBIPNWENCKAM-JTQLQIEISA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452771", + }, + { + IUPACInChIkey: "DBUAYOWCIUQXQW-UHFFFAOYSA-N", + dbId: "Q6T", + pubChemCompoundId: "304832", + name: "1,3-benzodioxole-4-carboxylic acid", + details: "1,3-benzodioxole-4-carboxylic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DBUAYOWCIUQXQW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/304832", + }, + { + IUPACInChIkey: "IUAFKLWCODTXIO-UHFFFAOYSA-N", + dbId: "Q6U", + pubChemCompoundId: "19261712", + name: "1-[4-(prop-2-yn-1-yl)piperazin-1-yl]ethan-1-one", + details: "1-[4-(prop-2-yn-1-yl)piperazin-1-yl]ethan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IUAFKLWCODTXIO-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/19261712", + }, + { + IUPACInChIkey: "UAJGNWGHSFBXPE-QMMMGPOBSA-N", + dbId: "Q7C", + pubChemCompoundId: "169452772", + name: "N~3~-acetyl-N~3~-[(3S)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-beta-alaninamide", + details: "N~3~-acetyl-N~3~-[(3S)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-beta-alaninamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UAJGNWGHSFBXPE-QMMMGPOBSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452772", + }, + { + IUPACInChIkey: "XFKXNYYYOGBBGS-UHFFFAOYSA-N", + dbId: "Q7R", + pubChemCompoundId: "885644", + name: "1-[4-(diphenylmethyl)piperazin-1-yl]ethan-1-one", + details: "1-[4-(diphenylmethyl)piperazin-1-yl]ethan-1-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XFKXNYYYOGBBGS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/885644", + }, + { + IUPACInChIkey: "YZWRRAZXWGNXFP-UHFFFAOYSA-N", + dbId: "Q83", + pubChemCompoundId: "167311807", + name: "7-(6-nitro-2,3-dihydroindol-1-yl)-7-oxidanylidene-heptanoic acid", + details: "7-(6-nitro-2,3-dihydroindol-1-yl)-7-oxidanylidene-heptanoic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YZWRRAZXWGNXFP-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/167311807", + }, + { + IUPACInChIkey: "HENQNXDSAFLWPN-UHFFFAOYSA-N", + dbId: "Q8I", + pubChemCompoundId: "82490608", + name: "1-(5-fluoro-1H-indol-3-yl)-N-methylmethanamine", + details: "1-(5-fluoro-1H-indol-3-yl)-N-methylmethanamine", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HENQNXDSAFLWPN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/82490608", + }, + { + IUPACInChIkey: "NKCRZXILCCSPCY-UHFFFAOYSA-N", + dbId: "Q8O", + pubChemCompoundId: "154851707", + name: "2-(1H-benzimidazol-6-yl)-N-(4-methylpyridin-3-yl)acetamide", + details: "2-(1H-benzimidazol-6-yl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NKCRZXILCCSPCY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154851707", + }, + { + IUPACInChIkey: "SNQHLYWSRJDLGK-FQEVSTJZSA-N", + dbId: "Q99", + pubChemCompoundId: "169408256", + name: + "N-[2-(3-chloro-5-{[(2S)-4-oxoazetidin-2-yl]oxy}phenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + details: + "N-[2-(3-chloro-5-{[(2S)-4-oxoazetidin-2-yl]oxy}phenoxy)ethyl]-2-oxo-1,2-dihydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SNQHLYWSRJDLGK-FQEVSTJZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408256", + }, + { + IUPACInChIkey: "QPUDXWFOZNQTRA-HXUWFJFHSA-N", + dbId: "QAO", + pubChemCompoundId: "168451681", + name: + "2-chloro-N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]acetamide", + details: + "2-chloro-N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QPUDXWFOZNQTRA-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168451681", + }, + { + IUPACInChIkey: "WPJAOHFPXGCVSV-HHHXNRCGSA-N", + dbId: "QBR", + pubChemCompoundId: "154878525", + name: + "N-(4-tert-butylphenyl)-N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]furan-2-carboxamide", + details: + "N-(4-tert-butylphenyl)-N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]furan-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WPJAOHFPXGCVSV-HHHXNRCGSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154878525", + }, + { + IUPACInChIkey: "RNKBROMGPBKNFK-KRWDZBQOSA-N", + dbId: "QC3", + pubChemCompoundId: "156906650", + name: "(3S)-3-(3-chlorophenyl)-1-(isoquinolin-4-yl)pyrrolidin-2-one", + details: "(3S)-3-(3-chlorophenyl)-1-(isoquinolin-4-yl)pyrrolidin-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RNKBROMGPBKNFK-KRWDZBQOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906650", + }, + { + IUPACInChIkey: "JCZDGTYSQGAPDN-KRWDZBQOSA-N", + dbId: "QCC", + pubChemCompoundId: "169408257", + name: + "2-(3-chloro-5-{[(2S)-4-oxoazetidin-2-yl]oxy}phenyl)-N-(4-methylpyridin-3-yl)acetamide", + details: + "2-(3-chloro-5-{[(2S)-4-oxoazetidin-2-yl]oxy}phenyl)-N-(4-methylpyridin-3-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JCZDGTYSQGAPDN-KRWDZBQOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408257", + }, + { + IUPACInChIkey: "CXQMRNJWEULDQY-AREMUKBSSA-N", + dbId: "QCO", + pubChemCompoundId: "169408258", + name: + "N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]-N-{4-[(propan-2-yl)oxy]phenyl}-1H-imidazole-4-carboxamide", + details: + "N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]-N-{4-[(propan-2-yl)oxy]phenyl}-1H-imidazole-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CXQMRNJWEULDQY-AREMUKBSSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408258", + }, + { + IUPACInChIkey: "RKWNGNYSSGAJBH-OAHLLOKOSA-N", + dbId: "QD4", + pubChemCompoundId: "169408259", + name: + "(4R)-6-chloro-N~4~-(isoquinolin-4-yl)-3,4-dihydroquinoline-1,4(2H)-dicarboxamide", + details: + "(4R)-6-chloro-N~4~-(isoquinolin-4-yl)-3,4-dihydroquinoline-1,4(2H)-dicarboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RKWNGNYSSGAJBH-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408259", + }, + { + IUPACInChIkey: "UJFDJUBIAPUKQV-UHFFFAOYSA-N", + dbId: "QD9", + pubChemCompoundId: "156906741", + name: + "N-[(3-chlorophenyl)methyl]-N-[5-(dimethylamino)pyridin-2-yl]-2-(isoquinolin-4-yl)acetamide", + details: + "N-[(3-chlorophenyl)methyl]-N-[5-(dimethylamino)pyridin-2-yl]-2-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UJFDJUBIAPUKQV-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906741", + }, + { + IUPACInChIkey: "WGORDSNJHZEQJN-OAHLLOKOSA-N", + dbId: "QDF", + pubChemCompoundId: "169408260", + name: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-2-oxo-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-2-oxo-1,2,3,4-tetrahydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WGORDSNJHZEQJN-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408260", + }, + { + IUPACInChIkey: "HVJFVWJFZCGHBH-UHFFFAOYSA-N", + dbId: "QDU", + pubChemCompoundId: "156906725", + name: "2-(2,5-difluorophenyl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(2,5-difluorophenyl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HVJFVWJFZCGHBH-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906725", + }, + { + IUPACInChIkey: "RMUFMFDOQHTPNN-UHFFFAOYSA-N", + dbId: "QE3", + pubChemCompoundId: "156906729", + name: "2-(5-chloropyridin-2-yl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(5-chloropyridin-2-yl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RMUFMFDOQHTPNN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906729", + }, + { + IUPACInChIkey: "UYNVMODNBIQBMV-BJQOMGFOSA-N", + dbId: "QEL", + pubChemCompoundId: "138753340", + name: "4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol", + details: "4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UYNVMODNBIQBMV-BJQOMGFOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/138753340", + }, + { + IUPACInChIkey: "IMZAGSRTOVZPED-UHFFFAOYSA-N", + dbId: "QER", + pubChemCompoundId: "156906716", + name: "2-(3-fluorophenyl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(3-fluorophenyl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IMZAGSRTOVZPED-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906716", + }, + { + IUPACInChIkey: "VGTLCIFBGULFDX-UHFFFAOYSA-N", + dbId: "QEX", + pubChemCompoundId: "156906719", + name: "N-(isoquinolin-4-yl)-2-(3-methylphenyl)acetamide", + details: "N-(isoquinolin-4-yl)-2-(3-methylphenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VGTLCIFBGULFDX-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906719", + }, + { + IUPACInChIkey: "IBEFUXAVGLACIF-UHFFFAOYSA-N", + dbId: "QF5", + pubChemCompoundId: "156906707", + name: "N-(isoquinolin-4-yl)-2-phenylacetamide", + details: "N-(isoquinolin-4-yl)-2-phenylacetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IBEFUXAVGLACIF-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906707", + }, + { + IUPACInChIkey: "RIBHDGSWGQEONR-UHFFFAOYSA-N", + dbId: "QF9", + pubChemCompoundId: "156906722", + name: "2-(3-chloro-5-cyanophenyl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(3-chloro-5-cyanophenyl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RIBHDGSWGQEONR-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906722", + }, + { + IUPACInChIkey: "XYWOJIRBYMBSKX-UHFFFAOYSA-N", + dbId: "QFL", + pubChemCompoundId: "156906713", + name: "2-(4-fluorophenyl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(4-fluorophenyl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XYWOJIRBYMBSKX-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906713", + }, + { + IUPACInChIkey: "BVFDAXUESDGGQS-UHFFFAOYSA-N", + dbId: "QFU", + pubChemCompoundId: "156906718", + name: "2-(3-cyanophenyl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(3-cyanophenyl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BVFDAXUESDGGQS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906718", + }, + { + IUPACInChIkey: "RXQWWUHGRJKJHB-UHFFFAOYSA-N", + dbId: "QG3", + pubChemCompoundId: "156906721", + name: "2-(3,5-difluorophenyl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(3,5-difluorophenyl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RXQWWUHGRJKJHB-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906721", }, { - IUPACInChIkey: "XPPKVPWEQAFLFU-UHFFFAOYSA-L", - dbId: "POP", - pubChemCompoundId: "4995", - name: "PYROPHOSPHATE 2-", - details: "PYROPHOSPHATE 2-", + IUPACInChIkey: "OGUUARWRDDBIAJ-QGZVFWFLSA-N", + dbId: "QGC", + pubChemCompoundId: "169408261", + name: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-1-[(4H-1,2,4-triazol-3-yl)methyl]-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-1-[(4H-1,2,4-triazol-3-yl)methyl]-1,2,3,4-tetrahydroquinoline-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XPPKVPWEQAFLFU-UHFFFAOYSA-L/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/4995", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OGUUARWRDDBIAJ-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408261", }, { - IUPACInChIkey: "WDVSHHCDHLJJJR-UHFFFAOYSA-N", - dbId: "PRL", - pubChemCompoundId: "7099", - name: "PROFLAVIN", - details: "PROFLAVIN", + IUPACInChIkey: "KPAUUUFZYYGHRE-QHCPKHFHSA-N", + dbId: "QGO", + pubChemCompoundId: "156906636", + name: + "(4S)-6-chloro-4-[2-(dimethylamino)-2-oxoethyl]-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-4-[2-(dimethylamino)-2-oxoethyl]-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WDVSHHCDHLJJJR-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/7099", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KPAUUUFZYYGHRE-QHCPKHFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906636", }, { - IUPACInChIkey: "HRSANNODOVBCST-UHFFFAOYSA-N", - dbId: "PRO", - pubChemCompoundId: "4930", - name: "PROLINE", - details: "PROLINE", + IUPACInChIkey: "WYMRTHFDSBYEJI-MRXNPFEDSA-N", + dbId: "QGX", + pubChemCompoundId: "169408262", + name: "(2R)-2-amino-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)acetamide", + details: "(2R)-2-amino-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)acetamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HRSANNODOVBCST-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/4930", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WYMRTHFDSBYEJI-MRXNPFEDSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408262", }, { - IUPACInChIkey: "UXKNAXNFIYFMIB-UHFFFAOYSA-N", - dbId: "PYD", - pubChemCompoundId: "445779", - name: "2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE", - details: "2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE", + IUPACInChIkey: "AHDULYSHSMKYBB-QRVBRYPASA-N", + dbId: "QH0", + pubChemCompoundId: "169452773", + name: + "(phenylmethyl) ~{N}-[(2~{S})-4-methyl-1-[[(2~{S})-4-nitro-1-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-pentan-2-yl]carbamate", + details: + "(phenylmethyl) ~{N}-[(2~{S})-4-methyl-1-[[(2~{S})-4-nitro-1-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-pentan-2-yl]carbamate", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UXKNAXNFIYFMIB-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/445779", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AHDULYSHSMKYBB-QRVBRYPASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452773", }, { - IUPACInChIkey: "DJXNJVFEFSWHLY-UHFFFAOYSA-N", - dbId: "Q3C", - pubChemCompoundId: "80971", - name: "quinoline-3-carboxylic acid", - details: "quinoline-3-carboxylic acid", + IUPACInChIkey: "FVAXWBDMZWOKGB-UHFFFAOYSA-N", + dbId: "QH6", + pubChemCompoundId: "156906712", + name: "2-(3-chloro-4-fluorophenyl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(3-chloro-4-fluorophenyl)-N-(isoquinolin-4-yl)acetamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DJXNJVFEFSWHLY-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/80971", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FVAXWBDMZWOKGB-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906712", }, { - IUPACInChIkey: "KLDKNBLMZUYYLD-CIEVZJJWSA-N", - dbId: "Q56", - pubChemCompoundId: "163321826", + IUPACInChIkey: "UETIOCMJDODDEB-CQSZACIVSA-N", + dbId: "QHI", + pubChemCompoundId: "169408263", name: - "N~2~-{[(naphthalen-2-yl)methoxy]carbonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide", + "(4R)-6,8-dichloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", details: - "N~2~-{[(naphthalen-2-yl)methoxy]carbonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide", + "(4R)-6,8-dichloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KLDKNBLMZUYYLD-CIEVZJJWSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/163321826", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UETIOCMJDODDEB-CQSZACIVSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408263", }, { - IUPACInChIkey: "DBUAYOWCIUQXQW-UHFFFAOYSA-N", - dbId: "Q6T", - pubChemCompoundId: "304832", - name: "1,3-benzodioxole-4-carboxylic acid", - details: "1,3-benzodioxole-4-carboxylic acid", + IUPACInChIkey: "ATZNGVMHQNZVPP-CYBMUJFWSA-N", + dbId: "QHU", + pubChemCompoundId: "169408264", + name: + "(4R)-6,7-dichloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6,7-dichloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DBUAYOWCIUQXQW-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/304832", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ATZNGVMHQNZVPP-CYBMUJFWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408264", }, { - IUPACInChIkey: "YZWRRAZXWGNXFP-UHFFFAOYSA-N", - dbId: "Q83", - pubChemCompoundId: "167311807", - name: "7-(6-nitro-2,3-dihydroindol-1-yl)-7-oxidanylidene-heptanoic acid", - details: "7-(6-nitro-2,3-dihydroindol-1-yl)-7-oxidanylidene-heptanoic acid", + IUPACInChIkey: "MTMXPPBZDNZMGK-NSHDSACASA-N", + dbId: "QI4", + pubChemCompoundId: "169408265", + name: "(2S)-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)propanamide", + details: "(2S)-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)propanamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YZWRRAZXWGNXFP-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/167311807", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MTMXPPBZDNZMGK-NSHDSACASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408265", }, { - IUPACInChIkey: "QPUDXWFOZNQTRA-HXUWFJFHSA-N", - dbId: "QAO", - pubChemCompoundId: "168451681", + IUPACInChIkey: "ALSINHANKODPSI-GOSISDBHSA-N", + dbId: "QI7", + pubChemCompoundId: "169408266", name: - "2-chloro-N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]acetamide", + "(4R)-6-chloro-1-[(1H-imidazol-2-yl)methyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", details: - "2-chloro-N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]acetamide", + "(4R)-6-chloro-1-[(1H-imidazol-2-yl)methyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QPUDXWFOZNQTRA-HXUWFJFHSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168451681", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ALSINHANKODPSI-GOSISDBHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408266", }, { - IUPACInChIkey: "UYNVMODNBIQBMV-BJQOMGFOSA-N", - dbId: "QEL", - pubChemCompoundId: "138753340", - name: "4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol", - details: "4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol", + IUPACInChIkey: "QFIUTQBIZOZBNY-IBGZPJMESA-N", + dbId: "QIB", + pubChemCompoundId: "156906814", + name: + "(4S)-6-chloro-4-hydroxy-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-4-hydroxy-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UYNVMODNBIQBMV-BJQOMGFOSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/138753340", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QFIUTQBIZOZBNY-IBGZPJMESA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906814", + }, + { + IUPACInChIkey: "ULOCCHXCKCKCRD-OAHLLOKOSA-N", + dbId: "QIM", + pubChemCompoundId: "169408267", + name: + "(4R)-6-chloro-N-[6-(methanesulfonyl)isoquinolin-4-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-[6-(methanesulfonyl)isoquinolin-4-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ULOCCHXCKCKCRD-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408267", }, { IUPACInChIkey: "ILIKJSAPLUUPEN-YMTOWFKASA-N", @@ -5947,6 +8804,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ILIKJSAPLUUPEN-YMTOWFKASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513297", }, + { + IUPACInChIkey: "LPKOUSTWJUXVBF-UHFFFAOYSA-N", + dbId: "QIQ", + pubChemCompoundId: "156906726", + name: "2-(5-chloropyridin-3-yl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(5-chloropyridin-3-yl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LPKOUSTWJUXVBF-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906726", + }, { IUPACInChIkey: "ILIKJSAPLUUPEN-OTYXRUKQSA-N", dbId: "QIR", @@ -5959,6 +8826,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ILIKJSAPLUUPEN-OTYXRUKQSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513298", }, + { + IUPACInChIkey: "TXAXJHHNYJHGRH-KRWDZBQOSA-N", + dbId: "QIT", + pubChemCompoundId: "169408268", + name: "(2S)-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)-2-(methylamino)acetamide", + details: "(2S)-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)-2-(methylamino)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TXAXJHHNYJHGRH-KRWDZBQOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408268", + }, { IUPACInChIkey: "CJCWGFRSMPSRDX-UHFFFAOYSA-N", dbId: "QIW", @@ -5971,6 +8848,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CJCWGFRSMPSRDX-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513236", }, + { + IUPACInChIkey: "NNQIVNFMEXUPCH-CYBMUJFWSA-N", + dbId: "QIZ", + pubChemCompoundId: "156906443", + name: + "(4R)-6-chloro-7-fluoro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-7-fluoro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NNQIVNFMEXUPCH-CYBMUJFWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906443", + }, { IUPACInChIkey: "QXNLGIPKEFPOOU-UHFFFAOYSA-N", dbId: "QJ0", @@ -5983,6 +8872,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QXNLGIPKEFPOOU-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513237", }, + { + IUPACInChIkey: "HQIMBBKRSDUGNW-QGZVFWFLSA-N", + dbId: "QJ6", + pubChemCompoundId: "169408269", + name: "(2R)-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)-2-methoxyacetamide", + details: "(2R)-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)-2-methoxyacetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HQIMBBKRSDUGNW-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408269", + }, { IUPACInChIkey: "JUCHDTFOJXKPLJ-NSHDSACASA-N", dbId: "QJC", @@ -5995,6 +8894,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JUCHDTFOJXKPLJ-NSHDSACASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164575903", }, + { + IUPACInChIkey: "FBODVAAXKKPILK-OAHLLOKOSA-N", + dbId: "QJF", + pubChemCompoundId: "169408270", + name: + "(4R)-6-chloro-N-(6-methoxyisoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(6-methoxyisoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FBODVAAXKKPILK-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408270", + }, { IUPACInChIkey: "REGCRCQNLPXESK-MADCSZMMSA-N", dbId: "QJG", @@ -6007,6 +8918,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/REGCRCQNLPXESK-MADCSZMMSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513239", }, + { + IUPACInChIkey: "XTRUZCCFIYMEIT-DEOSSOPVSA-N", + dbId: "QJL", + pubChemCompoundId: "169408271", + name: + "(4R)-6-chloro-4-{[(N,N-dimethylglycyl)amino]methyl}-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-4-{[(N,N-dimethylglycyl)amino]methyl}-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XTRUZCCFIYMEIT-DEOSSOPVSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408271", + }, { IUPACInChIkey: "UFHUWHHAKBBFLR-LURJTMIESA-N", dbId: "QJO", @@ -6017,6 +8940,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UFHUWHHAKBBFLR-LURJTMIESA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513240", }, + { + IUPACInChIkey: "IOZNTHKFTJIBSE-UHFFFAOYSA-N", + dbId: "QJR", + pubChemCompoundId: "156906657", + name: "2-(3,4-dichlorophenyl)-N-(2,7-naphthyridin-4-yl)acetamide", + details: "2-(3,4-dichlorophenyl)-N-(2,7-naphthyridin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IOZNTHKFTJIBSE-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906657", + }, { IUPACInChIkey: "ZXGIEJJPEJFTMR-GFCCVEGCSA-N", dbId: "QJU", @@ -6029,6 +8962,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZXGIEJJPEJFTMR-GFCCVEGCSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513241", }, + { + IUPACInChIkey: "BSTRMBRUYYSEKM-VWLOTQADSA-N", + dbId: "QK3", + pubChemCompoundId: "169408272", + name: + "(4R)-6-chloro-4-{[2-(1H-imidazol-1-yl)acetamido]methyl}-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-4-{[2-(1H-imidazol-1-yl)acetamido]methyl}-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BSTRMBRUYYSEKM-VWLOTQADSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408272", + }, { IUPACInChIkey: "ZSSRFZSFZVHJBJ-SNVBAGLBSA-N", dbId: "QK6", @@ -6039,6 +8984,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZSSRFZSFZVHJBJ-SNVBAGLBSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513242", }, + { + IUPACInChIkey: "YVSNGUCAHVBFFA-CQSZACIVSA-N", + dbId: "QKB", + pubChemCompoundId: "156906643", + name: + "(4R)-6-chloro-N-(6-fluoroisoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(6-fluoroisoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YVSNGUCAHVBFFA-CQSZACIVSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906643", + }, { IUPACInChIkey: "VROCEIAKWXKTQX-LLVKDONJSA-N", dbId: "QKC", @@ -6049,6 +9006,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VROCEIAKWXKTQX-LLVKDONJSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513243", }, + { + IUPACInChIkey: "CKFWJQDYTZGUBQ-INIZCTEOSA-N", + dbId: "QKI", + pubChemCompoundId: "169408273", + name: "(2S)-2-(3,4-dichlorophenyl)-2-hydroxy-N-(isoquinolin-4-yl)acetamide", + details: "(2S)-2-(3,4-dichlorophenyl)-2-hydroxy-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CKFWJQDYTZGUBQ-INIZCTEOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408273", + }, { IUPACInChIkey: "PQRRGZUIGKDGBP-ROUUACIJSA-N", dbId: "QKL", @@ -6061,6 +9028,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PQRRGZUIGKDGBP-ROUUACIJSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513244", }, + { + IUPACInChIkey: "RSRGRXAYHCGNSK-UHFFFAOYSA-N", + dbId: "QKR", + pubChemCompoundId: "156906696", + name: "2-(3,4-dichlorophenyl)-2,2-difluoro-N-(isoquinolin-4-yl)acetamide", + details: "2-(3,4-dichlorophenyl)-2,2-difluoro-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RSRGRXAYHCGNSK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906696", + }, { IUPACInChIkey: "PQRRGZUIGKDGBP-ZWKOTPCHSA-N", dbId: "QKX", @@ -6073,6 +9050,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PQRRGZUIGKDGBP-ZWKOTPCHSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513245", }, + { + IUPACInChIkey: "LTNIKFLJOUNFAI-UHFFFAOYSA-N", + dbId: "QL3", + pubChemCompoundId: "156906888", + name: + "N-(6-acetamidopyridin-3-yl)-N-[(3-chlorophenyl)methyl]-2-(isoquinolin-4-yl)acetamide", + details: + "N-(6-acetamidopyridin-3-yl)-N-[(3-chlorophenyl)methyl]-2-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LTNIKFLJOUNFAI-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906888", + }, { IUPACInChIkey: "IKFUIKKYPURVDW-UHFFFAOYSA-N", dbId: "QL6", @@ -6083,6 +9072,17 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IKFUIKKYPURVDW-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513246", }, + { + IUPACInChIkey: "NBMMVUFIILVGST-LJQANCHMSA-N", + dbId: "QLC", + pubChemCompoundId: "169408274", + name: "(2R)-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)-2-(2-methoxyethoxy)acetamide", + details: + "(2R)-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)-2-(2-methoxyethoxy)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NBMMVUFIILVGST-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408274", + }, { IUPACInChIkey: "FYBAGYYARXHEJD-GOEBONIOSA-N", dbId: "QLF", @@ -6095,6 +9095,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FYBAGYYARXHEJD-GOEBONIOSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513217", }, + { + IUPACInChIkey: "WFJMXJRCQHLHHH-QFIPXVFZSA-N", + dbId: "QLO", + pubChemCompoundId: "156906638", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-[2-(methylamino)-2-oxoethyl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-[2-(methylamino)-2-oxoethyl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WFJMXJRCQHLHHH-QFIPXVFZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906638", + }, { IUPACInChIkey: "FYBAGYYARXHEJD-ZBFHGGJFSA-N", dbId: "QLU", @@ -6107,6 +9119,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FYBAGYYARXHEJD-ZBFHGGJFSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513218", }, + { + IUPACInChIkey: "QOLVOMOIQPMUFC-NRFANRHFSA-N", + dbId: "QM3", + pubChemCompoundId: "169408276", + name: + "(1'P,3'S)-6-chloro-1'-(isoquinolin-4-yl)-2,3-dihydrospiro[[1]benzopyran-4,3'-pyrrolidine]-2',5'-dione", + details: + "(1'P,3'S)-6-chloro-1'-(isoquinolin-4-yl)-2,3-dihydrospiro[[1]benzopyran-4,3'-pyrrolidine]-2',5'-dione", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QOLVOMOIQPMUFC-NRFANRHFSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408276", + }, { IUPACInChIkey: "HQJPRWMHEFULOK-UHFFFAOYSA-N", dbId: "QM6", @@ -6118,6 +9142,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HQJPRWMHEFULOK-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513247", }, + { + IUPACInChIkey: "RPJBJMKATYTDKW-IBGZPJMESA-N", + dbId: "QM9", + pubChemCompoundId: "156906815", + name: + "(4S)-4-amino-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-4-amino-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RPJBJMKATYTDKW-IBGZPJMESA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906815", + }, { IUPACInChIkey: "QEXGILIVIRXXHM-UHFFFAOYSA-N", dbId: "QMF", @@ -6130,6 +9166,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QEXGILIVIRXXHM-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513248", }, + { + IUPACInChIkey: "PKWRGHQHQAGUOY-QGZVFWFLSA-N", + dbId: "QML", + pubChemCompoundId: "169452774", + name: + "(3S)-5-chloro-N-(isoquinolin-4-yl)-N-propanoyl-2,3-dihydro-1-benzofuran-3-carboxamide", + details: + "(3S)-5-chloro-N-(isoquinolin-4-yl)-N-propanoyl-2,3-dihydro-1-benzofuran-3-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PKWRGHQHQAGUOY-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452774", + }, { IUPACInChIkey: "GNIIMSGFFQRDIB-AEFFLSMTSA-N", dbId: "QMO", @@ -6142,6 +9190,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GNIIMSGFFQRDIB-AEFFLSMTSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513249", }, + { + IUPACInChIkey: "ZITSXTKDCXOESQ-VWLOTQADSA-N", + dbId: "QMX", + pubChemCompoundId: "169408278", + name: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-4-({[(1-methyl-1H-pyrazol-3-yl)methyl]amino}methyl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-4-({[(1-methyl-1H-pyrazol-3-yl)methyl]amino}methyl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZITSXTKDCXOESQ-VWLOTQADSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408278", + }, { IUPACInChIkey: "GNIIMSGFFQRDIB-FUHWJXTLSA-N", dbId: "QN0", @@ -6154,6 +9214,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GNIIMSGFFQRDIB-FUHWJXTLSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513250", }, + { + IUPACInChIkey: "WROWCVDJFRRWBJ-NDEPHWFRSA-N", + dbId: "QN9", + pubChemCompoundId: "156906579", + name: + "(4S)-6-chloro-4-{2-[4-(3-hydroxypropyl)piperazin-1-yl]-2-oxoethyl}-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-4-{2-[4-(3-hydroxypropyl)piperazin-1-yl]-2-oxoethyl}-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WROWCVDJFRRWBJ-NDEPHWFRSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906579", + }, { IUPACInChIkey: "LOAUVZALPPNFOQ-UHFFFAOYSA-N", dbId: "QNC", @@ -6176,6 +9248,17 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NPDVANGOGQJPGW-PXAZEXFGSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513251", }, + { + IUPACInChIkey: "SYSIIGBRVBHDHN-QGZVFWFLSA-N", + dbId: "QNU", + pubChemCompoundId: "156906351", + name: "(4S)-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SYSIIGBRVBHDHN-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906351", + }, { IUPACInChIkey: "NPDVANGOGQJPGW-YVEFUNNKSA-N", dbId: "QNV", @@ -6188,6 +9271,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NPDVANGOGQJPGW-YVEFUNNKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513252", }, + { + IUPACInChIkey: "GPTYSZBZQAEHFD-FQEVSTJZSA-N", + dbId: "QO0", + pubChemCompoundId: "156906655", + name: + "(4S)-6,7-dichloro-N-(isoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6,7-dichloro-N-(isoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GPTYSZBZQAEHFD-FQEVSTJZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906655", + }, { IUPACInChIkey: "NMUBYVYZKDCGHF-QAPCUYQASA-N", dbId: "QO3", @@ -6210,6 +9305,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WOYOJAPRKMBKEU-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/583823", }, + { + IUPACInChIkey: "CJNMPNBDTPWBLB-MRXNPFEDSA-N", + dbId: "QOC", + pubChemCompoundId: "169408280", + name: "(3R)-3-(3,4-dichlorophenyl)-1-(isoquinolin-4-yl)piperidin-2-one", + details: "(3R)-3-(3,4-dichlorophenyl)-1-(isoquinolin-4-yl)piperidin-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CJNMPNBDTPWBLB-MRXNPFEDSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408280", + }, { IUPACInChIkey: "NMUBYVYZKDCGHF-MAUKXSAKSA-N", dbId: "QOF", @@ -6222,6 +9327,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NMUBYVYZKDCGHF-MAUKXSAKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513254", }, + { + IUPACInChIkey: "FPNVOOOMGSKXIQ-UHFFFAOYSA-N", + dbId: "QOO", + pubChemCompoundId: "156906490", + name: + "2-{3-chloro-5-[4-(ethanesulfonyl)piperazin-1-yl]phenyl}-N-(isoquinolin-4-yl)acetamide", + details: + "2-{3-chloro-5-[4-(ethanesulfonyl)piperazin-1-yl]phenyl}-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FPNVOOOMGSKXIQ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906490", + }, { IUPACInChIkey: "QXKJWZYTSHGWOC-KDOFPFPSSA-N", dbId: "QOR", @@ -6234,6 +9351,42 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QXKJWZYTSHGWOC-KDOFPFPSSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513255", }, + { + IUPACInChIkey: "KPHTXNLGFDQMPU-QFIPXVFZSA-N", + dbId: "QOU", + pubChemCompoundId: "169408279", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-(2-methoxyethyl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-(2-methoxyethyl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KPHTXNLGFDQMPU-QFIPXVFZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408279", + }, + { + IUPACInChIkey: "SGXOKACJPFKOBB-HXPMCKFVSA-N", + dbId: "QP0", + pubChemCompoundId: "156907047", + name: + "(3R,4R)-6-chloro-N-(isoquinolin-4-yl)-3-methyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(3R,4R)-6-chloro-N-(isoquinolin-4-yl)-3-methyl-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SGXOKACJPFKOBB-HXPMCKFVSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907047", + }, + { + IUPACInChIkey: "RMXNRMBUTBCRQX-FQEVSTJZSA-N", + dbId: "QP6", + pubChemCompoundId: "156906412", + name: + "(4S)-6,8-difluoro-N-(isoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6,8-difluoro-N-(isoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RMXNRMBUTBCRQX-FQEVSTJZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906412", + }, { IUPACInChIkey: "QXKJWZYTSHGWOC-KBXCAEBGSA-N", dbId: "QP9", @@ -6258,6 +9411,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CXHYRAPCOSLYMC-PXAZEXFGSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513257", }, + { + IUPACInChIkey: "FBLHAFJQTKYFLC-FQEVSTJZSA-N", + dbId: "QPQ", + pubChemCompoundId: "156906348", + name: + "(4S)-6-chloro-7-fluoro-N-(isoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-7-fluoro-N-(isoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FBLHAFJQTKYFLC-FQEVSTJZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906348", + }, { IUPACInChIkey: "CXHYRAPCOSLYMC-YVEFUNNKSA-N", dbId: "QPX", @@ -6270,6 +9435,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CXHYRAPCOSLYMC-YVEFUNNKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513258", }, + { + IUPACInChIkey: "UTAUZKDGXZMBJU-OAHLLOKOSA-N", + dbId: "QQ6", + pubChemCompoundId: "169408281", + name: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzothiopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzothiopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UTAUZKDGXZMBJU-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408281", + }, { IUPACInChIkey: "ZNXPXZYKUWUFEH-SECBINFHSA-N", dbId: "QQ9", @@ -6280,6 +9457,17 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZNXPXZYKUWUFEH-SECBINFHSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155957300", }, + { + IUPACInChIkey: "MDXYQARUSPNBMR-OAQYLSRUSA-N", + dbId: "QQF", + pubChemCompoundId: "169408282", + name: "2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)-N~2~-(methoxyacetyl)-L-alaninamide", + details: + "2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)-N~2~-(methoxyacetyl)-L-alaninamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MDXYQARUSPNBMR-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408282", + }, { IUPACInChIkey: "GOCJXWMVGSTUHD-PBHICJAKSA-N", dbId: "QQI", @@ -6292,6 +9480,30 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GOCJXWMVGSTUHD-PBHICJAKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513260", }, + { + IUPACInChIkey: "FFTZSDWTZYJKTH-FCEWJHQRSA-N", + dbId: "QQL", + pubChemCompoundId: "169452775", + name: + "4-methoxy-~{N}-[(2~{S})-4-methyl-1-[[(2~{S})-4-nitro-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-pentan-2-yl]-1~{H}-indole-2-carboxamide", + details: + "4-methoxy-~{N}-[(2~{S})-4-methyl-1-[[(2~{S})-4-nitro-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-pentan-2-yl]-1~{H}-indole-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FFTZSDWTZYJKTH-FCEWJHQRSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169452775", + }, + { + IUPACInChIkey: "LWLQXUAOFURQPB-ZEQKJWHPSA-N", + dbId: "QQO", + pubChemCompoundId: "169408283", + name: + "(2R)-N-{(2R)-2-(3,4-dichlorophenyl)-1-[(isoquinolin-4-yl)amino]-1-oxopropan-2-yl}-4-(propan-2-yl)morpholine-2-carboxamide", + details: + "(2R)-N-{(2R)-2-(3,4-dichlorophenyl)-1-[(isoquinolin-4-yl)amino]-1-oxopropan-2-yl}-4-(propan-2-yl)morpholine-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LWLQXUAOFURQPB-ZEQKJWHPSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408283", + }, { IUPACInChIkey: "GOCJXWMVGSTUHD-WMLDXEAASA-N", dbId: "QQR", @@ -6304,6 +9516,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GOCJXWMVGSTUHD-WMLDXEAASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513261", }, + { + IUPACInChIkey: "PJTWPJYCTTZBKW-IRPSRAIASA-N", + dbId: "QQU", + pubChemCompoundId: "169408284", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-{2-oxo-2-[(2R)-2-(1H-pyrazol-4-yl)piperidin-1-yl]ethyl}-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-{2-oxo-2-[(2R)-2-(1H-pyrazol-4-yl)piperidin-1-yl]ethyl}-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PJTWPJYCTTZBKW-IRPSRAIASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408284", + }, { IUPACInChIkey: "YYYJOMDAFKUPDC-FUHWJXTLSA-N", dbId: "QR0", @@ -6316,6 +9540,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YYYJOMDAFKUPDC-FUHWJXTLSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513259", }, + { + IUPACInChIkey: "CDPYVHPXDFRJSH-AREMUKBSSA-N", + dbId: "QR5", + pubChemCompoundId: "169408285", + name: + "(2R)-2-[2-(3-cyclopropyl-2-oxoimidazolidin-1-yl)acetamido]-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)propanamide", + details: + "(2R)-2-[2-(3-cyclopropyl-2-oxoimidazolidin-1-yl)acetamido]-2-(3,4-dichlorophenyl)-N-(isoquinolin-4-yl)propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CDPYVHPXDFRJSH-AREMUKBSSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408285", + }, { IUPACInChIkey: "DCWUYIIPJAIWML-MAUKXSAKSA-N", dbId: "QR6", @@ -6328,6 +9564,30 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DCWUYIIPJAIWML-MAUKXSAKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513262", }, + { + IUPACInChIkey: "XZDUBNODKZYWIO-CJYOKPGZSA-N", + dbId: "QR9", + pubChemCompoundId: "169408286", + name: + "(4S)-4-{2-[(1R,4R)-5-acetyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-oxoethyl}-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-4-{2-[(1R,4R)-5-acetyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-oxoethyl}-6-chloro-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XZDUBNODKZYWIO-CJYOKPGZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408286", + }, + { + IUPACInChIkey: "KIVBNAMDYXZGMT-UHFFFAOYSA-N", + dbId: "QRF", + pubChemCompoundId: "156906487", + name: + "2-{3-chloro-5-[4-(furan-2-carbonyl)piperazin-1-yl]phenyl}-N-(isoquinolin-4-yl)acetamide", + details: + "2-{3-chloro-5-[4-(furan-2-carbonyl)piperazin-1-yl]phenyl}-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KIVBNAMDYXZGMT-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906487", + }, { IUPACInChIkey: "AIAOTJWQHRPTHB-ZBFHGGJFSA-N", dbId: "QRI", @@ -6340,6 +9600,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AIAOTJWQHRPTHB-ZBFHGGJFSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513264", }, + { + IUPACInChIkey: "CDOWQSLSBXGJJG-UPCLLVRISA-N", + dbId: "QRS", + pubChemCompoundId: "169408287", + name: + "(3S)-N-{(2R)-2-(3,4-dichlorophenyl)-1-[(isoquinolin-4-yl)amino]-1-oxopropan-2-yl}-1-methylpyrrolidine-3-carboxamide", + details: + "(3S)-N-{(2R)-2-(3,4-dichlorophenyl)-1-[(isoquinolin-4-yl)amino]-1-oxopropan-2-yl}-1-methylpyrrolidine-3-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CDOWQSLSBXGJJG-UPCLLVRISA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408287", + }, { IUPACInChIkey: "HULQKGAWTDMSSA-AEFFLSMTSA-N", dbId: "QRU", @@ -6352,6 +9624,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HULQKGAWTDMSSA-AEFFLSMTSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513220", }, + { + IUPACInChIkey: "JBTXEVNTEFVYSG-NRFANRHFSA-N", + dbId: "QS3", + pubChemCompoundId: "169408288", + name: + "(1'M,4S)-6-chloro-1'-(isoquinolin-4-yl)-3'-methyl-2,3-dihydrospiro[[1]benzopyran-4,4'-imidazolidine]-2',5'-dione", + details: + "(1'M,4S)-6-chloro-1'-(isoquinolin-4-yl)-3'-methyl-2,3-dihydrospiro[[1]benzopyran-4,4'-imidazolidine]-2',5'-dione", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JBTXEVNTEFVYSG-NRFANRHFSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408288", + }, { IUPACInChIkey: "AVBQUGKPWKWVAT-JGVFFNPUSA-N", dbId: "QS6", @@ -6362,6 +9646,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AVBQUGKPWKWVAT-JGVFFNPUSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513265", }, + { + IUPACInChIkey: "FZPBWXZGXXKTLK-IBGZPJMESA-N", + dbId: "QSF", + pubChemCompoundId: "169408289", + name: + "(3S)-5-chloro-N-(isoquinolin-4-yl)-3-methyl-2-oxo-2,3-dihydro-1H-indole-3-carboxamide", + details: + "(3S)-5-chloro-N-(isoquinolin-4-yl)-3-methyl-2-oxo-2,3-dihydro-1H-indole-3-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FZPBWXZGXXKTLK-IBGZPJMESA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408289", + }, { IUPACInChIkey: "HQLHPXNPOGHZFK-UHFFFAOYSA-N", dbId: "QSL", @@ -6374,6 +9670,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HQLHPXNPOGHZFK-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513268", }, + { + IUPACInChIkey: "QQWBTWVCIPHEIH-OSOCVKALSA-N", + dbId: "QSX", + pubChemCompoundId: "169408290", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-{2-[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-oxoethyl}-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-{2-[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-oxoethyl}-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QQWBTWVCIPHEIH-OSOCVKALSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408290", + }, { IUPACInChIkey: "HVWUCQLKBDJYJU-SECBINFHSA-N", dbId: "QT0", @@ -6386,6 +9694,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HVWUCQLKBDJYJU-SECBINFHSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513269", }, + { + IUPACInChIkey: "NHDKKXCWRNZVNJ-LJQANCHMSA-N", + dbId: "QT3", + pubChemCompoundId: "169408291", + name: + "(1R)-7-chloro-N-(isoquinolin-4-yl)-2-methyl-1,2,3,4-tetrahydroisoquinoline-1-carboxamide", + details: + "(1R)-7-chloro-N-(isoquinolin-4-yl)-2-methyl-1,2,3,4-tetrahydroisoquinoline-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NHDKKXCWRNZVNJ-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408291", + }, { IUPACInChIkey: "GCGYUCGJMQIASH-NSHDSACASA-N", dbId: "QT6", @@ -6397,6 +9717,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GCGYUCGJMQIASH-NSHDSACASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164575904", }, + { + IUPACInChIkey: "AJZWQKNTPFPYEK-UHFFFAOYSA-N", + dbId: "QTC", + pubChemCompoundId: "156906450", + name: "2-(3-chloro-5-ethylphenyl)-N-(isoquinolin-4-yl)acetamide", + details: "2-(3-chloro-5-ethylphenyl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AJZWQKNTPFPYEK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906450", + }, { IUPACInChIkey: "GUQNCACKKADRCK-GOSISDBHSA-N", dbId: "QTF", @@ -6409,6 +9739,17 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GUQNCACKKADRCK-GOSISDBHSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513271", }, + { + IUPACInChIkey: "RTYGDBGOBVKIGM-GOSISDBHSA-N", + dbId: "QTL", + pubChemCompoundId: "169408292", + name: "(1R)-7-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-1-carboxamide", + details: + "(1R)-7-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RTYGDBGOBVKIGM-GOSISDBHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408292", + }, { IUPACInChIkey: "SGZPNVIZJRFOKP-SFHVURJKSA-N", dbId: "QTO", @@ -6433,6 +9774,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IPBSEFPXJIGJOL-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155949746", }, + { + IUPACInChIkey: "BEMREGHUYXDNTR-MNNSJKJDSA-N", + dbId: "QU9", + pubChemCompoundId: "169408293", + name: + "(4S)-6-chloro-4-(2-{(2R)-2-[(1H-imidazol-1-yl)methyl]pyrrolidin-1-yl}-2-oxoethyl)-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-4-(2-{(2R)-2-[(1H-imidazol-1-yl)methyl]pyrrolidin-1-yl}-2-oxoethyl)-N-(isoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BEMREGHUYXDNTR-MNNSJKJDSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408293", + }, { IUPACInChIkey: "USMKACAPCCXDJA-SCZZXKLOSA-N", dbId: "QUC", @@ -6455,6 +9808,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/REFJWTPEDVJJIY-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/5280343", }, + { + IUPACInChIkey: "VTQUGRCHBZGAGI-LJQANCHMSA-N", + dbId: "QUQ", + pubChemCompoundId: "169408294", + name: + "(4S)-2-acetyl-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-2-acetyl-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VTQUGRCHBZGAGI-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408294", + }, { IUPACInChIkey: "TZMSGRKICMJVLM-CBAPKCEASA-N", dbId: "QUR", @@ -6467,6 +9832,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TZMSGRKICMJVLM-CBAPKCEASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513274", }, + { + IUPACInChIkey: "SVWQDFXKODKDNW-JOCHJYFZSA-N", + dbId: "QV0", + pubChemCompoundId: "167856813", + name: + "(3'R)-6-chloro-1'-(isoquinolin-4-yl)-2,3-dihydrospiro[[1]benzopyran-4,3'-piperidin]-2'-one", + details: + "(3'R)-6-chloro-1'-(isoquinolin-4-yl)-2,3-dihydrospiro[[1]benzopyran-4,3'-piperidin]-2'-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SVWQDFXKODKDNW-JOCHJYFZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/167856813", + }, { IUPACInChIkey: "TZMSGRKICMJVLM-VXNVDRBHSA-N", dbId: "QV1", @@ -6479,6 +9856,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TZMSGRKICMJVLM-VXNVDRBHSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155966886", }, + { + IUPACInChIkey: "RNKBROMGPBKNFK-QGZVFWFLSA-N", + dbId: "QV9", + pubChemCompoundId: "156906649", + name: "(3R)-3-(3-chlorophenyl)-1-(isoquinolin-4-yl)pyrrolidin-2-one", + details: "(3R)-3-(3-chlorophenyl)-1-(isoquinolin-4-yl)pyrrolidin-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RNKBROMGPBKNFK-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906649", + }, { IUPACInChIkey: "DUKMUYCXRFBQQS-UHFFFAOYSA-N", dbId: "QVC", @@ -6491,6 +9878,30 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DUKMUYCXRFBQQS-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155944029", }, + { + IUPACInChIkey: "VPVQGEOZXDRIEP-GFCCVEGCSA-N", + dbId: "QVG", + pubChemCompoundId: "156906437", + name: + "(4R)-6-chloro-7-fluoro-N-(6-fluoroisoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-7-fluoro-N-(6-fluoroisoquinolin-4-yl)-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VPVQGEOZXDRIEP-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906437", + }, + { + IUPACInChIkey: "ZVIGUBNCYLIRDY-QHCPKHFHSA-N", + dbId: "QVJ", + pubChemCompoundId: "169408295", + name: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-4-{[2-(methylamino)-2-oxoethoxy]methyl}-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-4-{[2-(methylamino)-2-oxoethoxy]methyl}-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZVIGUBNCYLIRDY-QHCPKHFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408295", + }, { IUPACInChIkey: "CHQWAWHCQBTQEW-UHFFFAOYSA-N", dbId: "QVL", @@ -6501,6 +9912,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CHQWAWHCQBTQEW-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513275", }, + { + IUPACInChIkey: "RQFXRLLVVUPDMA-GFCCVEGCSA-N", + dbId: "QVU", + pubChemCompoundId: "169408296", + name: + "(4R)-6,7-dichloro-N-(2,7-naphthyridin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: + "(4R)-6,7-dichloro-N-(2,7-naphthyridin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RQFXRLLVVUPDMA-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408296", + }, { IUPACInChIkey: "PYDRNAYFUJBXAX-AZUAARDMSA-N", dbId: "QVX", @@ -6513,6 +9936,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PYDRNAYFUJBXAX-AZUAARDMSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513276", }, + { + IUPACInChIkey: "PVUJOYSOOMMEIC-QGZVFWFLSA-N", + dbId: "QW1", + pubChemCompoundId: "169408297", + name: + "(4S)-6-chloro-N~4~-(isoquinolin-4-yl)-3,4-dihydroisoquinoline-2,4(1H)-dicarboxamide", + details: + "(4S)-6-chloro-N~4~-(isoquinolin-4-yl)-3,4-dihydroisoquinoline-2,4(1H)-dicarboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PVUJOYSOOMMEIC-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408297", + }, { IUPACInChIkey: "WXQXNCDNVPQRNY-QAPCUYQASA-N", dbId: "QW3", @@ -6537,6 +9972,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WXQXNCDNVPQRNY-MAUKXSAKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513278", }, + { + IUPACInChIkey: "NUXDKRDLDDGPBW-GFCCVEGCSA-N", + dbId: "QWL", + pubChemCompoundId: "156906436", + name: + "(4R)-6,7-dichloro-N-(6-fluoroisoquinolin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: + "(4R)-6,7-dichloro-N-(6-fluoroisoquinolin-4-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NUXDKRDLDDGPBW-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906436", + }, { IUPACInChIkey: "HUIMCJCWKPGPKG-WMLDXEAASA-N", dbId: "QWO", @@ -6549,6 +9996,17 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HUIMCJCWKPGPKG-WMLDXEAASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513281", }, + { + IUPACInChIkey: "GTVALCQWCWDFRA-LJQANCHMSA-N", + dbId: "QWU", + pubChemCompoundId: "169408298", + name: "(3S)-5-chloro-N-(isoquinolin-4-yl)-3-methyl-2,3-dihydro-1H-indole-3-carboxamide", + details: + "(3S)-5-chloro-N-(isoquinolin-4-yl)-3-methyl-2,3-dihydro-1H-indole-3-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GTVALCQWCWDFRA-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408298", + }, { IUPACInChIkey: "CCYMLLLLZCFHPI-QAPCUYQASA-N", dbId: "QWX", @@ -6561,6 +10019,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CCYMLLLLZCFHPI-QAPCUYQASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513279", }, + { + IUPACInChIkey: "SAWVWQKOOIRWCC-GFCCVEGCSA-N", + dbId: "QX3", + pubChemCompoundId: "169408299", + name: + "(4R)-6,7-dichloro-N-(4-cyclopropylpyridin-3-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + details: + "(4R)-6,7-dichloro-N-(4-cyclopropylpyridin-3-yl)-1,2,3,4-tetrahydroquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SAWVWQKOOIRWCC-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408299", + }, { IUPACInChIkey: "CCYMLLLLZCFHPI-MAUKXSAKSA-N", dbId: "QX5", @@ -6573,6 +10043,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CCYMLLLLZCFHPI-MAUKXSAKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513280", }, + { + IUPACInChIkey: "BSUXNZPXAUGDQM-UHFFFAOYSA-N", + dbId: "QX9", + pubChemCompoundId: "156906356", + name: "2-(3-chlorophenyl)-N-(6-methylisoquinolin-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(6-methylisoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BSUXNZPXAUGDQM-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906356", + }, { IUPACInChIkey: "DZWJUUHHWFVLBE-UHFFFAOYSA-N", dbId: "QXC", @@ -6583,6 +10063,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DZWJUUHHWFVLBE-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/110874954", }, + { + IUPACInChIkey: "MQGPZHKWCMCBLI-SOKVYYICSA-N", + dbId: "QXI", + pubChemCompoundId: "169408300", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-{2-[(4R,8S)-8-methyl-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl]-2-oxoethyl}-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-{2-[(4R,8S)-8-methyl-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl]-2-oxoethyl}-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MQGPZHKWCMCBLI-SOKVYYICSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408300", + }, { IUPACInChIkey: "AZZWDFMEYOBJAU-MRVPVSSYSA-N", dbId: "QXL", @@ -6593,6 +10085,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AZZWDFMEYOBJAU-MRVPVSSYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513284", }, + { + IUPACInChIkey: "QOGVQOIEARJILE-UHFFFAOYSA-N", + dbId: "QXR", + pubChemCompoundId: "156906369", + name: "N-(4-tert-butoxypyridin-3-yl)-2-(3-chlorophenyl)acetamide", + details: "N-(4-tert-butoxypyridin-3-yl)-2-(3-chlorophenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QOGVQOIEARJILE-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906369", + }, { IUPACInChIkey: "FIVRTGMLMASIKD-ZJUUUORDSA-N", dbId: "QXS", @@ -6603,6 +10105,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FIVRTGMLMASIKD-ZJUUUORDSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513282", }, + { + IUPACInChIkey: "LTODPBLUNCYZHX-UHFFFAOYSA-N", + dbId: "QXX", + pubChemCompoundId: "156907155", + name: "2-(3-chlorophenyl)-N-[4-(trifluoromethyl)pyridin-3-yl]acetamide", + details: "2-(3-chlorophenyl)-N-[4-(trifluoromethyl)pyridin-3-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LTODPBLUNCYZHX-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156907155", + }, { IUPACInChIkey: "FIVRTGMLMASIKD-VHSXEESVSA-N", dbId: "QY0", @@ -6613,6 +10125,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FIVRTGMLMASIKD-VHSXEESVSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513283", }, + { + IUPACInChIkey: "GMEVLWIDIJTOMX-JOCHJYFZSA-N", + dbId: "QY6", + pubChemCompoundId: "169408301", + name: + "(3R)-6'-chloro-1-(isoquinolin-4-yl)-2',3'-dihydro-1'H-spiro[piperidine-3,4'-quinolin]-2-one", + details: + "(3R)-6'-chloro-1-(isoquinolin-4-yl)-2',3'-dihydro-1'H-spiro[piperidine-3,4'-quinolin]-2-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GMEVLWIDIJTOMX-JOCHJYFZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408301", + }, { IUPACInChIkey: "HULQKGAWTDMSSA-WMZOPIPTSA-N", dbId: "QYC", @@ -6625,6 +10149,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HULQKGAWTDMSSA-WMZOPIPTSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513285", }, + { + IUPACInChIkey: "PAPXBUNGDDTTOJ-FQEVSTJZSA-N", + dbId: "QYI", + pubChemCompoundId: "156906261", + name: + "(4S)-6-chloro-N-(6-fluoroisoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-N-(6-fluoroisoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PAPXBUNGDDTTOJ-FQEVSTJZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906261", + }, { IUPACInChIkey: "HULQKGAWTDMSSA-FUHWJXTLSA-N", dbId: "QYJ", @@ -6637,6 +10173,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HULQKGAWTDMSSA-FUHWJXTLSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513219", }, + { + IUPACInChIkey: "AVYNUDKWZTWDST-LJQANCHMSA-N", + dbId: "QYN", + pubChemCompoundId: "169408302", + name: + "(4S)-6-chloro-2-(1H-imidazole-2-sulfonyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-(1H-imidazole-2-sulfonyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AVYNUDKWZTWDST-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408302", + }, { IUPACInChIkey: "JNVGUGBOYHSUKL-ZJUUUORDSA-N", dbId: "QYO", @@ -6647,6 +10195,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JNVGUGBOYHSUKL-ZJUUUORDSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513286", }, + { + IUPACInChIkey: "ZZQVZHXOXZIEHC-HXUWFJFHSA-N", + dbId: "QYR", + pubChemCompoundId: "169408303", + name: + "(4S)-6-chloro-2-(cyclopropanesulfonyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-(cyclopropanesulfonyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZZQVZHXOXZIEHC-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408303", + }, { IUPACInChIkey: "BHZBRFONZANPNK-FPXQBCRKSA-N", dbId: "QYS", @@ -6669,6 +10229,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JNVGUGBOYHSUKL-VHSXEESVSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513287", }, + { + IUPACInChIkey: "GYXPARZCBIHWKB-LJQANCHMSA-N", + dbId: "QZ0", + pubChemCompoundId: "169408304", + name: + "(4S)-6-chloro-N~4~-(isoquinolin-4-yl)-N~2~,N~2~-dimethyl-3,4-dihydroisoquinoline-2,4(1H)-dicarboxamide", + details: + "(4S)-6-chloro-N~4~-(isoquinolin-4-yl)-N~2~,N~2~-dimethyl-3,4-dihydroisoquinoline-2,4(1H)-dicarboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GYXPARZCBIHWKB-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408304", + }, { IUPACInChIkey: "QYGCDFUDMPADLQ-SECBINFHSA-N", dbId: "QZ6", @@ -6681,6 +10253,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QYGCDFUDMPADLQ-SECBINFHSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513288", }, + { + IUPACInChIkey: "POHNQKSSAWVPGD-LJQANCHMSA-N", + dbId: "QZC", + pubChemCompoundId: "169408305", + name: + "(4S)-6-chloro-2-(dimethylsulfamoyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-(dimethylsulfamoyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/POHNQKSSAWVPGD-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408305", + }, { IUPACInChIkey: "DRYOZRKBYUHNNN-GOSISDBHSA-N", dbId: "QZF", @@ -6693,98 +10277,310 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DRYOZRKBYUHNNN-GOSISDBHSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513289", }, + { + IUPACInChIkey: "DHYOVGSVGPDDRX-OPAMFIHVSA-N", + dbId: "QZL", + pubChemCompoundId: "169408306", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(3R)-3-methylpyrrolidine-1-sulfonyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(3R)-3-methylpyrrolidine-1-sulfonyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DHYOVGSVGPDDRX-OPAMFIHVSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408306", + }, { IUPACInChIkey: "FZCZCOHJHKTFMC-CDMKHQONSA-N", dbId: "QZO", pubChemCompoundId: "164513290", name: - "(1S,6R,7S)-3-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-azabicyclo[4.1.0]heptane-7-carboxylic acid", + "(1S,6R,7S)-3-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-azabicyclo[4.1.0]heptane-7-carboxylic acid", + details: + "(1S,6R,7S)-3-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-azabicyclo[4.1.0]heptane-7-carboxylic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FZCZCOHJHKTFMC-CDMKHQONSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513290", + }, + { + IUPACInChIkey: "DWQRAXAUIMRQLB-QHCPKHFHSA-N", + dbId: "QZU", + pubChemCompoundId: "169408307", + name: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-4-[(prop-2-enamido)methyl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-(isoquinolin-4-yl)-4-[(prop-2-enamido)methyl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DWQRAXAUIMRQLB-QHCPKHFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408307", + }, + { + IUPACInChIkey: "FZCZCOHJHKTFMC-UFGOTCBOSA-N", + dbId: "QZX", + pubChemCompoundId: "164513291", + name: + "(1R,6S,7R)-3-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-azabicyclo[4.1.0]heptane-7-carboxylic acid", + details: + "(1R,6S,7R)-3-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-azabicyclo[4.1.0]heptane-7-carboxylic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FZCZCOHJHKTFMC-UFGOTCBOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513291", + }, + { + IUPACInChIkey: "LZTSPUJFXOCHAI-HXUWFJFHSA-N", + dbId: "R08", + pubChemCompoundId: "169408308", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-(1-methyl-1H-pyrazole-5-carbonyl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-(1-methyl-1H-pyrazole-5-carbonyl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LZTSPUJFXOCHAI-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408308", + }, + { + IUPACInChIkey: "HVBAXYAKMOCXCC-LBPRGKRZSA-N", + dbId: "R0A", + pubChemCompoundId: "164513292", + name: + "[(6S)-8-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-5-oxa-8-azaspiro[3.5]nonan-6-yl]acetic acid", + details: + "[(6S)-8-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-5-oxa-8-azaspiro[3.5]nonan-6-yl]acetic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HVBAXYAKMOCXCC-LBPRGKRZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513292", + }, + { + IUPACInChIkey: "BNHZFFZRNBJNJB-LJQANCHMSA-N", + dbId: "R0F", + pubChemCompoundId: "169408309", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BNHZFFZRNBJNJB-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408309", + }, + { + IUPACInChIkey: "OVLJZTWXOSQLFV-QGZVFWFLSA-N", + dbId: "R0H", + pubChemCompoundId: "164513293", + name: + "methyl (3R)-1-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-(hydroxymethyl)pyrrolidine-3-carboxylate", + details: + "methyl (3R)-1-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-(hydroxymethyl)pyrrolidine-3-carboxylate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OVLJZTWXOSQLFV-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513293", + }, + { + IUPACInChIkey: "LNMHSQWGJNVQMD-LLVKDONJSA-N", + dbId: "R0L", + pubChemCompoundId: "164513294", + name: "(2R)-4-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)morpholine-2-carboxylic acid", + details: "(2R)-4-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)morpholine-2-carboxylic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LNMHSQWGJNVQMD-LLVKDONJSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513294", + }, + { + IUPACInChIkey: "XCYDEVNRWFWHLA-QFIPXVFZSA-N", + dbId: "R0Q", + pubChemCompoundId: "169408310", + name: + "methyl ({(4R)-6-chloro-4-[(isoquinolin-4-yl)carbamoyl]-3,4-dihydro-2H-1-benzopyran-4-yl}methyl)carbamate", + details: + "methyl ({(4R)-6-chloro-4-[(isoquinolin-4-yl)carbamoyl]-3,4-dihydro-2H-1-benzopyran-4-yl}methyl)carbamate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XCYDEVNRWFWHLA-QFIPXVFZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408310", + }, + { + IUPACInChIkey: "SKYVYAVECIKOMJ-QGZVFWFLSA-N", + dbId: "R0R", + pubChemCompoundId: "164513295", + name: + "(8R)-8-fluoro-6-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-2-oxa-6-azaspiro[3.4]octane-8-carboxylic acid", + details: + "(8R)-8-fluoro-6-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-2-oxa-6-azaspiro[3.4]octane-8-carboxylic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SKYVYAVECIKOMJ-QGZVFWFLSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513295", + }, + { + IUPACInChIkey: "SKYVYAVECIKOMJ-KRWDZBQOSA-N", + dbId: "R0W", + pubChemCompoundId: "164513296", + name: + "(8S)-8-fluoro-6-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-2-oxa-6-azaspiro[3.4]octane-8-carboxylic acid", + details: + "(8S)-8-fluoro-6-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-2-oxa-6-azaspiro[3.4]octane-8-carboxylic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SKYVYAVECIKOMJ-KRWDZBQOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513296", + }, + { + IUPACInChIkey: "BDYIWAGQQMTVBW-HXUWFJFHSA-N", + dbId: "R1I", + pubChemCompoundId: "169408311", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-(2-methoxyethyl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-(2-methoxyethyl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BDYIWAGQQMTVBW-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408311", + }, + { + IUPACInChIkey: "YMBXBLIFBSFTRM-UHFFFAOYSA-N", + dbId: "R1U", + pubChemCompoundId: "156906361", + name: "2-(3-chlorophenyl)-N-(1-methyl-1H-pyrazolo[4,3-c]pyridin-7-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(1-methyl-1H-pyrazolo[4,3-c]pyridin-7-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YMBXBLIFBSFTRM-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906361", + }, + { + IUPACInChIkey: "BKFTUQOQWCYOPO-GFCCVEGCSA-N", + dbId: "R2L", + pubChemCompoundId: "169408312", + name: + "(4R)-6-chloro-N-[4-methyl-5-(methylamino)pyridin-3-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4R)-6-chloro-N-[4-methyl-5-(methylamino)pyridin-3-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BKFTUQOQWCYOPO-GFCCVEGCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408312", + }, + { + IUPACInChIkey: "RZBYEPRBZPLACH-RBZQAINGSA-N", + dbId: "R2X", + pubChemCompoundId: "169408313", + name: + "(2S,5R)-N-{(1R)-1-(3-chlorophenyl)-2-[(isoquinolin-4-yl)amino]-2-oxoethyl}-5-(pyrrolidine-1-carbonyl)oxolane-2-carboxamide (non-preferred name)", + details: + "(2S,5R)-N-{(1R)-1-(3-chlorophenyl)-2-[(isoquinolin-4-yl)amino]-2-oxoethyl}-5-(pyrrolidine-1-carbonyl)oxolane-2-carboxamide (non-preferred name)", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RZBYEPRBZPLACH-RBZQAINGSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408313", + }, + { + IUPACInChIkey: "TWIVXCFEBRGEKY-UHFFFAOYSA-N", + dbId: "R30", + pubChemCompoundId: "56932132", + name: "N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}propanamide", + details: + "N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}propanamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TWIVXCFEBRGEKY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/56932132", + }, + { + IUPACInChIkey: "XTXMEPGJZZXFBA-HXUWFJFHSA-N", + dbId: "R3I", + pubChemCompoundId: "169408314", + name: + "(3S)-5-chloro-1'-(6-fluoroisoquinolin-4-yl)-2H-spiro[[1]benzofuran-3,3'-pyrrolidin]-2'-one", + details: + "(3S)-5-chloro-1'-(6-fluoroisoquinolin-4-yl)-2H-spiro[[1]benzofuran-3,3'-pyrrolidin]-2'-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XTXMEPGJZZXFBA-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408314", + }, + { + IUPACInChIkey: "JMLGBOOPVUWCHB-OAQYLSRUSA-N", + dbId: "R43", + pubChemCompoundId: "169408315", + name: + "(4S)-6-chloro-2-(3-cyanoazetidine-1-sulfonyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", details: - "(1S,6R,7S)-3-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-azabicyclo[4.1.0]heptane-7-carboxylic acid", + "(4S)-6-chloro-2-(3-cyanoazetidine-1-sulfonyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FZCZCOHJHKTFMC-CDMKHQONSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513290", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JMLGBOOPVUWCHB-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408315", }, { - IUPACInChIkey: "FZCZCOHJHKTFMC-UFGOTCBOSA-N", - dbId: "QZX", - pubChemCompoundId: "164513291", + IUPACInChIkey: "DAHOAXWCUDTPIS-HXUWFJFHSA-N", + dbId: "R4X", + pubChemCompoundId: "169408316", name: - "(1R,6S,7R)-3-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-azabicyclo[4.1.0]heptane-7-carboxylic acid", + "(4S)-2-(azetidine-1-sulfonyl)-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", details: - "(1R,6S,7R)-3-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-azabicyclo[4.1.0]heptane-7-carboxylic acid", + "(4S)-2-(azetidine-1-sulfonyl)-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FZCZCOHJHKTFMC-UFGOTCBOSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513291", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DAHOAXWCUDTPIS-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408316", }, { - IUPACInChIkey: "HVBAXYAKMOCXCC-LBPRGKRZSA-N", - dbId: "R0A", - pubChemCompoundId: "164513292", + IUPACInChIkey: "BOBUOSCSQDEHLU-OAQYLSRUSA-N", + dbId: "R5H", + pubChemCompoundId: "169408317", name: - "[(6S)-8-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-5-oxa-8-azaspiro[3.5]nonan-6-yl]acetic acid", + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-(3-methoxyazetidine-1-sulfonyl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", details: - "[(6S)-8-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-5-oxa-8-azaspiro[3.5]nonan-6-yl]acetic acid", + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-(3-methoxyazetidine-1-sulfonyl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HVBAXYAKMOCXCC-LBPRGKRZSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513292", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BOBUOSCSQDEHLU-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408317", }, { - IUPACInChIkey: "OVLJZTWXOSQLFV-QGZVFWFLSA-N", - dbId: "R0H", - pubChemCompoundId: "164513293", + IUPACInChIkey: "OANVIGJLLAVHQQ-NRFANRHFSA-N", + dbId: "R5O", + pubChemCompoundId: "169408318", name: - "methyl (3R)-1-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-(hydroxymethyl)pyrrolidine-3-carboxylate", + "(4S)-6-chloro-N-{6-[(methanesulfonyl)amino]isoquinolin-4-yl}-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", details: - "methyl (3R)-1-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-(hydroxymethyl)pyrrolidine-3-carboxylate", + "(4S)-6-chloro-N-{6-[(methanesulfonyl)amino]isoquinolin-4-yl}-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OVLJZTWXOSQLFV-QGZVFWFLSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513293", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OANVIGJLLAVHQQ-NRFANRHFSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408318", }, { - IUPACInChIkey: "LNMHSQWGJNVQMD-LLVKDONJSA-N", - dbId: "R0L", - pubChemCompoundId: "164513294", - name: "(2R)-4-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)morpholine-2-carboxylic acid", - details: "(2R)-4-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)morpholine-2-carboxylic acid", + IUPACInChIkey: "YJEUVMCEEMSKGZ-LJQANCHMSA-N", + dbId: "R66", + pubChemCompoundId: "156906160", + name: "(3R)-3-(3-chlorophenyl)-3-hydroxy-1-(isoquinolin-4-yl)pyrrolidin-2-one", + details: "(3R)-3-(3-chlorophenyl)-3-hydroxy-1-(isoquinolin-4-yl)pyrrolidin-2-one", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LNMHSQWGJNVQMD-LLVKDONJSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513294", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YJEUVMCEEMSKGZ-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156906160", }, { - IUPACInChIkey: "SKYVYAVECIKOMJ-QGZVFWFLSA-N", - dbId: "R0R", - pubChemCompoundId: "164513295", + IUPACInChIkey: "MJNZSTCPXGKUKK-NRFANRHFSA-N", + dbId: "R6L", + pubChemCompoundId: "169408319", name: - "(8R)-8-fluoro-6-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-2-oxa-6-azaspiro[3.4]octane-8-carboxylic acid", + "(4S)-6-chloro-4-methoxy-N-[7-(methylsulfamoyl)isoquinolin-4-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", details: - "(8R)-8-fluoro-6-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-2-oxa-6-azaspiro[3.4]octane-8-carboxylic acid", + "(4S)-6-chloro-4-methoxy-N-[7-(methylsulfamoyl)isoquinolin-4-yl]-3,4-dihydro-2H-1-benzopyran-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SKYVYAVECIKOMJ-QGZVFWFLSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513295", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MJNZSTCPXGKUKK-NRFANRHFSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408319", }, { - IUPACInChIkey: "SKYVYAVECIKOMJ-KRWDZBQOSA-N", - dbId: "R0W", - pubChemCompoundId: "164513296", + IUPACInChIkey: "JTYFNCRZNYLUFK-GOSISDBHSA-N", + dbId: "R76", + pubChemCompoundId: "169408321", name: - "(8S)-8-fluoro-6-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-2-oxa-6-azaspiro[3.4]octane-8-carboxylic acid", + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", details: - "(8S)-8-fluoro-6-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-2-oxa-6-azaspiro[3.4]octane-8-carboxylic acid", + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SKYVYAVECIKOMJ-KRWDZBQOSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513296", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JTYFNCRZNYLUFK-GOSISDBHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408321", }, { - IUPACInChIkey: "TWIVXCFEBRGEKY-UHFFFAOYSA-N", - dbId: "R30", - pubChemCompoundId: "56932132", - name: "N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}propanamide", + IUPACInChIkey: "KLGKDNQJTAVAQU-MRXNPFEDSA-N", + dbId: "R7F", + pubChemCompoundId: "169408320", + name: + "(4R)-6-chloro-N-[6-(2-hydroxypropan-2-yl)isoquinolin-4-yl]-1,2,3,4-tetrahydroquinoline-4-carboxamide", details: - "N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}propanamide", + "(4R)-6-chloro-N-[6-(2-hydroxypropan-2-yl)isoquinolin-4-yl]-1,2,3,4-tetrahydroquinoline-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TWIVXCFEBRGEKY-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/56932132", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KLGKDNQJTAVAQU-MRXNPFEDSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408320", }, { IUPACInChIkey: "VLKIRFAISMBUCB-UHFFFAOYSA-N", @@ -6796,6 +10592,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VLKIRFAISMBUCB-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/576829", }, + { + IUPACInChIkey: "FQAWNARVGLFFLT-FQEVSTJZSA-N", + dbId: "R87", + pubChemCompoundId: "169408322", + name: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + details: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-4-methoxy-3,4-dihydro-2H-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FQAWNARVGLFFLT-FQEVSTJZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408322", + }, { IUPACInChIkey: "LGWQYJCCERJRJX-MZKUHISZSA-N", dbId: "R8H", @@ -6808,6 +10616,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LGWQYJCCERJRJX-MZKUHISZSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156022756", }, + { + IUPACInChIkey: "LMKSIQRBKBYNDJ-HXUWFJFHSA-N", + dbId: "R8I", + pubChemCompoundId: "169408323", + name: + "(4S)-6-chloro-2-{2-[(cyanomethyl)amino]-2-oxoethyl}-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-{2-[(cyanomethyl)amino]-2-oxoethyl}-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LMKSIQRBKBYNDJ-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408323", + }, { IUPACInChIkey: "KZZPVTBGUAEVQI-IBGZPJMESA-N", dbId: "R8K", @@ -6820,6 +10640,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KZZPVTBGUAEVQI-IBGZPJMESA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513299", }, + { + IUPACInChIkey: "ULPUVHVLGAEZBJ-OAQYLSRUSA-N", + dbId: "R8O", + pubChemCompoundId: "169408324", + name: + "(4S)-6-chloro-2-[2-(cyclopropylamino)-2-oxoethyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[2-(cyclopropylamino)-2-oxoethyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ULPUVHVLGAEZBJ-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408324", + }, { IUPACInChIkey: "BNVOKYLFRJDXFX-CYBMUJFWSA-N", dbId: "R8R", @@ -6832,6 +10664,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BNVOKYLFRJDXFX-CYBMUJFWSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513300", }, + { + IUPACInChIkey: "WMOVBRSKQFDZDB-OAQYLSRUSA-N", + dbId: "R8X", + pubChemCompoundId: "169408325", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(2-methoxyethyl)(methyl)sulfamoyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(2-methoxyethyl)(methyl)sulfamoyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WMOVBRSKQFDZDB-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408325", + }, { IUPACInChIkey: "FUQOCUYHHLENJU-LLVKDONJSA-N", dbId: "R8Z", @@ -6844,6 +10688,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FUQOCUYHHLENJU-LLVKDONJSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513301", }, + { + IUPACInChIkey: "JGGCTEVCEKJRSX-HXUWFJFHSA-N", + dbId: "R95", + pubChemCompoundId: "169408326", + name: + "(4S)-6-chloro-2-[(cyanomethyl)(methyl)sulfamoyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[(cyanomethyl)(methyl)sulfamoyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JGGCTEVCEKJRSX-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408326", + }, { IUPACInChIkey: "REQNIKUYNKHSBT-UHFFFAOYSA-N", dbId: "R98", @@ -6854,6 +10710,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/REQNIKUYNKHSBT-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513302", }, + { + IUPACInChIkey: "KXCZEZCRICVIKU-UHFFFAOYSA-N", + dbId: "R9E", + pubChemCompoundId: "169408327", + name: "2-(3-chlorophenyl)-N-(7-fluoro-6-methoxyisoquinolin-4-yl)acetamide", + details: "2-(3-chlorophenyl)-N-(7-fluoro-6-methoxyisoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KXCZEZCRICVIKU-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408327", + }, { IUPACInChIkey: "LFMLBPCSGKLSSW-UHFFFAOYSA-N", dbId: "R9F", @@ -6864,6 +10730,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LFMLBPCSGKLSSW-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/156876771", }, + { + IUPACInChIkey: "GLLFHKJANJSNEG-HXUWFJFHSA-N", + dbId: "R9I", + pubChemCompoundId: "169408328", + name: + "methyl N-[(4S)-6-chloro-4-[(isoquinolin-4-yl)carbamoyl]-3,4-dihydroisoquinoline-2(1H)-sulfonyl]-N-methylglycinate", + details: + "methyl N-[(4S)-6-chloro-4-[(isoquinolin-4-yl)carbamoyl]-3,4-dihydroisoquinoline-2(1H)-sulfonyl]-N-methylglycinate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GLLFHKJANJSNEG-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408328", + }, { IUPACInChIkey: "JVQPJNYREDESAV-UHFFFAOYSA-N", dbId: "R9L", @@ -6876,6 +10754,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JVQPJNYREDESAV-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513303", }, + { + IUPACInChIkey: "NHHHIEXFSUFQCS-OAQYLSRUSA-N", + dbId: "R9R", + pubChemCompoundId: "169408329", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(3-methyl-1,1-dioxo-1lambda~6~-thietan-3-yl)methanesulfonyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(3-methyl-1,1-dioxo-1lambda~6~-thietan-3-yl)methanesulfonyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NHHHIEXFSUFQCS-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408329", + }, { IUPACInChIkey: "NESBXOSECIYAHI-GFCCVEGCSA-N", dbId: "R9U", @@ -6908,6 +10798,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YLUSMKAJIQOXPV-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/604519", }, + { + IUPACInChIkey: "XRLQZDQTHAVICV-OAQYLSRUSA-N", + dbId: "R9Z", + pubChemCompoundId: "169408330", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(1-methoxycyclopropyl)methanesulfonyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(1-methoxycyclopropyl)methanesulfonyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XRLQZDQTHAVICV-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408330", + }, { IUPACInChIkey: "XIVZXMMBMNXYDY-GHMZBOCLSA-N", dbId: "RA3", @@ -6920,6 +10822,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XIVZXMMBMNXYDY-GHMZBOCLSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513305", }, + { + IUPACInChIkey: "UZYMUGANHORAQE-HSZRJFAPSA-N", + dbId: "RAQ", + pubChemCompoundId: "169408331", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(oxan-4-yl)methanesulfonyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(oxan-4-yl)methanesulfonyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UZYMUGANHORAQE-HSZRJFAPSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408331", + }, { IUPACInChIkey: "RSIOYFDJMJLVBY-LLVKDONJSA-N", dbId: "RBB", @@ -6931,6 +10845,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RSIOYFDJMJLVBY-LLVKDONJSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513306", }, + { + IUPACInChIkey: "JKPQSZQLRZDMOG-OAQYLSRUSA-N", + dbId: "RBM", + pubChemCompoundId: "169408332", + name: + "(4S)-6-chloro-2-[(2-cyanoethyl)(methyl)sulfamoyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[(2-cyanoethyl)(methyl)sulfamoyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JKPQSZQLRZDMOG-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408332", + }, { IUPACInChIkey: "XWEGCZDYAZUMMD-SNVBAGLBSA-N", dbId: "RBO", @@ -6941,6 +10867,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XWEGCZDYAZUMMD-SNVBAGLBSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513307", }, + { + IUPACInChIkey: "PKNUWHGBAIVWIT-HXUWFJFHSA-N", + dbId: "RBX", + pubChemCompoundId: "169408333", + name: + "(4S)-6-chloro-2-[ethyl(methyl)sulfamoyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[ethyl(methyl)sulfamoyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PKNUWHGBAIVWIT-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408333", + }, { IUPACInChIkey: "XWEGCZDYAZUMMD-JTQLQIEISA-N", dbId: "RC3", @@ -6951,6 +10889,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XWEGCZDYAZUMMD-JTQLQIEISA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513308", }, + { + IUPACInChIkey: "GJPHCXZDDOVJHH-JOCHJYFZSA-N", + dbId: "RC9", + pubChemCompoundId: "169408334", + name: + "(4S)-6-chloro-2-[(1-cyanocyclobutyl)methanesulfonyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[(1-cyanocyclobutyl)methanesulfonyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GJPHCXZDDOVJHH-JOCHJYFZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408334", + }, { IUPACInChIkey: "RIJVOOFUJLZCSA-GOSISDBHSA-N", dbId: "RCR", @@ -6963,6 +10913,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RIJVOOFUJLZCSA-GOSISDBHSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513309", }, + { + IUPACInChIkey: "NPWJYOOGEVTHDL-UHFFFAOYSA-N", + dbId: "RD5", + pubChemCompoundId: "169408335", + name: + "2-(5-chloro-2-{[(methanesulfonyl)amino]methyl}phenyl)-N-(isoquinolin-4-yl)acetamide", + details: + "2-(5-chloro-2-{[(methanesulfonyl)amino]methyl}phenyl)-N-(isoquinolin-4-yl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NPWJYOOGEVTHDL-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408335", + }, { IUPACInChIkey: "RIJVOOFUJLZCSA-SFHVURJKSA-N", dbId: "RD6", @@ -6975,6 +10937,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RIJVOOFUJLZCSA-SFHVURJKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513310", }, + { + IUPACInChIkey: "PHRFKYXEKRVOIU-LJQANCHMSA-N", + dbId: "RDK", + pubChemCompoundId: "169408336", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-methyl-1,1-dioxo-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-4-methyl-1,1-dioxo-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PHRFKYXEKRVOIU-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408336", + }, { IUPACInChIkey: "GCIZFGPLNCVZMB-GFCCVEGCSA-N", dbId: "RDN", @@ -6986,6 +10960,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GCIZFGPLNCVZMB-GFCCVEGCSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513311", }, + { + IUPACInChIkey: "KEXXOTYEALJBRL-LJQANCHMSA-N", + dbId: "RDQ", + pubChemCompoundId: "169408337", + name: + "(4S)-6-chloro-N-{6-[(methanesulfonyl)amino]isoquinolin-4-yl}-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-{6-[(methanesulfonyl)amino]isoquinolin-4-yl}-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KEXXOTYEALJBRL-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408337", + }, { IUPACInChIkey: "LYLUBGOVYDDPIC-GFCCVEGCSA-N", dbId: "RDU", @@ -6998,6 +10984,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LYLUBGOVYDDPIC-GFCCVEGCSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513312", }, + { + IUPACInChIkey: "RGTAJMPNICITLK-HXUWFJFHSA-N", + dbId: "RDX", + pubChemCompoundId: "169408338", + name: + "(4S)-6-chloro-2-[(2-hydroxyethyl)(methyl)sulfamoyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[(2-hydroxyethyl)(methyl)sulfamoyl]-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RGTAJMPNICITLK-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408338", + }, { IUPACInChIkey: "SHGAZHPCJJPHSC-YCNIQYBTSA-N", dbId: "REA", @@ -7008,6 +11006,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SHGAZHPCJJPHSC-YCNIQYBTSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/444795", }, + { + IUPACInChIkey: "JYNPSSIRIGNSBA-VBKZILBWSA-N", + dbId: "REU", + pubChemCompoundId: "169408339", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(2S)-1-(methylamino)-1-oxopropan-2-yl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(2S)-1-(methylamino)-1-oxopropan-2-yl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JYNPSSIRIGNSBA-VBKZILBWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408339", + }, { IUPACInChIkey: "BXWPLXGLKXAQCW-GWCFXTLKSA-N", dbId: "RF0", @@ -7020,6 +11030,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BXWPLXGLKXAQCW-GWCFXTLKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513313", }, + { + IUPACInChIkey: "ZFCGSGJZJHDJGS-GOSISDBHSA-N", + dbId: "RFF", + pubChemCompoundId: "169408340", + name: + "(4S)-6-chloro-2-[(1-cyanocyclopropyl)methanesulfonyl]-N-(1-methyl-1H-pyrazolo[4,3-c]pyridin-7-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[(1-cyanocyclopropyl)methanesulfonyl]-N-(1-methyl-1H-pyrazolo[4,3-c]pyridin-7-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZFCGSGJZJHDJGS-GOSISDBHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408340", + }, { IUPACInChIkey: "JXLRADUCHRSAKP-NSHDSACASA-N", dbId: "RFI", @@ -7032,6 +11054,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JXLRADUCHRSAKP-NSHDSACASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513314", }, + { + IUPACInChIkey: "BDCZHNBCXCBWRA-HXUWFJFHSA-N", + dbId: "RFR", + pubChemCompoundId: "169408341", + name: + "(4S)-6-chloro-N-{6-[(methanesulfonyl)amino]isoquinolin-4-yl}-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-{6-[(methanesulfonyl)amino]isoquinolin-4-yl}-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BDCZHNBCXCBWRA-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408341", + }, { IUPACInChIkey: "JXLRADUCHRSAKP-LLVKDONJSA-N", dbId: "RFU", @@ -7044,6 +11078,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JXLRADUCHRSAKP-LLVKDONJSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513315", }, + { + IUPACInChIkey: "WWUGNTBTHKNOGA-LJQANCHMSA-N", + dbId: "RG3", + pubChemCompoundId: "169408342", + name: + "(4S)-6-chloro-N-[7-(methanesulfonyl)isoquinolin-4-yl]-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-[7-(methanesulfonyl)isoquinolin-4-yl]-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WWUGNTBTHKNOGA-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408342", + }, { IUPACInChIkey: "BPQSGQBVNCJOKS-LLVKDONJSA-N", dbId: "RG5", @@ -7055,6 +11101,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BPQSGQBVNCJOKS-LLVKDONJSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513316", }, + { + IUPACInChIkey: "OUTGZQNFEUVFAN-UHFFFAOYSA-N", + dbId: "RG9", + pubChemCompoundId: "169408343", + name: "2-(3-chlorophenyl)-N-[7-(2-hydroxypropan-2-yl)isoquinolin-4-yl]acetamide", + details: "2-(3-chlorophenyl)-N-[7-(2-hydroxypropan-2-yl)isoquinolin-4-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OUTGZQNFEUVFAN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408343", + }, { IUPACInChIkey: "RJMONMRVOQBIPJ-LBPRGKRZSA-N", dbId: "RGF", @@ -7067,6 +11123,54 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RJMONMRVOQBIPJ-LBPRGKRZSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513317", }, + { + IUPACInChIkey: "HSFVRLOBMRHDCQ-LJQANCHMSA-N", + dbId: "RGQ", + pubChemCompoundId: "169408344", + name: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HSFVRLOBMRHDCQ-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408344", + }, + { + IUPACInChIkey: "XGZIABVELMXRKW-HXUWFJFHSA-N", + dbId: "RGX", + pubChemCompoundId: "169408345", + name: + "(4S)-6-chloro-2-(cyclopropylsulfamoyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-(cyclopropylsulfamoyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XGZIABVELMXRKW-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408345", + }, + { + IUPACInChIkey: "MZECSNVKOADBBO-HXUWFJFHSA-N", + dbId: "RHI", + pubChemCompoundId: "169408346", + name: + "(4S)-6-chloro-N-[7-(methanesulfonyl)isoquinolin-4-yl]-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-[7-(methanesulfonyl)isoquinolin-4-yl]-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MZECSNVKOADBBO-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408346", + }, + { + IUPACInChIkey: "DEOCOIVMHQCEOX-OAHLLOKOSA-N", + dbId: "RI1", + pubChemCompoundId: "169408347", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-1,1-dioxo-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-1,1-dioxo-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DEOCOIVMHQCEOX-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408347", + }, { IUPACInChIkey: "NYJHYZIQBWNOCJ-SGTLLEGYSA-N", dbId: "RI3", @@ -7079,6 +11183,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NYJHYZIQBWNOCJ-SGTLLEGYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513318", }, + { + IUPACInChIkey: "LLZCKRVJSZRHHK-LJQANCHMSA-N", + dbId: "RI6", + pubChemCompoundId: "169408348", + name: + "(4S)-6-chloro-N-(7-chloroisoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(7-chloroisoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LLZCKRVJSZRHHK-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408348", + }, { IUPACInChIkey: "MJWKGJBWQCLDGE-NSHDSACASA-N", dbId: "RI7", @@ -7089,6 +11205,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MJWKGJBWQCLDGE-NSHDSACASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513319", }, + { + IUPACInChIkey: "UQYRJVFIAXFIFV-XMMPIXPASA-N", + dbId: "RIJ", + pubChemCompoundId: "169408349", + name: + "2-[(1'P,3'S)-6-chloro-1'-(isoquinolin-4-yl)-2',5'-dioxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + details: + "2-[(1'P,3'S)-6-chloro-1'-(isoquinolin-4-yl)-2',5'-dioxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UQYRJVFIAXFIFV-XMMPIXPASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408349", + }, { IUPACInChIkey: "USMUUUCYHOVMGT-LLVKDONJSA-N", dbId: "RIK", @@ -7100,6 +11228,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/USMUUUCYHOVMGT-LLVKDONJSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164575905", }, + { + IUPACInChIkey: "XNJZKRXHKUJCAT-UHFFFAOYSA-N", + dbId: "RIU", + pubChemCompoundId: "169408350", + name: "2-(3-chlorophenyl)-N-{6-[2-(dimethylamino)ethoxy]isoquinolin-4-yl}acetamide", + details: "2-(3-chlorophenyl)-N-{6-[2-(dimethylamino)ethoxy]isoquinolin-4-yl}acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XNJZKRXHKUJCAT-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408350", + }, { IUPACInChIkey: "NFUGNDSRCURWKQ-UHFFFAOYSA-N", dbId: "RIW", @@ -7110,6 +11248,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NFUGNDSRCURWKQ-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513321", }, + { + IUPACInChIkey: "BOQXHOIRFSIWNF-LJQANCHMSA-N", + dbId: "RIY", + pubChemCompoundId: "169408351", + name: + "(4S)-6-chloro-2-(ethylsulfamoyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-(ethylsulfamoyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BOQXHOIRFSIWNF-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408351", + }, { IUPACInChIkey: "VLGDVQRYEOXYDY-NEPJUHHUSA-N", dbId: "RIZ", @@ -7122,6 +11272,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VLGDVQRYEOXYDY-NEPJUHHUSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513322", }, + { + IUPACInChIkey: "OOJDKYAMUUAETB-UHFFFAOYSA-N", + dbId: "RJ3", + pubChemCompoundId: "169408352", + name: "4-[2-(3-chlorophenyl)acetamido]isoquinoline-7-carboxylic acid", + details: "4-[2-(3-chlorophenyl)acetamido]isoquinoline-7-carboxylic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OOJDKYAMUUAETB-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408352", + }, { IUPACInChIkey: "VLGDVQRYEOXYDY-NWDGAFQWSA-N", dbId: "RJ9", @@ -7134,6 +11294,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VLGDVQRYEOXYDY-NWDGAFQWSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513323", }, + { + IUPACInChIkey: "SCCMCXOVZPXNKG-GOSISDBHSA-N", + dbId: "RJF", + pubChemCompoundId: "169408353", + name: + "(4S)-6-chloro-2-[2-(methylamino)-2-oxoethyl]-N-(5-methylisoquinolin-4-yl)-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[2-(methylamino)-2-oxoethyl]-N-(5-methylisoquinolin-4-yl)-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SCCMCXOVZPXNKG-GOSISDBHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408353", + }, { IUPACInChIkey: "YVVRFBXSKUTJJG-UHFFFAOYSA-N", dbId: "RJL", @@ -7146,6 +11318,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YVVRFBXSKUTJJG-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513324", }, + { + IUPACInChIkey: "ZCROYMPHCXUWGH-GOSISDBHSA-N", + dbId: "RJO", + pubChemCompoundId: "169408354", + name: + "(4S)-6-chloro-N-(6-fluoroisoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(6-fluoroisoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZCROYMPHCXUWGH-GOSISDBHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408354", + }, { IUPACInChIkey: "LSGXMSZZZZALLZ-UHFFFAOYSA-N", dbId: "RJS", @@ -7158,6 +11342,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LSGXMSZZZZALLZ-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164575906", }, + { + IUPACInChIkey: "UKFWXTVAPKPVEE-UHFFFAOYSA-N", + dbId: "RJX", + pubChemCompoundId: "169408355", + name: "4-[2-(3-chlorophenyl)acetamido]isoquinoline-6-carboxylic acid", + details: "4-[2-(3-chlorophenyl)acetamido]isoquinoline-6-carboxylic acid", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UKFWXTVAPKPVEE-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408355", + }, { IUPACInChIkey: "BORZWBYDXGSJEW-UHFFFAOYSA-N", dbId: "RK0", @@ -7168,6 +11362,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BORZWBYDXGSJEW-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513326", }, + { + IUPACInChIkey: "YTZPJQXEGVHVLU-UHFFFAOYSA-N", + dbId: "RK6", + pubChemCompoundId: "169408356", + name: "4-[2-(3-chlorophenyl)acetamido]-N-methylisoquinoline-7-carboxamide", + details: "4-[2-(3-chlorophenyl)acetamido]-N-methylisoquinoline-7-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YTZPJQXEGVHVLU-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408356", + }, { IUPACInChIkey: "AUZRVQWOOJLPJO-UHFFFAOYSA-N", dbId: "RK9", @@ -7178,6 +11382,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AUZRVQWOOJLPJO-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513327", }, + { + IUPACInChIkey: "ZNASZZIYVWAOJK-OAQYLSRUSA-N", + dbId: "RKC", + pubChemCompoundId: "169408357", + name: + "(3'R)-6-chloro-1'-(isoquinolin-4-yl)-2,3-dihydrospiro[[1]benzopyran-4,3'-pyrrolidin]-2'-one", + details: + "(3'R)-6-chloro-1'-(isoquinolin-4-yl)-2,3-dihydrospiro[[1]benzopyran-4,3'-pyrrolidin]-2'-one", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZNASZZIYVWAOJK-OAQYLSRUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408357", + }, { IUPACInChIkey: "VCJDDYFVULHGFW-UHFFFAOYSA-N", dbId: "RKI", @@ -7188,6 +11404,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VCJDDYFVULHGFW-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513328", }, + { + IUPACInChIkey: "YDRXFINTBCAEPL-UHFFFAOYSA-N", + dbId: "RKR", + pubChemCompoundId: "169408358", + name: "2-(3-chlorophenyl)-N-[6-(dimethylamino)isoquinolin-4-yl]acetamide", + details: "2-(3-chlorophenyl)-N-[6-(dimethylamino)isoquinolin-4-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YDRXFINTBCAEPL-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408358", + }, { IUPACInChIkey: "QCPOODMPJHYVRY-ZDUSSCGKSA-N", dbId: "RKU", @@ -7200,6 +11426,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QCPOODMPJHYVRY-ZDUSSCGKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513329", }, + { + IUPACInChIkey: "NWQAGGFPSKOROJ-UHFFFAOYSA-N", + dbId: "RL0", + pubChemCompoundId: "169408359", + name: + "2-(3-chlorophenyl)-N-{6-[(methanesulfonyl)(methyl)amino]isoquinolin-4-yl}acetamide", + details: + "2-(3-chlorophenyl)-N-{6-[(methanesulfonyl)(methyl)amino]isoquinolin-4-yl}acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NWQAGGFPSKOROJ-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408359", + }, { IUPACInChIkey: "XUTVGWPXCMPLPZ-UHFFFAOYSA-N", dbId: "RL5", @@ -7212,6 +11450,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XUTVGWPXCMPLPZ-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513330", }, + { + IUPACInChIkey: "MQGFIRADDQPUFN-UHFFFAOYSA-N", + dbId: "RL8", + pubChemCompoundId: "169408360", + name: "4-[2-(3-chlorophenyl)acetamido]-N-methylisoquinoline-6-carboxamide", + details: "4-[2-(3-chlorophenyl)acetamido]-N-methylisoquinoline-6-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MQGFIRADDQPUFN-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408360", + }, { IUPACInChIkey: "JKFYNJOLPXQHQS-UHFFFAOYSA-N", dbId: "RL9", @@ -7222,6 +11470,17 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JKFYNJOLPXQHQS-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513331", }, + { + IUPACInChIkey: "MIPAPSMIEZDAGL-UHFFFAOYSA-N", + dbId: "RLH", + pubChemCompoundId: "169408361", + name: "2-(3-chlorophenyl)-N-{7-[2-(pyrrolidin-1-yl)ethoxy]isoquinolin-4-yl}acetamide", + details: + "2-(3-chlorophenyl)-N-{7-[2-(pyrrolidin-1-yl)ethoxy]isoquinolin-4-yl}acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MIPAPSMIEZDAGL-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408361", + }, { IUPACInChIkey: "CLXWTDODTCGGCR-UHFFFAOYSA-N", dbId: "RLN", @@ -7232,6 +11491,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CLXWTDODTCGGCR-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513332", }, + { + IUPACInChIkey: "TUGUABFGTODCQJ-TZIWHRDSSA-N", + dbId: "RLR", + pubChemCompoundId: "169408362", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(3R)-2-oxopyrrolidin-3-yl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(3R)-2-oxopyrrolidin-3-yl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/TUGUABFGTODCQJ-TZIWHRDSSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408362", + }, { IUPACInChIkey: "FSOPVDVKYHLXNE-GFCCVEGCSA-N", dbId: "RLU", @@ -7244,6 +11515,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FSOPVDVKYHLXNE-GFCCVEGCSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164575907", }, + { + IUPACInChIkey: "VLCYSYPHYNBYLW-UHFFFAOYSA-N", + dbId: "RM3", + pubChemCompoundId: "169408363", + name: "2-(3-chlorophenyl)-N-[7-(dimethylamino)isoquinolin-4-yl]acetamide", + details: "2-(3-chlorophenyl)-N-[7-(dimethylamino)isoquinolin-4-yl]acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VLCYSYPHYNBYLW-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408363", + }, { IUPACInChIkey: "BFCQGZXJYIJBQN-UHFFFAOYSA-N", dbId: "RM6", @@ -7256,6 +11537,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BFCQGZXJYIJBQN-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513333", }, + { + IUPACInChIkey: "LASXIBJOIXVTDT-UHFFFAOYSA-N", + dbId: "RMI", + pubChemCompoundId: "169408364", + name: "2-(3-chlorophenyl)-N-{7-[2-(dimethylamino)ethoxy]isoquinolin-4-yl}acetamide", + details: "2-(3-chlorophenyl)-N-{7-[2-(dimethylamino)ethoxy]isoquinolin-4-yl}acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LASXIBJOIXVTDT-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408364", + }, { IUPACInChIkey: "WARQQVLLUYXXAU-UHFFFAOYSA-N", dbId: "RMU", @@ -7278,6 +11569,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WQEPZBNLBWDIRZ-NRFANRHFSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/9798466", }, + { + IUPACInChIkey: "QXFKQZYRPVUBJK-UHFFFAOYSA-N", + dbId: "RN0", + pubChemCompoundId: "169408365", + name: "4-[2-(3-chlorophenyl)acetamido]isoquinolin-6-yl methanesulfonate", + details: "4-[2-(3-chlorophenyl)acetamido]isoquinolin-6-yl methanesulfonate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QXFKQZYRPVUBJK-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408365", + }, { IUPACInChIkey: "YHUMVPIVKSGDRU-UHFFFAOYSA-N", dbId: "RNC", @@ -7290,6 +11591,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YHUMVPIVKSGDRU-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513335", }, + { + IUPACInChIkey: "VNRACBLIZVOLEF-JOCHJYFZSA-N", + dbId: "RNI", + pubChemCompoundId: "169408366", + name: + "(4S)-6-chloro-2-[(1-cyanocyclopropyl)methanesulfonyl]-N-{7-[(methanesulfonyl)amino]isoquinolin-4-yl}-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[(1-cyanocyclopropyl)methanesulfonyl]-N-{7-[(methanesulfonyl)amino]isoquinolin-4-yl}-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VNRACBLIZVOLEF-JOCHJYFZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408366", + }, { IUPACInChIkey: "ZHMWBBORZYXPPK-JGVFFNPUSA-N", dbId: "RNL", @@ -7323,6 +11636,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XCWBRJUZKURZCA-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513337", }, + { + IUPACInChIkey: "IODVSEDZYFGXPU-UHFFFAOYSA-N", + dbId: "ROZ", + pubChemCompoundId: "169408367", + name: "4-[2-(3-chlorophenyl)acetamido]isoquinoline-6-carboxamide", + details: "4-[2-(3-chlorophenyl)acetamido]isoquinoline-6-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IODVSEDZYFGXPU-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408367", + }, { IUPACInChIkey: "KCUXIGLONPMWPT-UHFFFAOYSA-N", dbId: "RP0", @@ -7333,6 +11656,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KCUXIGLONPMWPT-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513338", }, + { + IUPACInChIkey: "CKGZDMAYPZCRDY-UHFFFAOYSA-N", + dbId: "RPK", + pubChemCompoundId: "169408368", + name: "N-(6-acetamidoisoquinolin-4-yl)-2-(3-chlorophenyl)acetamide", + details: "N-(6-acetamidoisoquinolin-4-yl)-2-(3-chlorophenyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CKGZDMAYPZCRDY-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408368", + }, { IUPACInChIkey: "UYBDWJKXHXPRQV-BXUZGUMPSA-N", dbId: "RPU", @@ -7345,6 +11678,30 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UYBDWJKXHXPRQV-BXUZGUMPSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513339", }, + { + IUPACInChIkey: "KZHDXVVSRJEQJU-XMMPIXPASA-N", + dbId: "RPZ", + pubChemCompoundId: "169408369", + name: + "2-[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + details: + "2-[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KZHDXVVSRJEQJU-XMMPIXPASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408369", + }, + { + IUPACInChIkey: "VVKKILAVDZOKCI-GOSISDBHSA-N", + dbId: "RQ6", + pubChemCompoundId: "169408370", + name: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VVKKILAVDZOKCI-GOSISDBHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408370", + }, { IUPACInChIkey: "SWEUDKUVJIPKFX-ZDUSSCGKSA-N", dbId: "RQ8", @@ -7368,6 +11725,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DQMGMSFESKLRGX-MRVPVSSYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164575908", }, + { + IUPACInChIkey: "GHTWIRSPUGHMTO-HXUWFJFHSA-N", + dbId: "RQF", + pubChemCompoundId: "169408372", + name: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-1-oxo-2-[2-oxo-2-(propylamino)ethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-1-oxo-2-[2-oxo-2-(propylamino)ethyl]-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GHTWIRSPUGHMTO-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408372", + }, { IUPACInChIkey: "OWEGWHBOCFMBLP-AWEZNQCLSA-N", dbId: "RQH", @@ -7390,6 +11759,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MWIHDBPJGZGAQB-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513342", }, + { + IUPACInChIkey: "CAOMTBMUDFASIS-UHFFFAOYSA-N", + dbId: "RQO", + pubChemCompoundId: "169408371", + name: "4-[2-(3-chlorophenyl)acetamido]-N,N-dimethylisoquinoline-6-carboxamide", + details: "4-[2-(3-chlorophenyl)acetamido]-N,N-dimethylisoquinoline-6-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CAOMTBMUDFASIS-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408371", + }, { IUPACInChIkey: "QXCOOMUNLBGYCR-SFYZADRCSA-N", dbId: "RQR", @@ -7402,6 +11781,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QXCOOMUNLBGYCR-SFYZADRCSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513343", }, + { + IUPACInChIkey: "HANIMTZEYQYKPD-UHFFFAOYSA-N", + dbId: "RR0", + pubChemCompoundId: "169408373", + name: + "(2r,4r)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-2,3-dihydro-4H-2,4-methano-1-benzopyran-4-carboxamide", + details: + "(2r,4r)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-2,3-dihydro-4H-2,4-methano-1-benzopyran-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HANIMTZEYQYKPD-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408373", + }, { IUPACInChIkey: "MNVMBEGUZDUKJW-UHFFFAOYSA-N", dbId: "RR3", @@ -7414,6 +11805,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MNVMBEGUZDUKJW-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513344", }, + { + IUPACInChIkey: "BLCZQPHMPCEAIL-HXUWFJFHSA-N", + dbId: "RRD", + pubChemCompoundId: "169408374", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-{2-[(oxetan-3-yl)amino]-2-oxoethyl}-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-{2-[(oxetan-3-yl)amino]-2-oxoethyl}-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BLCZQPHMPCEAIL-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408374", + }, { IUPACInChIkey: "KTTMBKKRQWCTBJ-WBMJQRKESA-N", dbId: "RRF", @@ -7426,6 +11829,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KTTMBKKRQWCTBJ-WBMJQRKESA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513345", }, + { + IUPACInChIkey: "ZFIJDHJQBMZSSD-AREMUKBSSA-N", + dbId: "RRU", + pubChemCompoundId: "169408375", + name: + "1-{[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + details: + "1-{[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZFIJDHJQBMZSSD-AREMUKBSSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408375", + }, { IUPACInChIkey: "KTTMBKKRQWCTBJ-BLLLJJGKSA-N", dbId: "RS0", @@ -7438,6 +11853,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KTTMBKKRQWCTBJ-BLLLJJGKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513346", }, + { + IUPACInChIkey: "MMRWQEDBDJLRBA-HXUWFJFHSA-N", + dbId: "RS6", + pubChemCompoundId: "169408376", + name: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-1-oxo-2-{2-oxo-2-[(propan-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(7-fluoroisoquinolin-4-yl)-1-oxo-2-{2-oxo-2-[(propan-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MMRWQEDBDJLRBA-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408376", + }, { IUPACInChIkey: "CXHYRAPCOSLYMC-SJCJKPOMSA-N", dbId: "RS9", @@ -7450,6 +11877,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CXHYRAPCOSLYMC-SJCJKPOMSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513347", }, + { + IUPACInChIkey: "DLGHRHRFJGLPSU-UHFFFAOYSA-N", + dbId: "RSL", + pubChemCompoundId: "169408377", + name: "4-[2-(3-chlorophenyl)acetamido]isoquinolin-7-yl methanesulfonate", + details: "4-[2-(3-chlorophenyl)acetamido]isoquinolin-7-yl methanesulfonate", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DLGHRHRFJGLPSU-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408377", + }, { IUPACInChIkey: "GHMLBKRAJCXXBS-UHFFFAOYSA-N", dbId: "RSR", @@ -7462,6 +11899,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GHMLBKRAJCXXBS-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/5054", }, + { + IUPACInChIkey: "PAAVFAOBFJLLJO-HXUWFJFHSA-N", + dbId: "RT4", + pubChemCompoundId: "169408378", + name: + "(4S)-6-chloro-2-[2-(cyclopropylamino)-2-oxoethyl]-N-(isoquinolin-4-yl)-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-[2-(cyclopropylamino)-2-oxoethyl]-N-(isoquinolin-4-yl)-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PAAVFAOBFJLLJO-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408378", + }, { IUPACInChIkey: "CDBGIGRGQZLBAF-SFHVURJKSA-N", dbId: "RT5", @@ -7474,6 +11923,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CDBGIGRGQZLBAF-SFHVURJKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513349", }, + { + IUPACInChIkey: "AHKRSFUFGSQVJJ-HXUWFJFHSA-N", + dbId: "RT9", + pubChemCompoundId: "169408379", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(1-methoxycyclopropyl)methanesulfonyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[(1-methoxycyclopropyl)methanesulfonyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AHKRSFUFGSQVJJ-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408379", + }, { IUPACInChIkey: "DEQJMLORKTWBPR-WMLDXEAASA-N", dbId: "RTI", @@ -7511,14 +11972,16 @@ export const data: Covid19Data = { externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513351", }, { - IUPACInChIkey: "VCYYRDKGHLOTQU-WCTZXXKLSA-N", - dbId: "RTV", - pubChemCompoundId: "444527", - name: "2-(acetylamino)-1,5-anhydro-2-deoxy-D-mannitol", - details: "2-(acetylamino)-1,5-anhydro-2-deoxy-D-mannitol", + IUPACInChIkey: "MYVKMPCLLUQWHY-HXUWFJFHSA-N", + dbId: "RV0", + pubChemCompoundId: "169408381", + name: + "(4S)-6-chloro-4-ethyl-N-(isoquinolin-4-yl)-1,1-dioxo-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + details: + "(4S)-6-chloro-4-ethyl-N-(isoquinolin-4-yl)-1,1-dioxo-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VCYYRDKGHLOTQU-WCTZXXKLSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/444527", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MYVKMPCLLUQWHY-HXUWFJFHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408381", }, { IUPACInChIkey: "ZBKHDPZXZUDEDP-UHFFFAOYSA-N", @@ -7552,6 +12015,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XGVGMKBKRWQGTN-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513353", }, + { + IUPACInChIkey: "IDFXYIJLVZRFSF-LJQANCHMSA-N", + dbId: "RVL", + pubChemCompoundId: "169408382", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[1-(methylcarbamoyl)cyclopropyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-[1-(methylcarbamoyl)cyclopropyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IDFXYIJLVZRFSF-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408382", + }, { IUPACInChIkey: "SILGAHKEYSAGRL-SNVBAGLBSA-N", dbId: "RVO", @@ -7572,6 +12047,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SDWIOXKHTFOULX-AFCXAGJDSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/100252", }, + { + IUPACInChIkey: "HAFJUHKWFUKUJR-OAHLLOKOSA-N", + dbId: "RVR", + pubChemCompoundId: "169408383", + name: + "(4S)-6-chloro-1,1-dioxo-N-(5,6,7,8-tetrahydroisoquinolin-4-yl)-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + details: + "(4S)-6-chloro-1,1-dioxo-N-(5,6,7,8-tetrahydroisoquinolin-4-yl)-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HAFJUHKWFUKUJR-OAHLLOKOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408383", + }, { IUPACInChIkey: "BJZXTCJBAZHJRX-RBUKOAKNSA-N", dbId: "RVS", @@ -7595,6 +12082,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JUSMHIGDXPKSID-QYESYBIKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/29987437", }, + { + IUPACInChIkey: "MZGOULQVWGBQGW-MCMMXHMISA-N", + dbId: "RW0", + pubChemCompoundId: "169408384", + name: + "(3R,4S)-6-chloro-N-[7-(methanesulfonyl)isoquinolin-4-yl]-3-methyl-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(3R,4S)-6-chloro-N-[7-(methanesulfonyl)isoquinolin-4-yl]-3-methyl-2-[2-(methylamino)-2-oxoethyl]-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MZGOULQVWGBQGW-MCMMXHMISA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408384", + }, { IUPACInChIkey: "ZHFXJVHZUDTZGC-FZMZJTMJSA-N", dbId: "RW5", @@ -7607,6 +12106,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZHFXJVHZUDTZGC-FZMZJTMJSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513229", }, + { + IUPACInChIkey: "ZIZXURDLSUGNHT-XMMPIXPASA-N", + dbId: "RW9", + pubChemCompoundId: "169408385", + name: + "2-[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-1,2'-dioxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + details: + "2-[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-1,2'-dioxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZIZXURDLSUGNHT-XMMPIXPASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408385", + }, { IUPACInChIkey: "AOHBVEDXTIZALI-HNNXBMFYSA-N", dbId: "RWC", @@ -7629,6 +12140,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QGSVLNUQBAPFJD-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513208", }, + { + IUPACInChIkey: "OLOUVJHSJAVGMH-IBGZPJMESA-N", + dbId: "RWO", + pubChemCompoundId: "169408386", + name: + "(4R)-6-chloro-4-methyl-1,1-dioxo-N-(5,6,7,8-tetrahydroisoquinolin-4-yl)-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + details: + "(4R)-6-chloro-4-methyl-1,1-dioxo-N-(5,6,7,8-tetrahydroisoquinolin-4-yl)-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OLOUVJHSJAVGMH-IBGZPJMESA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408386", + }, { IUPACInChIkey: "LEHSMGCFXRLFLE-SNVBAGLBSA-N", dbId: "RWQ", @@ -7639,6 +12162,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LEHSMGCFXRLFLE-SNVBAGLBSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513186", }, + { + IUPACInChIkey: "OLOUVJHSJAVGMH-LJQANCHMSA-N", + dbId: "RWT", + pubChemCompoundId: "169408387", + name: + "(4S)-6-chloro-4-methyl-1,1-dioxo-N-(5,6,7,8-tetrahydroisoquinolin-4-yl)-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + details: + "(4S)-6-chloro-4-methyl-1,1-dioxo-N-(5,6,7,8-tetrahydroisoquinolin-4-yl)-1,2,3,4-tetrahydro-1lambda~6~,2-benzothiazine-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OLOUVJHSJAVGMH-LJQANCHMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408387", + }, { IUPACInChIkey: "NVNVGIHHTGVADY-AWEZNQCLSA-N", dbId: "RXI", @@ -7651,6 +12186,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NVNVGIHHTGVADY-AWEZNQCLSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513211", }, + { + IUPACInChIkey: "HGSRDUTVEZMNMN-XMMPIXPASA-N", + dbId: "RXU", + pubChemCompoundId: "169408388", + name: + "2-[(3'S)-6-chloro-2'-oxo-1'-(5,6,7,8-tetrahydroisoquinolin-4-yl)-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + details: + "2-[(3'S)-6-chloro-2'-oxo-1'-(5,6,7,8-tetrahydroisoquinolin-4-yl)-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HGSRDUTVEZMNMN-XMMPIXPASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408388", + }, { IUPACInChIkey: "RYLGZXYODNRSDR-UHFFFAOYSA-N", dbId: "RXX", @@ -7696,6 +12243,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UYUBQOHPPHHZPI-DZGCQCFKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513213", }, + { + IUPACInChIkey: "FLBSSPVVUCLCOS-SSEXGKCCSA-N", + dbId: "RYB", + pubChemCompoundId: "169408389", + name: + "1-{[(3'S)-6-chloro-1'-{6-[2-(dimethylamino)ethoxy]isoquinolin-4-yl}-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + details: + "1-{[(3'S)-6-chloro-1'-{6-[2-(dimethylamino)ethoxy]isoquinolin-4-yl}-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FLBSSPVVUCLCOS-SSEXGKCCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408389", + }, { IUPACInChIkey: "UYUBQOHPPHHZPI-HIFRSBDPSA-N", dbId: "RYC", @@ -7752,6 +12311,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FSJZPCQWTVULBE-QMMMGPOBSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513199", }, + { + IUPACInChIkey: "JZJCSVMJFIAMQB-XMMPIXPASA-N", + dbId: "RZF", + pubChemCompoundId: "169408390", + name: + "2-[(3'S)-6-chloro-1'-(6-chloroisoquinolin-4-yl)-1,2'-dioxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + details: + "2-[(3'S)-6-chloro-1'-(6-chloroisoquinolin-4-yl)-1,2'-dioxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylacetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JZJCSVMJFIAMQB-XMMPIXPASA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408390", + }, { IUPACInChIkey: "XLOVNJUCAFIANM-UHFFFAOYSA-N", dbId: "RZG", @@ -7804,6 +12375,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MVJDUNKELBBNKM-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/24701445", }, + { + IUPACInChIkey: "FLEUPKADUSMVNQ-RUZDIDTESA-N", + dbId: "RZU", + pubChemCompoundId: "169408391", + name: + "1-[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-1,2'-dioxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylcyclopropane-1-carboxamide", + details: + "1-[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-1,2'-dioxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-methylcyclopropane-1-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FLEUPKADUSMVNQ-RUZDIDTESA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408391", + }, { IUPACInChIkey: "UCQXDGPOPJQAQB-CTNGQTDRSA-N", dbId: "S09", @@ -7828,6 +12411,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UCQXDGPOPJQAQB-PZJWPPBQSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513216", }, + { + IUPACInChIkey: "RIGXBQKBYSFBJB-HHHXNRCGSA-N", + dbId: "S0X", + pubChemCompoundId: "169408392", + name: + "2-[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-(cyclopropylmethyl)acetamide", + details: + "2-[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-(cyclopropylmethyl)acetamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RIGXBQKBYSFBJB-HHHXNRCGSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408392", + }, { IUPACInChIkey: "QZUXMBWCGJKNAA-JKSUJKDBSA-N", dbId: "S1F", @@ -7840,6 +12435,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QZUXMBWCGJKNAA-JKSUJKDBSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513221", }, + { + IUPACInChIkey: "SGZDWTLRWWIYQR-MUUNZHRXSA-N", + dbId: "S1L", + pubChemCompoundId: "169408394", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-{2-[3-(morpholin-4-yl)anilino]-2-oxoethyl}-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-{2-[3-(morpholin-4-yl)anilino]-2-oxoethyl}-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SGZDWTLRWWIYQR-MUUNZHRXSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408394", + }, { IUPACInChIkey: "ASNUGOSBOWLSJV-NSHDSACASA-N", dbId: "S1O", @@ -7852,6 +12459,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ASNUGOSBOWLSJV-NSHDSACASA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513197", }, + { + IUPACInChIkey: "DCLQGAIWDISPHM-SSEXGKCCSA-N", + dbId: "S1U", + pubChemCompoundId: "169408393", + name: + "(4S)-6-chloro-2-{2-[4-(4-ethylpiperazin-1-yl)anilino]-2-oxoethyl}-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-{2-[4-(4-ethylpiperazin-1-yl)anilino]-2-oxoethyl}-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DCLQGAIWDISPHM-SSEXGKCCSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408393", + }, { IUPACInChIkey: "YTJWUPQJUKAHJM-ZWKOTPCHSA-N", dbId: "S1X", @@ -7886,6 +12505,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DVCWUTSWCVQZSC-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/961874", }, + { + IUPACInChIkey: "QLTJDOSMDPTNNG-HSZRJFAPSA-N", + dbId: "S39", + pubChemCompoundId: "169408395", + name: + "(4S)-2-{2-[(1,3-benzothiazol-5-yl)amino]-2-oxoethyl}-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-2-{2-[(1,3-benzothiazol-5-yl)amino]-2-oxoethyl}-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QLTJDOSMDPTNNG-HSZRJFAPSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408395", + }, { IUPACInChIkey: "PRFABXNJKOXNTN-QMMMGPOBSA-N", dbId: "S3E", @@ -7908,6 +12539,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/DOFJBAVHDFWANZ-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513227", }, + { + IUPACInChIkey: "NSMAAPODQLIULZ-HFJWLAOPSA-N", + dbId: "S3X", + pubChemCompoundId: "169408396", + name: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-(2-{[(1S)-1-(4-nitrophenyl)ethyl]amino}-2-oxoethyl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-N-(isoquinolin-4-yl)-2-(2-{[(1S)-1-(4-nitrophenyl)ethyl]amino}-2-oxoethyl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/NSMAAPODQLIULZ-HFJWLAOPSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408396", + }, { IUPACInChIkey: "JURSYTNKCJMCTM-MRVPVSSYSA-N", dbId: "S4F", @@ -7942,6 +12585,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JMIDLJFHIRGERG-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155966885", }, + { + IUPACInChIkey: "LNPBEFQJZLIQLX-ZRIUDJFOSA-N", + dbId: "S4X", + pubChemCompoundId: "169408397", + name: + "(4S)-6-chloro-2-(2-{[(1r,3R,5R,7S)-3-hydroxyadamantan-1-yl]amino}-2-oxoethyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-6-chloro-2-(2-{[(1r,3R,5R,7S)-3-hydroxyadamantan-1-yl]amino}-2-oxoethyl)-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/LNPBEFQJZLIQLX-ZRIUDJFOSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408397", + }, { IUPACInChIkey: "RJFXVLMCNRXHDX-UHFFFAOYSA-N", dbId: "S50", @@ -7976,6 +12631,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CMNAMTJQXKKSGP-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/2741922", }, + { + IUPACInChIkey: "MHRZZVXEQPCPTK-AREMUKBSSA-N", + dbId: "S5L", + pubChemCompoundId: "169408398", + name: + "(4S)-2-[2-(4-acetamidoanilino)-2-oxoethyl]-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + details: + "(4S)-2-[2-(4-acetamidoanilino)-2-oxoethyl]-6-chloro-N-(isoquinolin-4-yl)-1,2,3,4-tetrahydroisoquinoline-4-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MHRZZVXEQPCPTK-AREMUKBSSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408398", + }, { IUPACInChIkey: "QXWCPCWNFDNBBL-OPRDCNLKSA-N", dbId: "S5O", @@ -8018,6 +12685,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OHVACHOAZRWEJX-QMMMGPOBSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155956975", }, + { + IUPACInChIkey: "WAAAIQKYRCBKNL-MYUZEXMDSA-N", + dbId: "S6K", + pubChemCompoundId: "169408399", + name: + "1-{[(3'S,4'R)-6-chloro-1'-(isoquinolin-4-yl)-4'-methyl-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + details: + "1-{[(3'S,4'R)-6-chloro-1'-(isoquinolin-4-yl)-4'-methyl-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/WAAAIQKYRCBKNL-MYUZEXMDSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408399", + }, { IUPACInChIkey: "LHAVLCJMCJXCKW-VIFPVBQESA-N", dbId: "S6N", @@ -8050,6 +12729,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OYRHWZOYGOUXNC-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/741243", }, + { + IUPACInChIkey: "BPMHGPSPIBHHKD-KMRXNPHXSA-N", + dbId: "S7C", + pubChemCompoundId: "169408400", + name: + "1-{[(3'S,4'R)-6-chloro-4'-ethyl-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + details: + "1-{[(3'S,4'R)-6-chloro-4'-ethyl-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BPMHGPSPIBHHKD-KMRXNPHXSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408400", + }, { IUPACInChIkey: "YJMLTHJLDUBVIC-VIFPVBQESA-N", dbId: "S7D", @@ -8114,6 +12805,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FYLGKPVWPNAHEF-UHFFFAOYSA-O/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164513234", }, + { + IUPACInChIkey: "KBMBYPWORLDFDP-HHHXNRCGSA-N", + dbId: "S7U", + pubChemCompoundId: "169408401", + name: + "1-{[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-piperidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + details: + "1-{[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-piperidine]-2(3H)-sulfonyl]methyl}cyclopropane-1-carbonitrile", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KBMBYPWORLDFDP-HHHXNRCGSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169408401", + }, { IUPACInChIkey: "WQNIKIMRIXHNFF-GFCCVEGCSA-N", dbId: "S7V", @@ -8260,16 +12963,6 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/PTTXNOSMDBWCQD-UHFFFAOYSA-J/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/6398953", }, - { - IUPACInChIkey: "GECHUMIMRBOMGK-UHFFFAOYSA-N", - dbId: "SFY", - pubChemCompoundId: "5336", - name: "4-amino-N-(pyridin-2-yl)benzenesulfonamide", - details: "4-amino-N-(pyridin-2-yl)benzenesulfonamide", - imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GECHUMIMRBOMGK-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/5336", - }, { IUPACInChIkey: "OBZJZDHRXBKKTJ-JTFADIMSSA-N", dbId: "SGV", @@ -9992,16 +14685,16 @@ export const data: Covid19Data = { externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154573649", }, { - IUPACInChIkey: "HIQXVKIISKTUPK-FTZGMBJCSA-N", + IUPACInChIkey: "FRACPXUHUTXLCX-CGBRIMPHSA-N", dbId: "V9R", - pubChemCompoundId: "166642334", + pubChemCompoundId: "168475494", name: "~{tert}-butyl ~{N}-[1-[(2~{R})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate", details: "~{tert}-butyl ~{N}-[1-[(2~{R})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate", imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HIQXVKIISKTUPK-FTZGMBJCSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/166642334", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/FRACPXUHUTXLCX-CGBRIMPHSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168475494", }, { IUPACInChIkey: "QMJFETCLZITVFG-MRXNPFEDSA-N", @@ -10215,6 +14908,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MPMTWRHFCLPCDF-OJJQZRKESA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155804578", }, + { + IUPACInChIkey: "QJXJXBXFIOTYHB-UUOKFMHZSA-N", + dbId: "VSN", + pubChemCompoundId: "135410865", + name: "5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine", + details: "5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QJXJXBXFIOTYHB-UUOKFMHZSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/135410865", + }, { IUPACInChIkey: "HGFZDZZEWWPKIB-UHFFFAOYSA-N", dbId: "VVD", @@ -10225,16 +14928,6 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/HGFZDZZEWWPKIB-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/19261749", }, - { - IUPACInChIkey: "MRTGYFRQZQCITC-UHFFFAOYSA-N", - dbId: "VVG", - pubChemCompoundId: "4693938", - name: "N-(2-fluorophenyl)ethanesulfonamide", - details: "N-(2-fluorophenyl)ethanesulfonamide", - imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MRTGYFRQZQCITC-UHFFFAOYSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/4693938", - }, { IUPACInChIkey: "UXPPTRFZLSZETL-UHFFFAOYSA-N", dbId: "VVJ", @@ -10617,6 +15310,16 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QELUYTUMUWHWMC-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/4021", }, + { + IUPACInChIkey: "VSXNZKCCQSDVAD-ZCFIWIBFSA-N", + dbId: "W1S", + pubChemCompoundId: "96053363", + name: "(8S)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-8-carboxamide", + details: "(8S)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-8-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VSXNZKCCQSDVAD-ZCFIWIBFSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/96053363", + }, { IUPACInChIkey: "JQSGNNVZAVLVHV-UHFFFAOYSA-N", dbId: "W1V", @@ -10659,6 +15362,17 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/VZERDZVLLIAWDV-SKDRFNHKSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155294421", }, + { + IUPACInChIkey: "", + dbId: "W28", + pubChemCompoundId: "", + name: + "N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-1H-indole-2-carboxamide", + details: + "N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-1H-indole-2-carboxamide", + imageLink: "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey//PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/", + }, { IUPACInChIkey: "FANJRWOXJRSBJO-SFYZADRCSA-N", dbId: "W2A", @@ -11348,15 +16062,28 @@ export const data: Covid19Data = { externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/22931034", }, { - IUPACInChIkey: "", + IUPACInChIkey: "SEDQMDCLDZNPIX-HNNXBMFYSA-N", + dbId: "WOH", + pubChemCompoundId: "162680084", + name: + "benzyl {(2S)-1-[2-(3-amino-3-oxopropyl)-2-(chloroacetyl)hydrazinyl]-4-methyl-1-oxopentan-2-yl}carbamate (non-preferred name)", + details: + "benzyl {(2S)-1-[2-(3-amino-3-oxopropyl)-2-(chloroacetyl)hydrazinyl]-4-methyl-1-oxopentan-2-yl}carbamate (non-preferred name)", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/SEDQMDCLDZNPIX-HNNXBMFYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/162680084", + }, + { + IUPACInChIkey: "AVAISVNJDSSFQV-UDQBHXPNSA-N", dbId: "WOK", - pubChemCompoundId: "", + pubChemCompoundId: "169491046", name: "(1R,2S,5S)-N-{(1S,2S)-1-(5-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", details: "(1R,2S,5S)-N-{(1S,2S)-1-(5-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", - imageLink: "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey//PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AVAISVNJDSSFQV-UDQBHXPNSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169491046", }, { IUPACInChIkey: "PANGDCFLXUDHDI-UHFFFAOYSA-N", @@ -11550,6 +16277,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/BOTWCSZQXQBVCZ-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/28742932", }, + { + IUPACInChIkey: "UJLGWNDCUWVLAK-ZOQUXTDFSA-N", + dbId: "WSB", + pubChemCompoundId: "154724555", + name: + "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine", + details: + "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UJLGWNDCUWVLAK-ZOQUXTDFSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/154724555", + }, { IUPACInChIkey: "OBDJLTJVFBLJIR-UHFFFAOYSA-N", dbId: "WSG", @@ -11705,16 +16444,6 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YCKAXCQPMUENML-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/165416234", }, - { - IUPACInChIkey: "MWDGBNUBPZOQNW-VIFPVBQESA-N", - dbId: "WW1", - pubChemCompoundId: "164575911", - name: "3-{[(2R)-2-phenylpropyl]sulfanyl}-7H-[1,2,4]triazolo[4,3-b][1,2,4]triazole", - details: "3-{[(2R)-2-phenylpropyl]sulfanyl}-7H-[1,2,4]triazolo[4,3-b][1,2,4]triazole", - imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MWDGBNUBPZOQNW-VIFPVBQESA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/164575911", - }, { IUPACInChIkey: "XUBYDFCDYPJZTA-SNVBAGLBSA-N", dbId: "WW4", @@ -11928,18 +16657,6 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IKONPSAKEQUJQO-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/90481251", }, - { - IUPACInChIkey: "RZITUVZKCFWKQP-LLVKDONJSA-N", - dbId: "WXT", - pubChemCompoundId: "165416596", - name: - "1-methyl-N-{(2S)-3-methyl-2-[(9H-purin-6-yl)amino]butyl}cyclobutane-1-carboxamide", - details: - "1-methyl-N-{(2S)-3-methyl-2-[(9H-purin-6-yl)amino]butyl}cyclobutane-1-carboxamide", - imageLink: - "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RZITUVZKCFWKQP-LLVKDONJSA-N/PNG", - externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/165416596", - }, { IUPACInChIkey: "HCXYCGJASBHJRP-CQSZACIVSA-N", dbId: "WXX", @@ -12066,6 +16783,42 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/QEDNABCLVCJRLV-UHFFFAOYSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/586354", }, + { + IUPACInChIkey: "IAIXUKUDGNIVRC-ZYRLFZHTSA-N", + dbId: "X6O", + pubChemCompoundId: "168654897", + name: + "(1R,2S,5S)-N-{(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + details: + "(1R,2S,5S)-N-{(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IAIXUKUDGNIVRC-ZYRLFZHTSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168654897", + }, + { + IUPACInChIkey: "KOJLJTKYOSKMNV-YTNBPZCUSA-N", + dbId: "X6T", + pubChemCompoundId: "168654898", + name: + "(1R,2S,5S)-N-{(2S,3R)-4-(3,3-dimethylazetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + details: + "(1R,2S,5S)-N-{(2S,3R)-4-(3,3-dimethylazetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/KOJLJTKYOSKMNV-YTNBPZCUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168654898", + }, + { + IUPACInChIkey: "GUMSXYQAJLBYRA-UYYZUGKPSA-N", + dbId: "X70", + pubChemCompoundId: "168654899", + name: + "(1R,2S,5S)-N-{(2S,3R)-4-(3,3-difluoroazetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + details: + "(1R,2S,5S)-N-{(2S,3R)-4-(3,3-difluoroazetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/GUMSXYQAJLBYRA-UYYZUGKPSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168654899", + }, { IUPACInChIkey: "MUNFBYOTGGMQOS-XMMPIXPASA-N", dbId: "X77", @@ -12090,6 +16843,30 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RYGJIKURQDMMQZ-YUDQIZAISA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155289416", }, + { + IUPACInChIkey: "XDHKGBBFOISQMJ-AMQFHODYSA-N", + dbId: "X9Z", + pubChemCompoundId: "168654900", + name: + "(1R,2S,5S)-N-[(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-(2-oxopyrrolidin-1-yl)butan-2-yl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + details: + "(1R,2S,5S)-N-[(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-(2-oxopyrrolidin-1-yl)butan-2-yl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/XDHKGBBFOISQMJ-AMQFHODYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168654900", + }, + { + IUPACInChIkey: "CEVFDXICNWCNKE-NLNBCDFGSA-N", + dbId: "XA8", + pubChemCompoundId: "168654901", + name: + "(1R,2S,5S)-N-[(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-(2-oxopiperidin-1-yl)butan-2-yl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + details: + "(1R,2S,5S)-N-[(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-(2-oxopiperidin-1-yl)butan-2-yl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/CEVFDXICNWCNKE-NLNBCDFGSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168654901", + }, { IUPACInChIkey: "LRFVTYWOQMYALW-UHFFFAOYSA-N", dbId: "XAN", @@ -12134,6 +16911,26 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZIDTZUSIKUZLIR-BJLQDIEVSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/165430684", }, + { + IUPACInChIkey: "MMOUYBCDJMEUFG-DUXPYHPUSA-N", + dbId: "XDU", + pubChemCompoundId: "5721553", + name: "4-[(E)-2-(2,4-dichlorophenyl)ethenyl]-6-(trifluoromethyl)pyrimidin-2-ol", + details: "4-[(E)-2-(2,4-dichlorophenyl)ethenyl]-6-(trifluoromethyl)pyrimidin-2-ol", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MMOUYBCDJMEUFG-DUXPYHPUSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/5721553", + }, + { + IUPACInChIkey: "IBPXEUWFSZDIPG-UHFFFAOYSA-N", + dbId: "XE0", + pubChemCompoundId: "168665403", + name: "4-[2-(2,4-dichlorophenyl)ethyl]-6-(trifluoromethyl)pyrimidin-2-ol", + details: "4-[2-(2,4-dichlorophenyl)ethyl]-6-(trifluoromethyl)pyrimidin-2-ol", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/IBPXEUWFSZDIPG-UHFFFAOYSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168665403", + }, { IUPACInChIkey: "KXGLBZMRWKVPSY-UHFFFAOYSA-N", dbId: "XEY", @@ -12227,6 +17024,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AGWHKDXHVADVIY-JLEJFLCFSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/165430687", }, + { + IUPACInChIkey: "OJDYQRNEDPEFMJ-VPMCDZTMSA-N", + dbId: "XIO", + pubChemCompoundId: "168654903", + name: + "[(2~{S})-2-[[4-(2-azanylethanoylamino)-7-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-4-[3-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-3-oxidanylidene-propyl]-7-oxidanylidene-heptanoyl]amino]-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]propanoyl]oxysodium", + details: + "[(2~{S})-2-[[4-(2-azanylethanoylamino)-7-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-4-[3-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-3-oxidanylidene-propyl]-7-oxidanylidene-heptanoyl]amino]-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]propanoyl]oxysodium", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/OJDYQRNEDPEFMJ-VPMCDZTMSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/168654903", + }, { IUPACInChIkey: "IAJLTMBBAVVMQO-UHFFFAOYSA-N", dbId: "XIY", @@ -12613,6 +17422,18 @@ export const data: Covid19Data = { "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/AFONNBAHWVWJGI-XKEITGKGSA-N/PNG", externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/155804610", }, + { + IUPACInChIkey: "MSAKMAGHNICQTP-KBCNZALWSA-N", + dbId: "Y8O", + pubChemCompoundId: "169491069", + name: + "(1R,2S,5S)-3-[N-(difluoroacetyl)-3-methyl-L-valyl]-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide", + details: + "(1R,2S,5S)-3-[N-(difluoroacetyl)-3-methyl-L-valyl]-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide", + imageLink: + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MSAKMAGHNICQTP-KBCNZALWSA-N/PNG", + externalLink: "https://pubchem.ncbi.nlm.nih.gov/compound/169491069", + }, { IUPACInChIkey: "ZIWRGXZFSGDQST-REFFYEJJSA-N", dbId: "Y8S", @@ -13849,6 +18670,8 @@ export const data: Covid19Data = { xRef: ["IDR"], }, ], + Organisms: [], + Ligands: [], RefModelSources: [ { name: "CERES", @@ -13874,6 +18697,12 @@ export const data: Covid19Data = { "The Image Data Resource (IDR) is a public repository of image datasets from published scientific studies, where the community can submit, search and access high-quality bio-image data.", externalLink: "https://idr.openmicroscopy.org/", }, + { + name: "NMR", + description: + "The international Covid19-NMR-Consortium project works to determine RNA and protein structures of SARS-CoV-2 and to investigate the drugability of those structures by small molecules.", + externalLink: "", + }, ], RefModelMethods: [ { @@ -13911,432361 +18740,13 @@ export const data: Covid19Data = { "High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets. (Source Accession: EFO_0007553)", externalLink: "https://idr.openmicroscopy.org/", }, - ], - Structures: [ - { - title: - "Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S486-505", - emdb: null, - pdb: { - dbId: "8CMB", - method: "X-RAY DIFFRACTION", - keywords: - "HLA-II, HLA-DR, HLA-DR1, human leukocyte antigen, major histocompatibility complex, major histocompatibility complex class 2, SARS-CoV-2, coronavirus, COVID-19, Spike, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CMB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cmb_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cmb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01903", - organism: "9606", - name: "HLA class II histocompatibility antigen, DR alpha chain", - details: "", - altNames: "MHC class II antigen DRA", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", "UFULAYFCSOUIOV-UHFFFAOYSA-N"], - dbauthors: ["MacLachlan, B.J.", "Mason, G.H.", "Godkin, A.J.", "Rizkallah, P.J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37471227", - title: - "Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.", - journal: "Cell Rep 42: 112827-112827 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112827", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37471227", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, Y.", - "Mason, G.H.", - "Scourfield, D.O.", - "Greenshields-Watson, A.", - "Haigh, T.A.", - "Sewell, A.K.", - "Long, H.M.", - "Gallimore, A.M.", - "Rizkallah, P.", - "MacLachlan, B.J.", - "Godkin, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cmb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cmb", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI33", - emdb: null, - pdb: { - dbId: "7UUD", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7UUD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uud_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uud", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GKUBEDOOUKCUOW-YTNBPZCUSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36629751", - title: - "A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.", - journal: "Acs Chem.Biol. 18: 449-455 (2023), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.2c00695", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36629751", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, K.S.", - "Blankenship, L.R.", - "Kuo, S.A.", - "Sheng, Y.J.", - "Li, P.", - "Fierke, C.A.", - "Russell, D.H.", - "Yan, X.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uud_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uud", - }, - }, - { - title: "SARS-CoV-2 Beta RBD in complex with human ACE2 and S304 Fab and S309 Fab", - emdb: null, - pdb: { - dbId: "8DF5", - method: "X-RAY DIFFRACTION", - keywords: - "RBD, SARS-CoV-2, COVID, S309, beta, B.1.351, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, VIRAL PROTEIN, VIRAL PROTEIN-Hydrolase-Immune System complex", - refModels: [ - { - emdbId: null, - pdbId: "8DF5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8df5_final.pdb", - externalLink: "https://pdb-redo.eu/db/8df5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "S309 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "S309 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "S304 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "S304 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: [ - "McCallum, M.", - "Seattle Structural Genomics Center for Infectious Disease (SSGCID)", - "Snell, G.", - "Veesler, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dodecameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35762884", - title: - "Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution.", - journal: "Science 377: 420-424 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abo7896", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35762884", - pubDate: "2022", - abstract: "", - authors: [ - "Starr, T.N. (0000-0001-6713-6904)", - "Greaney, A.J. (0000-0001-7202-3349)", - "Hannon, W.W. (0000-0002-6014-4749)", - "Loes, A.N. (0000-0002-8659-0149)", - "Hauser, K.", - "Dillen, J.R. (0000-0003-0702-5991)", - "Ferri, E. (0000-0002-8672-4733)", - "Farrell, A.G. (0000-0002-1389-0992)", - "Dadonaite, B. (0000-0003-0908-6982)", - "McCallum, M. (0000-0001-8398-8330)", - "Matreyek, K.A. (0000-0001-9149-551X)", - "Corti, D. (0000-0002-5797-1364)", - "Veesler, D. (0000-0002-6019-8675)", - "Snell, G. (0000-0003-1475-659X)", - "Bloom, J.D. (0000-0003-1267-3408)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8df5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8df5", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with 5-Iodotubercidin", - emdb: null, - pdb: { - dbId: "8OV3", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, methyltransferase, complex, inhibitor, SARS-CoV-2", - refModels: [ - { - emdbId: null, - pdbId: "8OV3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ov3_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ov3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "WHSIXKUPQCKWBY-IOSLPCCCSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - "Kiene, A.", - "Galchenkova, M. (0000-0001-8676-0091)", - "Garcia, Y. (0000-0002-9592-2141)", - "Ehr, C. (0000-0003-1428-0042)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ov3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ov3", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 RBD in complex with the ridge-binding nAb EH8 isolated from a nonvaccinated pediatric patient", - emdb: null, - pdb: { - dbId: "7UL0", - method: "X-RAY DIFFRACTION", - keywords: - "Pediatric neutralizing mAb, RBD-ridge-targeting, bind to both closed and open SARS-CoV-2 spike, Class-2 RBD-binding antibody, VIRAL PROTEIN, VIRAL PROTEIN-Immune System complex", - refModels: [ - { - emdbId: null, - pdbId: "7UL0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ul0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ul0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of EH8", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of EH8", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: [ - "Chen, Y. (0000-0001-5380-2339)", - "Tolbert, W.D. (0000-0001-7549-9596)", - "Bai, X. (0000-0002-0920-2472)", - "Pazgier, M. (0000-0003-0594-5057)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36514310", - title: - "Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD.", - journal: "Iscience 26: 105783-105783 (2023), 2589-0042", - doi: "https://doi.org/10.1016/j.isci.2022.105783", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36514310", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, Y.", - "Prevost, J.", - "Ullah, I.", - "Romero, H.", - "Lisi, V.", - "Tolbert, W.D.", - "Grover, J.R.", - "Ding, S.", - "Gong, S.Y.", - "Beaudoin-Bussieres, G.", - "Gasser, R.", - "Benlarbi, M.", - "Vezina, D.", - "Anand, S.P.", - "Chatterjee, D.", - "Goyette, G.", - "Grunst, M.W.", - "Yang, Z.", - "Bo, Y.", - "Zhou, F.", - "Beland, K.", - "Bai, X.", - "Zeher, A.R.", - "Huang, R.K.", - "Nguyen, D.N.", - "Sherburn, R.", - "Wu, D.", - "Piszczek, G.", - "Pare, B.", - "Matthies, D.", - "Xia, D.", - "Richard, J.", - "Kumar, P.", - "Mothes, W.", - "Cote, M.", - "Uchil, P.D.", - "Lavallee, V.P.", - "Smith, M.A.", - "Pazgier, M.", - "Haddad, E.", - "Finzi, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ul0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ul0", - }, - }, - { - title: - "Crystal Structure of SARS CoV-2 Mpro with Pfizer Intravenous Inhibitor PF-00835231", - emdb: null, - pdb: { - dbId: "8DSU", - method: "X-RAY DIFFRACTION", - keywords: - "Coronavirus, COVID-19, COVID, PROTEASE, DRUG RESISTANCE, COMPLEX, HYDROLASE, DURG DISCOVERY, MAIN PROTEASE, MPRO, SUBSTRATE COMPLEX, Pfizer IV compound, PF-00835231, VIRAL PROTEIN, VIRAL PROTEIN-HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DSU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dsu_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dsu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "FDQSUXUTXIGUIA-PRIDNEQBSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Shaqra, A.M. (0000-0001-6994-2416)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36992489", - title: - "Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses.", - journal: "Viruses 15 (2023), 1999-4915", - doi: "https://doi.org/10.3390/v15030781", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36992489", - pubDate: "2023", - abstract: "", - authors: [ - "Zvornicanin, S.N.", - "Shaqra, A.M.", - "Huang, Q.J.", - "Ornelas, E.", - "Moghe, M.", - "Knapp, M.", - "Moquin, S.", - "Dovala, D.", - "Schiffer, C.A.", - "Kurt Yilmaz, N.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dsu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dsu", - }, - }, - { - title: "SARS-CoV-2 specific private TCR RLQ7 in complex with RLQ-T1006I-HLA-A2", - emdb: null, - pdb: { - dbId: "8GON", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Private TCR, TCR-p-HLA, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "8GON", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gon_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gon", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2", - details: - "Lysine at N-terminal is used for biochemical assays; two serines were added at N-terminal to increase the peptide solubility in PBS", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "SARS-CoV-2 specific private TCR RLQ7 alpha", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "SARS-CoV-2 specific private TCR RLQ7 beta", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UWHCKJMYHZGTIT-UHFFFAOYSA-N"], - dbauthors: ["Wu, D. (0000-0003-2086-0190)", "Mariuzza, R.A. (0000-0003-0748-5875)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36806685", - title: - "Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor (TCR) diversity.", - journal: "J.Biol.Chem. 299: 103035-103035 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103035", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36806685", - pubDate: "2023", - abstract: "", - authors: [ - "Wu, D.", - "Efimov, G.A.", - "Bogolyubova, A.V.", - "Pierce, B.G.", - "Mariuzza, R.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gon_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gon", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with tubercidin", - emdb: null, - pdb: { - dbId: "8BSD", - method: "X-RAY DIFFRACTION", - keywords: "Methyltransferase, Complex, Inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8BSD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8bsd_final.pdb", - externalLink: "https://pdb-redo.eu/db/8bsd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "HDZZVAMISRMYHH-KCGFPETGSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Sprenger, J. (0000-0001-7977-3484)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8bsd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8bsd", - }, - }, - { - title: "The complex structure of WT-Mpro", - emdb: null, - pdb: { - dbId: "7XQ7", - method: "X-RAY DIFFRACTION", - keywords: "Protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7XQ7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xq7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xq7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: ["Sahoo, P.", "Lenka, D.R.", "Kumar, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36650888", - title: - "Detailed Insights into the Inhibitory Mechanism of New Ebselen Derivatives against Main Protease (M pro ) of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2).", - journal: "Acs Pharmacol Transl Sci 6: 171-180 (2023), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00203", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36650888", - pubDate: "2023", - abstract: "", - authors: [ - "Sahoo, P.", - "Lenka, D.R.", - "Batabyal, M. (0000-0002-0587-2874)", - "Pain, P.K.", - "Kumar, S. (0000-0003-0658-8709)", - "Manna, D.", - "Kumar, A. (0000-0003-4675-6623)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xq7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xq7", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CL protease in complex with a phenyl sulfane inhibitor", - emdb: null, - pdb: { - dbId: "8E63", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, Viral Protein-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8E63", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e63_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e63", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "AUIXPEVQDXBTHO-QUJKESNLSA-N", - "AUIXPEVQDXBTHO-DBSRCYSRSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Lovell, S. (0000-0002-3215-4472)", - "Liu, L. (0000-0003-0514-281X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Madden, T.K.", - "Groutas, W.C. (0000-0001-5248-7912)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e63_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e63", - }, - }, - { - title: "SARS-CoV-2 Main Protease adduct with Au(PEt3)Br", - emdb: null, - pdb: { - dbId: "8B0T", - method: "X-RAY DIFFRACTION", - keywords: "NSP5, Mpro, SARS_CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8B0T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8b0t_final.pdb", - externalLink: "https://pdb-redo.eu/db/8b0t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZBKIUFWVEIBQRT-UHFFFAOYSA-N"], - dbauthors: [ - "Massai, L.", - "Grifagni, D.", - "De Santis, A.", - "Geri, A.", - "Calderone, V.", - "Cantini, F.", - "Banci, L.", - "Messori, L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36421689", - title: - "Gold-Based Metal Drugs as Inhibitors of Coronavirus Proteins: The Inhibition of SARS-CoV-2 Main Protease by Auranofin and Its Analogs.", - journal: "Biomolecules 12 (2022), 2218-273X", - doi: "https://doi.org/10.3390/biom12111675", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36421689", - pubDate: "2022", - abstract: "", - authors: [ - "Massai, L. (0000-0003-0765-1802)", - "Grifagni, D.", - "De Santis, A.", - "Geri, A.", - "Cantini, F. (0000-0003-0526-6732)", - "Calderone, V. (0000-0002-7963-6241)", - "Banci, L. (0000-0003-0562-5774)", - "Messori, L. (0000-0002-9490-8014)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8b0t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8b0t", - }, - }, - { - title: "The complex structure of mutant Mpro with inhibitor", - emdb: null, - pdb: { - dbId: "7XQ6", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Cov-2, VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7XQ6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xq6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xq6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: ["Sahoo, P.", "Lenka, D.R.", "Kumar, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36650888", - title: - "Detailed Insights into the Inhibitory Mechanism of New Ebselen Derivatives against Main Protease (M pro ) of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2).", - journal: "Acs Pharmacol Transl Sci 6: 171-180 (2023), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00203", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36650888", - pubDate: "2023", - abstract: "", - authors: [ - "Sahoo, P.", - "Lenka, D.R.", - "Batabyal, M. 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(0000-0003-4675-6623)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xq6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xq6", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD) in complex with 1D1 Fab", - emdb: null, - pdb: { - dbId: "8BSE", - method: "X-RAY DIFFRACTION", - keywords: - "ANTIBODY, VIRUS, COMPLEX, SARS-COV-2, VIRAL PROTEIN COMPLEX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8BSE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8bse_final.pdb", - externalLink: "https://pdb-redo.eu/db/8bse", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "1D1 FAB HEAVY CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "1D1 FAB LIGHT CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "PQYJRMFWJJONBO-UHFFFAOYSA-N", - ], - dbauthors: [ - "Welin, M. (0000-0001-5786-1600)", - "Kimbung, Y.R.", - "Focht, D.", - "Pisitkun, T.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "unidentified baculovirus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD) in complex with 1D1 Fab", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Boonkrai, C.", - "Cotrone, T.S.", - "Chaisuriyong, W.", - "Tantawichien, T.", - "Thisyakorn, U.", - "Fernandez, S.", - "Hunsawong, T.", - "Reed, M.", - "Focht, D.", - "Kimbung, Y.R.", - "Welin, M.", - "Wongtangprasert, T.", - "Audomsun, T.", - "Phakham, T.", - "Attakitbancha, C.", - "Saelao, P.", - "Pisitkun, P.", - "Srisawat, N.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8bse_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8bse", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin", - emdb: null, - pdb: { - dbId: "8OV2", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, methyltransferase, complex, inhibitor", - refModels: [ - { - emdbId: null, - pdbId: "8OV2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ov2_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ov2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "OBZJZDHRXBKKTJ-JTFADIMSSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - "Kiene, A.", - "Galchenkova, M. (0000-0001-8676-0091)", - "Garcia, Y. (0000-0002-9592-2141)", - "Ehr, C. (0000-0003-1428-0042)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ov2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ov2", - }, - }, - { - title: - "SARS-CoV-2 non-structural protein-1 (nsp1) in complex with 4-(2-aminothiazol-4-yl)phenol", - emdb: null, - pdb: { - dbId: "8AYS", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, non-structural protein-1, fragment hit, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8AYS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ays_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ays", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Host translation inhibitor nsp1", - details: "", - altNames: "Leader protein,Non-structural protein 1,nsp1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QGSJYYIRAFRPIT-UHFFFAOYSA-N"], - dbauthors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Kozielski, F. (0000-0001-6096-9102)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36293303", - title: - "Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening.", - journal: "Int J Mol Sci 23 (2022), 1422-0067", - doi: "https://doi.org/10.1021/ci200227u", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36293303", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S. (0000-0002-2070-7770)", - "Lou, J.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Haider, S. (0000-0003-2650-2925)", - "Kozielski, F. (0000-0001-6096-9102)", - "Ma, S.", - "Mykhaylyk, V. (0000-0003-0106-2724)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ays_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ays", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI85", - emdb: null, - pdb: { - dbId: "7UUE", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7UUE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uue_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uue", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OLDUWPOLRQOLGJ-QURRFSBHSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36629751", - title: - "A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.", - journal: "Acs Chem.Biol. 18: 449-455 (2023), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.2c00695", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36629751", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, K.S.", - "Blankenship, L.R.", - "Kuo, S.A.", - "Sheng, Y.J.", - "Li, P.", - "Fierke, C.A.", - "Russell, D.H.", - "Yan, X.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uue_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uue", - }, - }, - { - title: - "Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530", - emdb: null, - pdb: { - dbId: "8CMC", - method: "X-RAY DIFFRACTION", - keywords: - "HLA-II, HLA-DR, HLA-DR1, human leukocyte antigen, major histocompatibility complex, major histocompatibility complex class 2, SARS-CoV-2, coronavirus, COVID-19, Spike, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CMC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cmc_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cmc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01903", - organism: "9606", - name: "HLA class II histocompatibility antigen, DR alpha chain", - details: "", - altNames: "MHC class II antigen DRA", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - ], - dbauthors: [ - "MacLachlan, B.J. (0000-0002-2685-2733)", - "Mason, G.H. (0000-0002-7844-7190)", - "Sourfield, D.O. (0000-0002-0836-7718)", - "Godkin, A.J. (0000-0002-1910-7567)", - "Rizkallah, P.J. (0000-0002-9290-0369)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37471227", - title: - "Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.", - journal: "Cell Rep 42: 112827-112827 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112827", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37471227", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, Y.", - "Mason, G.H.", - "Scourfield, D.O.", - "Greenshields-Watson, A.", - "Haigh, T.A.", - "Sewell, A.K.", - "Long, H.M.", - "Gallimore, A.M.", - "Rizkallah, P.", - "MacLachlan, B.J.", - "Godkin, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cmc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cmc", - }, - }, - { - title: - "Structure of SARS-CoV-2 Gamma variant receptor-binding domain complexed with high affinity human ACE2 mutant (T27F,R273Q)", - emdb: null, - pdb: { - dbId: "7WNM", - method: "X-RAY DIFFRACTION", - keywords: "complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WNM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wnm_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wnm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Ma, R.Y.", "Han, P.C.", "Wang, Q.H.", "Han, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35013100", - title: - "A binding-enhanced but enzymatic activity-eliminated human ACE2 efficiently neutralizes SARS-CoV-2 variants.", - journal: "Signal Transduct Target Ther 7: 10-10 (2022), 2059-3635", - doi: "https://doi.org/10.1038/s41392-021-00821-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35013100", - pubDate: "2022", - abstract: "", - authors: [ - "Zheng, A.", - "Wu, L.", - "Ma, R. (0000-0002-6152-9050)", - "Han, P.", - "Huang, B.", - "Qiao, C.", - "Wang, Q. (0000-0003-3768-0401)", - "Tan, W.", - "Gao, G.F. (0000-0002-3869-615X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wnm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wnm", - }, - }, - { - title: "Co-structure of SARS-CoV-2 (COVID-19 with covalent pyrazoline based inhibitors", - emdb: null, - pdb: { - dbId: "8SKH", - method: "X-RAY DIFFRACTION", - keywords: "sars2, mpro, inhibitor, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8SKH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8skh_final.pdb", - externalLink: "https://pdb-redo.eu/db/8skh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "KRLGZQHRFNNZBX-GMAHTHKFSA-N"], - dbauthors: ["Ornelas, E.", "Knapp, M.S."], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "37069799", - title: - "Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors.", - journal: "Chembiochem: e202300116-e202300116 (2023), 1439-7633", - doi: "https://doi.org/10.1002/cbic.202300116", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37069799", - pubDate: "2023", - abstract: "", - authors: [ - "Moon, P.", - "Zammit, C.M.", - "Shao, Q.", - "Dovala, D.", - "Boike, L.", - "Henning, N.J.", - "Knapp, M.", - "Spradlin, J.N.", - "Ward, C.C.", - "Wolleb, H.", - "Fuller, D.", - "Blake, G.", - "Murphy, J.P.", - "Wang, F.", - "Lu, Y.", - "Moquin, S.A.", - "Tandeske, L.", - "Hesse, M.J.", - "McKenna, J.M.", - "Tallarico, J.A.", - "Schirle, M.", - "Toste, F.D. (0000-0001-8018-2198)", - "Nomura, D.K. (0000-0003-1614-8360)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8skh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8skh", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with MTA", - emdb: null, - pdb: { - dbId: "8C5M", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, methyltransferase, complex, inhibitor", - refModels: [ - { - emdbId: null, - pdbId: "8C5M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8c5m_final.pdb", - externalLink: "https://pdb-redo.eu/db/8c5m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "WUUGFSXJNOTRMR-IOSLPCCCSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - "Kiene, A.", - "Galchenkova, M. (0000-0001-8676-0091)", - "Garcia, Y. (0000-0002-9592-2141)", - "Ehr, C. (0000-0003-1428-0042)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8c5m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8c5m", - }, - }, - { - title: - "Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp4-nsp5 (C4) cut site sequence", - emdb: null, - pdb: { - dbId: "8DRR", - method: "X-RAY DIFFRACTION", - keywords: "Viral protease, SARS-CoV-2, HY, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8DRR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8drr_final.pdb", - externalLink: "https://pdb-redo.eu/db/8drr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: [ - "Lee, J. (0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. 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(0000-0003-2086-0190)", "Mariuzza, R.A. (0000-0003-0748-5875)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36806685", - title: - "Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor (TCR) diversity.", - journal: "J.Biol.Chem. 299: 103035-103035 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103035", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36806685", - pubDate: "2023", - abstract: "", - authors: [ - "Wu, D.", - "Efimov, G.A.", - "Bogolyubova, A.V.", - "Pierce, B.G.", - "Mariuzza, R.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gom_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gom", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 Main Protease after incubation with Sulfo-Calpeptin", - emdb: null, - pdb: { - dbId: "7Z3U", - method: "X-RAY DIFFRACTION", - keywords: - "main protease, MPro, cystein protease, drug development, drug target, peptide-like inhibitor, SARS-CoV-2, COVID-19, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7Z3U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7z3u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7z3u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "JDNZSBPOIODDLU-ROUUACIJSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Falke, S. (0000-0003-3409-1791)", - "Reinke, P.Y.A. (0000-0002-7354-0839)", - "Lieske, J. (0000-0002-5439-5082)", - "Ewert, W. (0000-0001-8626-4864)", - "Loboda, J. (0000-0002-9601-3484)", - "Rahmani Mashhour, A. (0000-0001-9177-5589)", - "Hauser, M.", - "Karnicar, K. (0000-0002-7033-9224)", - "Usenik, A. (0000-0003-2366-2886)", - "Lindic, N. (0000-0001-7681-3436)", - "Lach, M.", - "Boehler, H.", - "Beck, T.", - "Cox, R.", - "Chapman, H.N. (0000-0002-4655-1743)", - "Hinrichs, W. (0000-0002-0435-4565)", - "Turk, D. (0000-0003-0205-6609)", - "Guenther, S. (0000-0002-7329-6653)", - "Meents, A. (0000-0001-6078-4095)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Sulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Reinke, P.Y.A. (0000-0002-7354-0839)", - "Falke, S. (0000-0003-3409-1791)", - "Lieske, J. (0000-0002-5439-5082)", - "Ewert, W. (0000-0001-8626-4864)", - "Loboda, J. (0000-0002-9601-3484)", - "Rahmani Mashhour, A. (0000-0001-9177-5589)", - "Hauser, M.", - "Karnicar, K. (0000-0002-7033-9224)", - "Usenik, A. (0000-0003-2366-2886)", - "Lindic, N. (0000-0001-7681-3436)", - "Lach, M.", - "Boehler, H.", - "Beck, T.", - "Cox, R.", - "Chapman, H.N. (0000-0002-4655-1743)", - "Hinrichs, W. (0000-0002-0435-4565)", - "Turk, D. (0000-0003-0205-6609)", - "Guenther, S. (0000-0002-7329-6653)", - "Meents, A. (0000-0001-6078-4095)", - "Afonine, P.V.", - "Grosse-Kunstleve, R.W.", - "Echols, N.", - "Headd, J.J.", - "Moriarty, N.W.", - "Mustyakimov, M.", - "Terwilliger, T.C.", - "Urzhumtsev, A.", - "Zwart, P.H.", - "Adams, P.D.", - ], - }, - { - pmID: "22505256", - title: - "Towards automated crystallographic structure refinement with phenix.refine.", - journal: - "Acta Crystallogr D Biol Crystallogr 68: 352-367 (2012), 1399-0047", - doi: "https://doi.org/10.1107/S0907444912001308", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/22505256", - pubDate: "2012", - abstract: "", - authors: [ - "Reinke, P.Y.A. (0000-0002-7354-0839)", - "Falke, S. (0000-0003-3409-1791)", - "Lieske, J. (0000-0002-5439-5082)", - "Ewert, W. (0000-0001-8626-4864)", - "Loboda, J. (0000-0002-9601-3484)", - "Rahmani Mashhour, A. (0000-0001-9177-5589)", - "Hauser, M.", - "Karnicar, K. (0000-0002-7033-9224)", - "Usenik, A. (0000-0003-2366-2886)", - "Lindic, N. (0000-0001-7681-3436)", - "Lach, M.", - "Boehler, H.", - "Beck, T.", - "Cox, R.", - "Chapman, H.N. (0000-0002-4655-1743)", - "Hinrichs, W. (0000-0002-0435-4565)", - "Turk, D. (0000-0003-0205-6609)", - "Guenther, S. (0000-0002-7329-6653)", - "Meents, A. (0000-0001-6078-4095)", - "Afonine, P.V.", - "Grosse-Kunstleve, R.W.", - "Echols, N.", - "Headd, J.J.", - "Moriarty, N.W.", - "Mustyakimov, M.", - "Terwilliger, T.C.", - "Urzhumtsev, A.", - "Zwart, P.H.", - "Adams, P.D.", - "Anson, B. (0000-0003-2670-974X)", - "Ghosh, A.K.", - "Mesecar, A. (0000-0002-1241-2577)", - "Bunkoczi, G.", - "Chen, V.B.", - "Davis, I.W.", - "Hung, L.W.", - "Kapral, G.J.", - "McCoy, A.J.", - "Oeffner, R.", - "Read, R.J.", - "Richardson, D.C.", - "Richardson, J.S.", - "Sander, S. (0000-0002-7985-2526)", - "Tidow, H. (0000-0002-4702-9332)", - "Fliegert, R.", - "Sandmann, M.", - "Liebschner, D. (0000-0003-3921-3209)", - "Afonine, P.V. (0000-0002-5052-991X)", - "Baker, M.L.", - "Croll, T.I.", - "Hintze, B. (0000-0002-4871-2096)", - "Hung, L.W. (0000-0001-6690-8458)", - "Jain, S.", - "Moriarty, N.W. (0000-0001-8857-9464)", - "Oeffner, R.D. (0000-0003-3107-2202)", - "Poon, B.K. (0000-0001-9633-6067)", - "Prisant, M.G.", - "Read, R.J. (0000-0001-8273-0047)", - "Sammito, M.D.", - "Sobolev, O.V. (0000-0002-0623-3214)", - "Stockwell, D.H.", - "Terwilliger, T.C. (0000-0001-6384-0320)", - "Urzhumtsev, A.G.", - "Videau, L.L.", - "Williams, C.J.", - "Adams, P.D. (0000-0001-9333-8219)", - "Aksu, M.", - "Kumar, P.", - "Guttler, T.", - "Taxer, W.", - "Gregor, K.", - "Mussil, B.", - "Rymarenko, O.", - "Stegmann, K.M.", - "Dickmanns, A.", - "Gerber, S.", - "Reineking, W.", - "Schulz, C.", - "Henneck, T.", - "Mohamed, A.", - "Pohlmann, G.", - "Ramazanoglu, M.", - "Mese, K.", - "Gross, U.", - "Ben-Yedidia, T.", - "Ovadia, O.", - "Fischer, D.W.", - "Kamensky, M.", - "Reichman, A.", - "Baumgartner, W.", - "von Kockritz-Blickwede, M.", - "Dobbelstein, M.", - "Gorlich, D.", - "Kabsch, W.", - "Emsley, P.", - "Lohkamp, B.", - "Scott, W.G.", - "Cowtan, K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z3u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z3u", - }, - }, - { - title: "Structure of SARS-CoV2 PLpro bound to a covalent inhibitor", - emdb: null, - pdb: { - dbId: "8EUA", - method: "X-RAY DIFFRACTION", - keywords: - "PLpro, SARS-CoV2, Covalent inhibitor, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8EUA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8eua_final.pdb", - externalLink: "https://pdb-redo.eu/db/8eua", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "KCRIVPTZKJZJHI-GOSISDBHSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: [ - "Mathews, I.I. (0000-0001-6254-3519)", - "Pokhrel, S. (0000-0001-5712-2824)", - "Wakatsuki, S. (0000-0001-5896-7968)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36977673", - title: - "Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2.", - journal: "Nat Commun 14: 1733-1733 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-37254-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36977673", - pubDate: "2023", - abstract: "", - authors: [ - "Sanders, B.C. (0000-0001-9754-1687)", - "Pokhrel, S. (0000-0003-2258-8768)", - "Labbe, A.D.", - "Mathews, I.I. (0000-0001-6254-3519)", - "Cooper, C.J.", - "Davidson, R.B.", - "Phillips, G. (0000-0001-5858-3825)", - "Weiss, K.L. (0000-0002-6486-8007)", - "Zhang, Q.", - "O'Neill, H. (0000-0003-2966-5527)", - "Kaur, M.", - "Schmidt, J.G. (0000-0002-8192-9940)", - "Reichard, W.", - "Surendranathan, S.", - "Parvathareddy, J.", - "Phillips, L.", - "Rainville, C.", - "Sterner, D.E.", - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Babnigg, G. (0000-0002-9838-1803)", - "Moriarty, N.W. (0000-0001-8857-9464)", - "Adams, P.D. (0000-0001-9333-8219)", - "Joachimiak, A. (0000-0003-2535-6209)", - "Hurst, B.L. (0000-0003-1025-5878)", - "Kumar, S. (0000-0002-1940-772X)", - "Butt, T.R.", - "Jonsson, C.B. (0000-0002-2640-7672)", - "Ferrins, L. (0000-0001-8992-0919)", - "Wakatsuki, S. (0000-0001-5896-7968)", - "Galanie, S. (0000-0001-5712-2568)", - "Head, M.S.", - "Parks, J.M. (0000-0002-3103-9333)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8eua_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8eua", - }, - }, - { - title: - "SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01", - emdb: null, - pdb: { - dbId: "7SA2", - method: "X-RAY DIFFRACTION", - keywords: - "human leukocyte antigen, major histocompatibility complex, HLA-A2, HLA-A*02:01, VVFLHVTYV, SARS-CoV-2, spike, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7SA2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sa2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sa2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2' peptide VVFLHVTYV", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WLZRMCYVCSSEQC-UHFFFAOYSA-N", "FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: ["Szeto, C. (0000-0003-3784-5210)", "Gras, S. (0000-0001-7416-038X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Szeto, C. (0000-0003-3784-5210)", - "Gras, S. (0000-0001-7416-038X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sa2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sa2", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI42", - emdb: null, - pdb: { - dbId: "7S75", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S75", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s75_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s75", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YJDABKUOTKRKDF-RZCQQDKOSA-N"], - dbauthors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Sankaran, B. (0000-0002-3266-8131)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35839690", - title: - "A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114596-114596 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839690", - pubDate: "2022", - abstract: "", - authors: [ - "Alugubelli, Y.R.", - "Geng, Z.Z.", - "Yang, K.S.", - "Shaabani, N.", - "Khatua, K.", - "Ma, X.R.", - "Vatansever, E.C.", - "Cho, C.C.", - "Ma, Y.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s75_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s75", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibodies WRAIR-2063 and WRAIR-2151", - emdb: null, - pdb: { - dbId: "8EOO", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, immune system, complex, human antibodies", - refModels: [ - { - emdbId: null, - pdbId: "8EOO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8eoo_final.pdb", - externalLink: "https://pdb-redo.eu/db/8eoo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2151 antibody Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2151 antibody Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "WRAIR-2063 antibody Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "WRAIR-2063 antibody Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Jensen, J.L. (0000-0002-8818-7513)", - "Sankhala, R.S. (0000-0001-8639-5290)", - "Joyce, M.G. (0000-0002-6808-7232)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37395646", - title: - "Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity.", - journal: "J.Virol. 97: e0159622-e0159622 (2023), 1098-5514", - doi: "https://doi.org/10.1128/jvi.01596-22", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37395646", - pubDate: "2023", - abstract: "", - authors: [ - "Jensen, J.L.", - "Sankhala, R.S.", - "Dussupt, V.", - "Bai, H.", - "Hajduczki, A.", - "Lal, K.G.", - "Chang, W.C.", - "Martinez, E.J.", - "Peterson, C.E.", - "Golub, E.S.", - "Rees, P.A.", - "Mendez-Rivera, L.", - "Zemil, M.", - "Kavusak, E.", - "Mayer, S.V. (0000-0002-5767-8870)", - "Wieczorek, L.", - "Kannan, S.", - "Doranz, B.J.", - "Davidson, E.", - "Yang, E.S.", - "Zhang, Y.", - "Chen, M.", - "Choe, M.", - "Wang, L.", - "Gromowski, G.D.", - "Koup, R.A.", - "Michael, N.L.", - "Polonis, V.R. (0000-0002-4827-9923)", - "Rolland, M. (0000-0003-3650-8490)", - "Modjarrad, K.", - "Krebs, S.J.", - "Joyce, M.G. (0000-0002-6808-7232)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8eoo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8eoo", - }, - }, - { - title: - "Crystal Structure of Human Fab S24-1063 in the Complex with the N-teminal Domain of Nucleocapsid Protein from SARS CoV-2", - emdb: null, - pdb: { - dbId: "7STR", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Coronavirus 2, Nucleocapsid protein, Human antibody Fab, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7STR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7str_final.pdb", - externalLink: "https://pdb-redo.eu/db/7str", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Fab S24-1063, Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab S24-1063, Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of Human Fab S24-1063 in the Complex with the N-teminal Domain of Nucleocapsid Protein from SARS CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7str_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7str", - }, - }, - { - title: "SARS-CoV-2-Beta-RBD and CB6-092-Fab complex", - emdb: null, - pdb: { - dbId: "7XEG", - method: "X-RAY DIFFRACTION", - keywords: - "complex, antibody, receptor, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7XEG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xeg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xeg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CB6-092-Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CB6-092-Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wang, Y.", "Feng, Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2-Beta-RBD and CB6-092-Fab complex", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Wang, Y.", "Feng, Y."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xeg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xeg", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CL protease in complex with a m-chlorophenyl dimethyl sulfane inhibitor", - emdb: null, - pdb: { - dbId: "8E61", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, Viral protein-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8E61", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e61_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e61", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "MOYGJNHMYWCTOO-SXTKRDDTSA-N", - "MOYGJNHMYWCTOO-BCSOYYNPSA-N", - ], - dbauthors: [ - "Lovell, S. (0000-0002-3215-4472)", - "Liu, L. (0000-0003-0514-281X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Madden, T.K.", - "Groutas, W.C. (0000-0001-5248-7912)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e61_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e61", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with AG7404", - emdb: null, - pdb: { - dbId: "7ZQV", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Inhibitor, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZQV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zqv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zqv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WVFVHUYBPRBKRA-UEXGIBASSA-N"], - dbauthors: [ - "Fabrega-Ferrer, M. (0000-0001-9471-0473)", - "Herrera-Morande, A.", - "Perez-Saavedra, J. (0000-0003-0829-6056)", - "Coll, M. (0000-0003-4471-8674)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36336176", - title: - "Structure and inhibition of SARS-CoV-1 and SARS-CoV-2 main proteases by oral antiviral compound AG7404.", - journal: "Antiviral Res. 208: 105458-105458 (2022), 0166-3542", - doi: "https://doi.org/10.1016/j.antiviral.2022.105458", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36336176", - pubDate: "2022", - abstract: "", - authors: [ - "Fabrega-Ferrer, M.", - "Herrera-Morande, A.", - "Muriel-Goni, S.", - "Perez-Saavedra, J.", - "Bueno, P.", - "Castro, V.", - "Garaigorta, U.", - "Gastaminza, P.", - "Coll, M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zqv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zqv", - }, - }, - { - title: - "Crystal Structure of Human Fab S24-1379 in the Complex with the N-teminal Domain of Nucleocapsid Protein from SARS CoV-2", - emdb: null, - pdb: { - dbId: "7STS", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Coronavirus 2, Nucleocapsid protein, Human antibody Fab, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7STS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sts_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sts", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Fab S24-1379, heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab S24-1379, light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of Human Fab S24-1379 in the Complex with the N-teminal Domain of Nucleocapsid Protein from SARS CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sts_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sts", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI38", - emdb: null, - pdb: { - dbId: "7S74", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S74", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s74_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s74", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AXOUOMLRYWWRDK-XLAORIBOSA-N"], - dbauthors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Sankaran, B. (0000-0002-3266-8131)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35839690", - title: - "A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114596-114596 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839690", - pubDate: "2022", - abstract: "", - authors: [ - "Alugubelli, Y.R.", - "Geng, Z.Z.", - "Yang, K.S.", - "Shaabani, N.", - "Khatua, K.", - "Ma, X.R.", - "Vatansever, E.C.", - "Cho, C.C.", - "Ma, Y.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s74_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s74", - }, - }, - { - title: "Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004", - emdb: null, - pdb: { - dbId: "8G62", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, coronavirus, SARS, COV-2, papain-like protease, IDP51000, IDP52003, remodilin, Center for Structural Biology of Infectious Diseases, CSBID, HYDROLASE-HYDROLASE INHIBITOR complex, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8G62", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8g62_final.pdb", - externalLink: "https://pdb-redo.eu/db/8g62", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "JTGUXSIYSIXMPK-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - ], - dbauthors: [ - "Tesar, C.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Luci, D.", - "Kales, S.", - "Simeonov, A.", - "Rai, G.", - "Drayman, N.", - "Tay, S.", - "Oakes, S.", - "Rosner, M.", - "Chen, B.", - "Dulin, N.", - "Solway, J.", - "Center for Structural Biology of Infectious Diseases (CSBID)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Jedrzejczak, R.", - "Luci, D.", - "Kales, S.", - "Simeonov, A.", - "Rai, G.", - "Drayman, N.", - "Tay, S.", - "Oakes, S.", - "Rosner, M.", - "Chen, B.", - "Dulin, N.", - "Solway, J.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Center for Structural Biology of Infectious Diseases (CSBID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8g62_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8g62", - }, - }, - { - title: - "SARS-CoV-2 3CLPro in complex with N-(4-(1H-pyrazol-4-yl)phenyl)-N-(3-chlorobenzyl)-2-(pyridin-3-yl)acetamide", - emdb: null, - pdb: { - dbId: "7TEK", - method: "X-RAY DIFFRACTION", - keywords: - "Inhibitor, Complex, Protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TEK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tek_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tek", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LLFIKGDQQRLTFJ-UHFFFAOYSA-N"], - dbauthors: [ - "Goins, C.M. (0000-0002-6617-4877)", - "Stauffer, S.R. (0000-0002-6332-1827)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 3CL-protease inhibitors derived from ML300: investigation of P1 and replacements of the 1,2,3-benzotriazole", - journal: "Med.Chem.Res. (2023), 1054-2523", - doi: "https://doi.org/10.1007/s00044-023-03108-9", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Hooper, A.", - "Macdonald, J.D.", - "Reilly, B.", - "Maw, J.", - "Wirrick, A.P.", - "Han, S.H.", - "Lindsey, A.A.", - "Rico, E.G.", - "Romigh, T.", - "Goins, C.M.", - "Wang, N.S.", - "Stauffer, S.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tek_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tek", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab", - emdb: null, - pdb: { - dbId: "8BSF", - method: "X-RAY DIFFRACTION", - keywords: - "ANTIBODY, VIRUS, COMPLEX, SARS-COV-2, VIRAL PROTEIN COMPLEX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8BSF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8bsf_final.pdb", - externalLink: "https://pdb-redo.eu/db/8bsf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "3D2 FAB HEAVY CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "3D2 FAB LIGHT CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Welin, M. (0000-0001-5786-1600)", - "Kimbung, Y.R.", - "Focht, D.", - "Pisitkun, T.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "unidentified baculovirus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Boonkrai, C.", - "Cotrone, T.S.", - "Chaisuriyong, W.", - "Tantawichien, T.", - "Thisyakorn, U.", - "Fernandez, S.", - "Hunsawong, T.", - "Reed, M.", - "Focht, D.", - "Kimbung, Y.R.", - "Welin, M.", - "Wongtangprasert, T.", - "Audomsun, T.", - "Phakham, T.", - "Attakitbancha, C.", - "Saelao, P.", - "Pisitkun, P.", - "Srisawat, N.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8bsf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8bsf", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide", - emdb: null, - pdb: { - dbId: "8AAA", - method: "X-RAY DIFFRACTION", - keywords: "sRBD, Stapled peptide, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8AAA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8aaa_final.pdb", - externalLink: "https://pdb-redo.eu/db/8aaa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Stapled peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AEPJNZPJFYDQLM-UHFFFAOYSA-N"], - dbauthors: [ - "Brear, P. (0000-0002-4045-0474)", - "Chen, L. (0000-0003-1776-3146)", - "Gaynor, K. (0000-0003-0461-810X)", - "Harman, M. (0000-0002-3667-5929)", - "Dods, R. (0000-0003-4014-7499)", - "Hyvonen, M. (0000-0001-8683-4070)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37328472", - title: - "Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2.", - journal: "Nat Commun 14: 3583-3583 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-39158-1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37328472", - pubDate: "2023", - abstract: "", - authors: [ - "Gaynor, K.U. (0000-0003-0461-810X)", - "Vaysburd, M.", - "Harman, M.A.J. (0000-0002-3667-5929)", - "Albecka, A.", - "Jeffrey, P.", - "Beswick, P.", - "Papa, G. (0000-0002-5215-0014)", - "Chen, L. (0000-0003-1776-3146)", - "Mallery, D. (0000-0003-2713-5215)", - "McGuinness, B.", - "Van Rietschoten, K.", - "Stanway, S.", - "Brear, P. (0000-0002-4045-0474)", - "Lulla, A.", - "Ciazynska, K. (0000-0002-9899-2428)", - "Chang, V.T. (0000-0001-7047-9019)", - "Sharp, J. (0000-0001-8482-5736)", - "Neary, M.", - "Box, H.", - "Herriott, J.", - "Kijak, E.", - "Tatham, L.", - "Bentley, E.G.", - "Sharma, P.", - "Kirby, A.", - "Han, X.", - "Stewart, J.P. (0000-0002-8928-2037)", - "Owen, A. (0000-0002-9819-7651)", - "Briggs, J.A.G. (0000-0003-3990-6910)", - "Hyvonen, M. (0000-0001-8683-4070)", - "Skynner, M.J. (0000-0001-6586-9055)", - "James, L.C. (0000-0003-2131-0334)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8aaa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8aaa", - }, - }, - { - title: - "Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp6-nsp7 (C6) cut site sequence", - emdb: null, - pdb: { - dbId: "8DRS", - method: "X-RAY DIFFRACTION", - keywords: "Viral protease, SARS-CoV-2, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8DRS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8drs_final.pdb", - externalLink: "https://pdb-redo.eu/db/8drs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lee, J. (0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. (0000-0002-7408-5487)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8drs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8drs", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with ADP", - emdb: null, - pdb: { - dbId: "8OV1", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, methyltransferase, complex, inhibitor, SARS-Cov-2", - refModels: [ - { - emdbId: null, - pdbId: "8OV1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ov1_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ov1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "XTWYTFMLZFPYCI-KQYNXXCUSA-N", - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - "Kiene, A.", - "Galchenkova, M. (0000-0001-8676-0091)", - "Garcia, Y. (0000-0002-9592-2141)", - "Ehr, C. (0000-0003-1428-0042)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ov1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ov1", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with AMP", - emdb: null, - pdb: { - dbId: "8OTO", - method: "X-RAY DIFFRACTION", - keywords: "Methyltransferase, protein complex, Inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8OTO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8oto_final.pdb", - externalLink: "https://pdb-redo.eu/db/8oto", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "UDMBCSSLTHHNCD-KQYNXXCUSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - "Kiene, A.", - "Galchenkova, M. (0000-0001-8676-0091)", - "Garcia, Y. (0000-0002-9592-2141)", - "Ehr, C. (0000-0003-1428-0042)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8oto_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8oto", - }, - }, - { - title: "Crystal structure of the SARS-Cov-2 RBD in complex with Fab 2303", - emdb: null, - pdb: { - dbId: "7WBZ", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7WBZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wbz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wbz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "2303 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "2303 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Xiang, Y.", "Ma, B."], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera aff. frugiperda 1 BOLD-2017", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35931732", - title: - "Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies.", - journal: "Commun Biol 5: 789-789 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03739-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35931732", - pubDate: "2022", - abstract: "", - authors: [ - "Li, R.", - "Mor, M. (0000-0003-1361-4151)", - "Ma, B.", - "Clark, A.E. (0000-0003-1687-416X)", - "Alter, J.", - "Werbner, M.", - "Lee, J.C. (0000-0001-5465-3670)", - "Leibel, S.L.", - "Carlin, A.F. (0000-0002-1669-8066)", - "Dessau, M. (0000-0002-1954-3625)", - "Gal-Tanamy, M.", - "Croker, B.A. (0000-0002-0885-3599)", - "Xiang, Y. (0000-0003-0230-9522)", - "Freund, N.T. (0000-0002-5386-502X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wbz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wbz", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166N Mutant", - emdb: null, - pdb: { - dbId: "8DDI", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, Mutation, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DDI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ddi_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ddi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Jacobs, L.M.C. (0000-0002-9939-653X)", - "Chen, Y. (0000-0002-5115-3600)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35982672", - title: - "A yeast-based system to study SARS-CoV-2 M pro structure and to identify nirmatrelvir resistant mutations.", - journal: "Biorxiv (2022)", - doi: "https://doi.org/10.1101/2022.08.06.503039", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35982672", - pubDate: "2022", - abstract: "", - authors: [ - "Ou, J.", - "Lewandowski, E.M.", - "Hu, Y.", - "Lipinski, A.A.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Zhang, X.", - "Bikowitz, M.J.", - "Langlais, P.", - "Tan, H.", - "Wang, J.", - "Chen, Y.", - "Choy, J.S. (0000-0001-9196-3280)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ddi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ddi", - }, - }, - { - title: - "Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S761-775", - emdb: null, - pdb: { - dbId: "8CMD", - method: "X-RAY DIFFRACTION", - keywords: - "HLA-II, HLA-DR, HLA-DR1, human leukocyte antigen, major histocompatibility complex, major histocompatibility complex class 2, SARS-CoV-2, coronavirus, COVID-19, Spike, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CMD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cmd_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cmd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01903", - organism: "9606", - name: "HLA class II histocompatibility antigen, DR alpha chain", - details: "", - altNames: "MHC class II antigen DRA", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "MacLachlan, B.J. (0000-0002-2685-2733)", - "Mason, G.H. (0000-0002-7844-7190)", - "Sourfield, D.O. (0000-0002-0836-7718)", - "Godkin, A.J. (0000-0002-1910-7567)", - "Rizkallah, P.J. (0000-0002-9290-0369)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37471227", - title: - "Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.", - journal: "Cell Rep 42: 112827-112827 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112827", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37471227", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, Y.", - "Mason, G.H.", - "Scourfield, D.O.", - "Greenshields-Watson, A.", - "Haigh, T.A.", - "Sewell, A.K.", - "Long, H.M.", - "Gallimore, A.M.", - "Rizkallah, P.", - "MacLachlan, B.J.", - "Godkin, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cmd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cmd", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI12", - emdb: null, - pdb: { - dbId: "7UUB", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7UUB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uub_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uub", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BYTYQUJNXNJHDG-CMOCDZPBSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36629751", - title: - "A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.", - journal: "Acs Chem.Biol. 18: 449-455 (2023), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.2c00695", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36629751", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, K.S.", - "Blankenship, L.R.", - "Kuo, S.A.", - "Sheng, Y.J.", - "Li, P.", - "Fierke, C.A.", - "Russell, D.H.", - "Yan, X.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uub_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uub", - }, - }, - { - title: - "SARS-CoV-2 non-structural protein-1 (nsp1) in complex with 1-(2-(3-chlorophenyl)thiazol-4-yl)-N-methylmethanamine", - emdb: null, - pdb: { - dbId: "8AZ9", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, non-structural protein-1, fragment hit, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8AZ9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8az9_final.pdb", - externalLink: "https://pdb-redo.eu/db/8az9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Host translation inhibitor nsp1", - details: "", - altNames: "Leader protein,Non-structural protein 1,nsp1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YHQACXKNKUPSSA-UHFFFAOYSA-N"], - dbauthors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Kozielski, F. (0000-0001-6096-9102)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36293303", - title: - "Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening.", - journal: "Int J Mol Sci 23 (2022), 1422-0067", - doi: "https://doi.org/10.1021/ci200227u", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36293303", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S. (0000-0002-2070-7770)", - "Lou, J.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Haider, S. (0000-0003-2650-2925)", - "Kozielski, F. (0000-0001-6096-9102)", - "Ma, S.", - "Mykhaylyk, V. (0000-0003-0106-2724)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8az9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8az9", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166R Mutant in Complex with Inhibitor GC376", - emdb: null, - pdb: { - dbId: "8DDM", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, Mutation, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DDM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ddm_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ddm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35982672", - title: - "A yeast-based system to study SARS-CoV-2 M pro structure and to identify nirmatrelvir resistant mutations.", - journal: "Biorxiv (2022)", - doi: "https://doi.org/10.1101/2022.08.06.503039", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35982672", - pubDate: "2022", - abstract: "", - authors: [ - "Ou, J.", - "Lewandowski, E.M.", - "Hu, Y.", - "Lipinski, A.A.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Zhang, X.", - "Bikowitz, M.J.", - "Langlais, P.", - "Tan, H.", - "Wang, J.", - "Chen, Y.", - "Choy, J.S. (0000-0001-9196-3280)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ddm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ddm", - }, - }, - { - title: - "Structure of SARS-CoV-2 Mpro in complex with the nsp13-nsp14 (C13) cut site sequence (form 2)", - emdb: null, - pdb: { - dbId: "8DS2", - method: "X-RAY DIFFRACTION", - keywords: "Viral protease, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DS2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ds2_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ds2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: [ - "Lee, J. (0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. (0000-0002-7408-5487)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ds2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ds2", - }, - }, - { - title: - "SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01", - emdb: null, - pdb: { - dbId: "7UM2", - method: "X-RAY DIFFRACTION", - keywords: - "human leukocyte antigen, major histocompatibility complex, HLA-A2, HLA-A*02:01, SARS-CoV-2, Spike, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7UM2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7um2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7um2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q53Z42", - organism: "9606", - name: "HLA class I antigen", - details: "", - altNames: - "HLA class I histocompatibility antigen,HLA class I histocompatibility antigen A alpha chain,A alpha chain,MHC class I antigen,MHC class I protein,MHC class I protein (HLA-A)", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "WLZRMCYVCSSEQC-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Szeto, C. (0000-0003-3784-5210)", "Gras, S. (0000-0001-7416-038X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Szeto, C. (0000-0003-3784-5210)", - "Gras, S. (0000-0001-7416-038X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7um2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7um2", - }, - }, - { - title: "Structure of P4A2 Fab in complex with Spike-RBD from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7WVL", - method: "X-RAY DIFFRACTION", - keywords: - "Fab, Spike-RBD, complex, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7WVL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wvl_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wvl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "10090", - name: "P4A2 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "P4A2 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Narayanan, N. (0000-0001-8327-1559)", - "Nair, D.T. (0000-0002-0677-9444)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36508467", - title: - "A broadly neutralizing monoclonal antibody overcomes the mutational landscape of emerging SARS-CoV-2 variants of concern.", - journal: "Plos Pathog. 18: e1010994-e1010994 (2022), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1010994", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36508467", - pubDate: "2022", - abstract: "", - authors: [ - "Parray, H.A.", - "Narayanan, N.", - "Garg, S.", - "Rizvi, Z.A.", - "Shrivastava, T.", - "Kushwaha, S.", - "Singh, J.", - "Murugavelu, P.", - "Anantharaj, A.", - "Mehdi, F.", - "Raj, N.", - "Singh, S.", - "Dandotiya, J.", - "Lukose, A.", - "Jamwal, D.", - "Kumar, S.", - "Chiranjivi, A.", - "Dhyani, S.", - "Mishra, N.", - "Jakhar, K.", - "Sonar, S.", - "Panchal, A.K.", - "Tripathy, M.R.", - "Chowdhury, S.R.", - "Ahmed, S.", - "Samal, S.", - "Mani, S.", - "Bhattacharyya, S.", - "Das, S.", - "Sinha, S.", - "Luthra, K.", - "Batra, G.", - "Sehgal, D.", - "Medigeshi, G.R.", - "Sharma, C.", - "Awasthi, A.", - "Garg, P.K.", - "Nair, D.T.", - "Kumar, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wvl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wvl", - }, - }, - { - title: - "Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp9-nsp10 (C9) cut site sequence", - emdb: null, - pdb: { - dbId: "8DRW", - method: "X-RAY DIFFRACTION", - keywords: "Viral protease, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DRW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8drw_final.pdb", - externalLink: "https://pdb-redo.eu/db/8drw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: - "Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase,nsp9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "JLFNLZLINWHATN-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Lee, J. (0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. 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(0000-0003-4310-7898)", - "Li, Y.", - "Yoon, C.", - "Huang, Q.", - "Hu, B.", - "You, J.", - "Quan, B.", - "Zhao, X.", - "Guo, N.", - "Zhang, S.", - "Ma, R.", - "Zhang, J.", - "Wang, Y.", - "Yang, R.", - "Nan, J.", - "Xu, H.", - "Wang, F.", - "Lei, J. (0000-0001-9326-0554)", - "Chu, H. 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(0000-0002-9560-5082)", - "Damfo, S.", - "Kozielski, F. (0000-0001-6096-9102)", - "Haider, S. (0000-0003-2650-2925)", - "Borsatto, A. (0000-0002-8889-6491)", - "Galdadas, I. (0000-0003-2136-9723)", - "Estarellas, C. (0000-0002-0944-9053)", - "Gervasio, F.L. 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(0000-0002-9723-4756)", - "Han, Y.", - "Zhou, R.", - "Zhou, Y.", - "Lei, J. (0000-0001-9326-0554)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wzo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wzo", - }, - }, - { - title: "14-3-3 in complex with SARS-COV2 N phospho-peptide", - emdb: null, - pdb: { - dbId: "7ZIT", - method: "X-RAY DIFFRACTION", - keywords: "covid, coronavirus, N-phosphopeptide, PROTEIN BINDING", - refModels: [ - { - emdbId: null, - pdbId: "7ZIT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zit_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zit", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P63104", - organism: "9606", - name: "14-3-3 protein zeta/delta", - details: "", - altNames: "Protein kinase C inhibitor protein 1,KCIP-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "WPYMKLBDIGXBTP-UHFFFAOYSA-N", - ], - dbauthors: ["Eisenreichova, A.", "Boura, E."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35781025", - title: - "Structural basis for SARS-CoV-2 nucleocapsid (N) protein recognition by 14-3-3 proteins.", - journal: "J.Struct.Biol. 214: 107879-107879 (2022), 1095-8657", - doi: "https://doi.org/10.1016/j.jsb.2022.107879", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35781025", - pubDate: "2022", - abstract: "", - authors: ["Eisenreichova, A.", "Boura, E."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zit_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zit", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI34", - emdb: null, - pdb: { - dbId: "7S70", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S70", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s70_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s70", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CYAFTCDKLGXDCI-BLTUZGSGSA-N"], - dbauthors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Sankaran, B. (0000-0002-3266-8131)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35839690", - title: - "A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114596-114596 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839690", - pubDate: "2022", - abstract: "", - authors: [ - "Alugubelli, Y.R.", - "Geng, Z.Z.", - "Yang, K.S.", - "Shaabani, N.", - "Khatua, K.", - "Ma, X.R.", - "Vatansever, E.C.", - "Cho, C.C.", - "Ma, Y.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s70_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s70", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with antibody CC12.1 Fab and nanobody Nb-C4-255", - emdb: null, - pdb: { - dbId: "8ELQ", - method: "X-RAY DIFFRACTION", - keywords: - "synthetic, nanobody, SARS-CoV-2, coronavirus, neutralization, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8ELQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8elq_final.pdb", - externalLink: "https://pdb-redo.eu/db/8elq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "32630", - name: "Nanobody Nb-C4-255", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.1 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.1 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Liu, H. 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(0009-0000-4564-8132)", - "Liu, J. (0000-0002-6038-593X)", - "Stanfield, R.L. (0000-0001-9521-9184)", - "Zhu, X. (0000-0002-6021-3740)", - "Turner, H.L.", - "Sok, D.", - "Huang, P.S. (0000-0002-7948-2895)", - "Burton, D.R. (0000-0001-6711-9864)", - "Ward, A.B. (0000-0001-7153-3769)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Jardine, J.G. (0000-0001-8951-1074)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8elq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8elq", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CL protease in complex with a benzimidazole dimethyl sulfane inhibitor", - emdb: null, - pdb: { - dbId: "8E64", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, Viral Protein-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8E64", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e64_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e64", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NRGPZDKZNYWRRP-BCSOYYNPSA-N", "NRGPZDKZNYWRRP-SXTKRDDTSA-N"], - dbauthors: [ - "Lovell, S. (0000-0002-3215-4472)", - "Liu, L. (0000-0003-0514-281X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Madden, T.K.", - "Groutas, W.C. (0000-0001-5248-7912)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e64_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e64", - }, - }, - { - title: "SARS-COV-2 Main Protease adduct with Au(NHC)Cl", - emdb: null, - pdb: { - dbId: "8B0S", - method: "X-RAY DIFFRACTION", - keywords: "NSP5, Mpro, SARS_COv-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8B0S", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8b0s_final.pdb", - externalLink: "https://pdb-redo.eu/db/8b0s", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZBKIUFWVEIBQRT-UHFFFAOYSA-N"], - dbauthors: [ - "Massai, L.", - "Grifagni, D.", - "Geri, A.", - "Calderone, V.", - "Cantini, F.", - "Banci, L.", - "Messori, L.", - "Desantis, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36421689", - title: - "Gold-Based Metal Drugs as Inhibitors of Coronavirus Proteins: The Inhibition of SARS-CoV-2 Main Protease by Auranofin and Its Analogs.", - journal: "Biomolecules 12 (2022), 2218-273X", - doi: "https://doi.org/10.3390/biom12111675", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36421689", - pubDate: "2022", - abstract: "", - authors: [ - "Massai, L. 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(0000-0002-3215-4472)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Groutas, W.C. (0000-0001-5248-7912)", - "Machen, A.J. (0000-0003-0625-3415)", - "Dampalla, C.S. (0000-0002-8199-2376)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e5x_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e5x", - }, - }, - { - title: "A dual Inhibitor Against Main Protease", - emdb: null, - pdb: { - dbId: "7V1T", - method: "X-RAY DIFFRACTION", - keywords: - "drug design, Dual Inhibitor, Main Protease, COVID-19, SARS-CoV-2, VIRUS, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7V1T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7v1t_final.pdb", - externalLink: "https://pdb-redo.eu/db/7v1t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JAMVFKPFIUKEMG-UHFFFAOYSA-N"], - dbauthors: [ - "Yu, W.Y. 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(0000-0002-3215-4472)", - "Liu, L. (0000-0003-0514-281X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Groutas, W.C. (0000-0001-5248-7912)", - "Miller, M.J. (0000-0002-8199-2376)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e65_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e65", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with antibody CC12.1 Fab and nanobody Nb-C4-240", - emdb: null, - pdb: { - dbId: "8ELP", - method: "X-RAY DIFFRACTION", - keywords: - "synthetic, nanobody, SARS-CoV-2, coronavirus, neutralization, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8ELP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8elp_final.pdb", - externalLink: "https://pdb-redo.eu/db/8elp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "32630", - name: "Nanobody Nb-C4-240", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.1 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.1 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Liu, H. (0000-0002-2412-7853)", "Wilson, I.A. (0000-0002-6469-2419)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37276407", - title: - "Fully synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins.", - journal: - "Proc.Natl.Acad.Sci.USA 120: e2216612120-e2216612120 (2023), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2216612120", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37276407", - pubDate: "2023", - abstract: "", - authors: [ - "Misson Mindrebo, L. (0000-0001-6318-1126)", - "Liu, H. (0000-0002-2412-7853)", - "Ozorowski, G. (0000-0002-9695-8138)", - "Tran, Q. (0000-0002-1250-5853)", - "Woehl, J. (0000-0001-7374-0059)", - "Khalek, I.", - "Smith, J.M. (0009-0000-1554-6768)", - "Barman, S.", - "Zhao, F. (0000-0002-3172-1340)", - "Keating, C.", - "Limbo, O. (0000-0003-1686-1414)", - "Verma, M. (0009-0000-4564-8132)", - "Liu, J. (0000-0002-6038-593X)", - "Stanfield, R.L. (0000-0001-9521-9184)", - "Zhu, X. (0000-0002-6021-3740)", - "Turner, H.L.", - "Sok, D.", - "Huang, P.S. (0000-0002-7948-2895)", - "Burton, D.R. (0000-0001-6711-9864)", - "Ward, A.B. (0000-0001-7153-3769)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Jardine, J.G. (0000-0001-8951-1074)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8elp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8elp", - }, - }, - { - title: - "Crystal Structure of Human Fab S24-188 in the complex with the N-teminal Domain of Nucleocapsid protein from SARS CoV-2", - emdb: null, - pdb: { - dbId: "7SUE", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Coronavirus 2, Nucleocapsid protein, Human antibody Fab, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7SUE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sue_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sue", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "S24-188 Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "S24-188 Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of Human Fab S24-188 in the complex with the N-teminal Domain of Nucleocapsid protein from SARS CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sue_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sue", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-1H1 Fab", - emdb: null, - pdb: { - dbId: "7XS8", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7XS8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xs8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xs8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "P5S-1H1 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P5S-1H1 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Wang, X.", "Wang, Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36914890", - title: - "Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.", - journal: "Nat.Immunol. 24: 690-699 (2023), 1529-2916", - doi: "https://doi.org/10.1038/s41590-023-01449-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36914890", - pubDate: "2023", - abstract: "", - authors: [ - "Ju, B.", - "Zhang, Q.", - "Wang, Z.", - "Aw, Z.Q. (0000-0002-6097-4099)", - "Chen, P. (0000-0002-9041-8392)", - "Zhou, B.", - "Wang, R. (0000-0002-8040-7913)", - "Ge, X.", - "Lv, Q.", - "Cheng, L.", - "Zhang, R. (0000-0003-0024-389X)", - "Wong, Y.H.", - "Chen, H.", - "Wang, H.", - "Shan, S. (0000-0002-7184-6818)", - "Liao, X.", - "Shi, X.", - "Liu, L.", - "Chu, J.J.H. (0000-0002-1673-6819)", - "Wang, X. (0000-0003-3136-8070)", - "Zhang, Z. (0000-0002-3544-1389)", - "Zhang, L. (0000-0003-4931-509X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xs8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xs8", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI35", - emdb: null, - pdb: { - dbId: "7S71", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S71", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s71_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s71", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NSGOBCXXBBPKSX-FQCPSNFCSA-N"], - dbauthors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Sankaran, B. (0000-0002-3266-8131)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35839690", - title: - "A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114596-114596 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839690", - pubDate: "2022", - abstract: "", - authors: [ - "Alugubelli, Y.R.", - "Geng, Z.Z.", - "Yang, K.S.", - "Shaabani, N.", - "Khatua, K.", - "Ma, X.R.", - "Vatansever, E.C.", - "Cho, C.C.", - "Ma, Y.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s71_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s71", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 BA.2 receptor binding domain in complex with neutralizing antibody 20A7", - emdb: null, - pdb: { - dbId: "8GB8", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, antibody, spike, receptor binding domain, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8GB8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gb8_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gb8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9544", - name: "20A7 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9544", - name: "20A7 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "DHMQDGOQFOQNFH-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - ], - dbauthors: ["Wilson, I.A. (0000-0002-6469-2419)", "Yuan, M. (0000-0001-9754-4503)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37163615", - title: - "Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.", - journal: "Sci Transl Med 15: eadg7404-eadg7404 (2023), 1946-6242", - doi: "https://doi.org/10.1126/scitranslmed.adg7404", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37163615", - pubDate: "2023", - abstract: "", - authors: [ - "Feng, Y. (0000-0001-8550-2787)", - "Yuan, M. (0000-0001-9754-4503)", - "Powers, J.M. (0000-0002-0485-9109)", - "Hu, M. (0000-0003-4495-7501)", - "Munt, J.E.", - "Arunachalam, P.S. (0000-0003-0090-5689)", - "Leist, S.R. (0000-0002-4989-5381)", - "Bellusci, L. (0000-0001-9945-1706)", - "Kim, J. (0000-0001-5443-8997)", - "Sprouse, K.R. (0000-0003-0007-2226)", - "Adams, L.E. (0000-0001-7780-9973)", - "Sundaramurthy, S. (0009-0004-7066-5662)", - "Zhu, X. (0000-0002-6021-3740)", - "Shirreff, L.M. (0000-0002-8403-451X)", - "Mallory, M.L. (0000-0003-0768-572X)", - "Scobey, T.D.", - "Moreno, A. (0000-0002-3031-7194)", - "O'Hagan, D.T.", - "Kleanthous, H.", - "Villinger, F.J. (0000-0002-7790-2008)", - "Veesler, D. (0000-0002-6019-8675)", - "King, N.P. (0000-0002-2978-4692)", - "Suthar, M.S. (0000-0002-2686-8380)", - "Khurana, S. (0000-0002-0593-7965)", - "Baric, R.S. (0000-0001-6827-8701)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Pulendran, B. (0000-0001-6517-4333)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gb8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gb8", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 main protease in complex with SY110", - emdb: null, - pdb: { - dbId: "8HHU", - method: "X-RAY DIFFRACTION", - keywords: - "Severe acute respiratory syndrome coronavirus 2, main protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8HHU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hhu_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hhu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PYEYIJGOSSTTFY-XCJLJZCSSA-N"], - dbauthors: [ - "Zeng, R. (0000-0001-9716-6354)", - "Xie, L.W. (0000-0002-4024-4988)", - "Huang, C. (0000-0003-0951-3411)", - "Wang, K. (0000-0002-8549-8973)", - "Liu, Y.Z. (0000-0001-7433-5119)", - "Yang, S.Y. (0000-0001-5147-3746)", - "Lei, J. (0000-0001-9326-0554)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36928316", - title: - "A new generation M pro inhibitor with potent activity against SARS-CoV-2 Omicron variants.", - journal: - "Signal Transduct Target Ther 8: 128-128 (2023), 2059-3635", - doi: "https://doi.org/10.1038/s41392-023-01392-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36928316", - pubDate: "2023", - abstract: "", - authors: [ - "Huang, C.", - "Shuai, H.", - "Qiao, J.", - "Hou, Y.", - "Zeng, R.", - "Xia, A. (0000-0002-2695-3024)", - "Xie, L.", - "Fang, Z. (0000-0003-4310-7898)", - "Li, Y.", - "Yoon, C.", - "Huang, Q.", - "Hu, B.", - "You, J.", - "Quan, B.", - "Zhao, X.", - "Guo, N.", - "Zhang, S.", - "Ma, R.", - "Zhang, J.", - "Wang, Y.", - "Yang, R.", - "Nan, J.", - "Xu, H.", - "Wang, F.", - "Lei, J. (0000-0001-9326-0554)", - "Chu, H. (0000-0003-2855-9837)", - "Yang, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hhu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hhu", - }, - }, - { - title: - "Fab arm of antibodies 4G1-C2 and 10G4 bound to CoV-2 receptor binding domain (RBD)", - emdb: null, - pdb: { - dbId: "8CWK", - method: "X-RAY DIFFRACTION", - keywords: - "antibody, CoV-2, receptor binding domain, class 5 epitope, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CWK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cwk_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cwk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of Fab arm of antibody 10G4", - details: "Heavy chain of Fab arm of antibody 10G4", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of Fab arm of antibody 10G4", - details: "Light chain of Fab arm of antibody 10G4", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of Fab arm of antibody 4G1-C2", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q6GMX0", - organism: "9606", - name: "Light chain of Fab arm of antibody 4G1-C2", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Langley, D.B. (0000-0003-2752-0041)", - "Christ, D. (0000-0002-7313-3977)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Neutralization of CoV-2 omicron sublineages by affinity-matured class 5 antibodies", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Langley, D.B.", "Christ, D."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cwk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cwk", - }, - }, - { - title: - "Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp8-nsp9 (C8) cut site sequence", - emdb: null, - pdb: { - dbId: "8DRV", - method: "X-RAY DIFFRACTION", - keywords: "Viral protease, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DRV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8drv_final.pdb", - externalLink: "https://pdb-redo.eu/db/8drv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: - "Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase,nsp8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JLFNLZLINWHATN-UHFFFAOYSA-N"], - dbauthors: [ - "Lee, J. (0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Vuckovic, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. (0000-0002-7408-5487)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8drv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8drv", - }, - }, - { - title: "Crystal structure of Ubl1 (residues 18-111) of SARS-CoV-2", - emdb: null, - pdb: { - dbId: "8HDA", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Nsp3, Ubl1, N-terminus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8HDA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hda_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hda", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Lei, J. (0000-0001-9326-0554)", "Ni, X.C. (0000-0002-9723-4756)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Crystal structure of Ubl1 (residues 18-111) of SARS-CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Ni, X.C. (0000-0002-9723-4756)", - "Lei, J. (0000-0001-9326-0554)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hda_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hda", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) H163A Mutant Apo Structure", - emdb: null, - pdb: { - dbId: "8DDL", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, SARS-CoV-2, 3CL-like, disulfide bond, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8DDL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ddl_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ddl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "A0A8B1JQ63", - organism: "2697049", - name: "ORF1a polyprotein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ZIBGPFATKBEMQZ-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Tran, N. (0000-0002-9372-9444)", - "McLeod, M.J. (0000-0001-5540-916X)", - "Kalyaanamoorthy, S. (0000-0003-0854-6449)", - "Ganesan, A. (0000-0001-8689-943X)", - "Holyoak, T. (0000-0002-7329-1115)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Revealing An Oxidized Conformation of the SARS-CoV-2 Main Protease: Detailing the Peculiar Features of the H163A Mutant Crystal Structure", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Tran, N.", - "Dasari, S.", - "Barwell, S.", - "McLeod, M.J.", - "Kalyaanamoorthy, S.", - "Holyoak, T.", - "Ganesan, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ddl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ddl", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with Toyocamycin", - emdb: null, - pdb: { - dbId: "8OV4", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, methyltransferase, complex, inhibitor, SARS-CoV-2", - refModels: [ - { - emdbId: null, - pdbId: "8OV4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ov4_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ov4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "XOKJUSAYZUAMGJ-WOUKDFQISA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of theSARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Falke, S. (0000-0003-3409-1791)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ov4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ov4", - }, - }, - { - title: - "SARS-CoV-2 non-structural protein-1 (nsp1) in complex with 2-(benzylamino)ethan-1-ol", - emdb: null, - pdb: { - dbId: "8AZ8", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, non-structural protein-1, fragment hit, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8AZ8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8az8_final.pdb", - externalLink: "https://pdb-redo.eu/db/8az8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Host translation inhibitor nsp1", - details: "", - altNames: "Leader protein,Non-structural protein 1,nsp1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XNIOWJUQPMKCIJ-UHFFFAOYSA-N"], - dbauthors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Kozielski, F. (0000-0001-6096-9102)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36293303", - title: - "Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening.", - journal: "Int J Mol Sci 23 (2022), 1422-0067", - doi: "https://doi.org/10.1021/ci200227u", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36293303", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S. (0000-0002-2070-7770)", - "Lou, J.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Haider, S. (0000-0003-2650-2925)", - "Kozielski, F. (0000-0001-6096-9102)", - "Ma, S.", - "Mykhaylyk, V. (0000-0003-0106-2724)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8az8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8az8", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 omicron variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab", - emdb: null, - pdb: { - dbId: "7YOW", - method: "X-RAY DIFFRACTION", - keywords: - "spike, coronavirus omicron strain, viral protein, Fab, VIRAL PROTEIN-IMMUNE SYSTEM complex, VIRUS, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7YOW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7yow_final.pdb", - externalLink: "https://pdb-redo.eu/db/7yow", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Yamamoto, A. (0000-0002-2928-2828)", - "Higashiura, A. (0000-0001-8448-9349)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37041231", - title: - "Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.", - journal: "Commun Biol 6: 395-395 (2023), 2399-3642", - doi: "https://doi.org/10.1038/s42003-023-04782-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37041231", - pubDate: "2023", - abstract: "", - authors: [ - "Shitaoka, K. (0000-0002-2070-1520)", - "Higashiura, A.", - "Kawano, Y.", - "Yamamoto, A.", - "Mizoguchi, Y.", - "Hashiguchi, T. (0000-0001-7578-7571)", - "Nishimichi, N.", - "Huang, S.", - "Ito, A. (0000-0002-7552-0073)", - "Ohki, S.", - "Kanda, M.", - "Taniguchi, T.", - "Yoshizato, R.", - "Azuma, H.", - "Kitajima, Y.", - "Yokosaki, Y.", - "Okada, S. (0000-0002-4622-5657)", - "Sakaguchi, T. (0000-0002-3754-1252)", - "Yasuda, T. (0000-0001-9997-6852)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7yow_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7yow", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 papain-like protease (C111S mutant)", - emdb: null, - pdb: { - dbId: "7YBG", - method: "X-RAY DIFFRACTION", - keywords: - "Severe acute respiratory syndrome coronavirus 2, papain-like protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7YBG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ybg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ybg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VHJLVAABSRFDPM-IMJSIDKUSA-N", - "OFOBLEOULBTSOW-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: ["Zeng, R. (0000-0001-9716-6354)", "Lei, J. (0000-0001-9326-0554)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of the SARS-CoV-2 papain-like protease (C111S mutant)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zeng, R.", "Lei, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ybg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ybg", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI19", - emdb: null, - pdb: { - dbId: "7UUC", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7UUC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uuc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uuc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QFKWZICTDWNTDA-MYGLTJDJSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36629751", - title: - "A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.", - journal: "Acs Chem.Biol. 18: 449-455 (2023), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.2c00695", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36629751", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, K.S.", - "Blankenship, L.R.", - "Kuo, S.A.", - "Sheng, Y.J.", - "Li, P.", - "Fierke, C.A.", - "Russell, D.H.", - "Yan, X.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uuc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uuc", - }, - }, - { - title: - "Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Membrane peptide M176-190", - emdb: null, - pdb: { - dbId: "8CME", - method: "X-RAY DIFFRACTION", - keywords: - "HLA-II, HLA-DR, HLA-DR1, human leukocyte antigen, major histocompatibility complex, major histocompatibility complex class 2, SARS-CoV-2, coronavirus, COVID-19, Membrane, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CME", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cme_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cme", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01903", - organism: "9606", - name: "HLA class II histocompatibility antigen, DR alpha chain", - details: "", - altNames: "MHC class II antigen DRA", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC5", - organism: null, - name: "Membrane protein", - details: "", - altNames: "M,E1 glycoprotein,Matrix glycoprotein,Membrane glycoprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SXGZJKUKBWWHRA-UHFFFAOYSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "MacLachlan, B.J. (0000-0002-2685-2733)", - "Mason, G.H. (0000-0002-7844-7190)", - "Sourfield, D.O. (0000-0002-0836-7718)", - "Godkin, A.J. (0000-0002-1910-7567)", - "Rizkallah, P.J. (0000-0002-9290-0369)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37471227", - title: - "Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.", - journal: "Cell Rep 42: 112827-112827 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112827", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37471227", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, Y.", - "Mason, G.H.", - "Scourfield, D.O.", - "Greenshields-Watson, A.", - "Haigh, T.A.", - "Sewell, A.K.", - "Long, H.M.", - "Gallimore, A.M.", - "Rizkallah, P.", - "MacLachlan, B.J.", - "Godkin, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cme_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cme", - }, - }, - { - title: - "Crystal structure of X77 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2 in spacegroup P2(1)2(1)2(1).", - emdb: null, - pdb: { - dbId: "7PHZ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN, X77", - refModels: [ - { - emdbId: null, - pdbId: "7PHZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7phz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7phz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MUNFBYOTGGMQOS-XMMPIXPASA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of X77 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2 in spacegroup P2(1)2(1)2(1).", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Costanzi, E.", "Demitri, N.", "Storici, P."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7phz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7phz", - }, - }, - { - title: - "Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide (orf1ab)6420-6434", - emdb: null, - pdb: { - dbId: "8CMG", - method: "X-RAY DIFFRACTION", - keywords: - "HLA-II, HLA-DR, HLA-DR1, human leukocyte antigen, major histocompatibility complex, major histocompatibility complex class 2, SARS-CoV-2, coronavirus, COVID-19, nsp14, orf1ab, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CMG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cmg_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cmg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01903", - organism: "9606", - name: "HLA class II histocompatibility antigen, DR alpha chain", - details: "", - altNames: "MHC class II antigen DRA", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 7", - details: "", - altNames: "nsp7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "MacLachlan, B.J. (0000-0002-2685-2733)", - "Mason, G.H. (0000-0002-7844-7190)", - "Sourfield, D.O. (0000-0002-0836-7718)", - "Godkin, A.J. (0000-0002-1910-7567)", - "Rizkallah, P.J. (0000-0002-9290-0369)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37471227", - title: - "Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.", - journal: "Cell Rep 42: 112827-112827 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112827", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37471227", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, Y.", - "Mason, G.H.", - "Scourfield, D.O.", - "Greenshields-Watson, A.", - "Haigh, T.A.", - "Sewell, A.K.", - "Long, H.M.", - "Gallimore, A.M.", - "Rizkallah, P.", - "MacLachlan, B.J.", - "Godkin, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cmg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cmg", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI8", - emdb: null, - pdb: { - dbId: "7UUA", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7UUA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uua_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uua", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YIWYOEOSWRXENJ-FFXRMZKPSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36629751", - title: - "A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.", - journal: "Acs Chem.Biol. 18: 449-455 (2023), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.2c00695", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36629751", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, K.S.", - "Blankenship, L.R.", - "Kuo, S.A.", - "Sheng, Y.J.", - "Li, P.", - "Fierke, C.A.", - "Russell, D.H.", - "Yan, X.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uua_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uua", - }, - }, - { - title: - "Virtual screening for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors", - emdb: null, - pdb: { - dbId: "8DII", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, MPro, nsp7, COVID-19, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DII", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dii_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dii", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "GDUZGWMNCDBRFJ-AWEZNQCLSA-N"], - dbauthors: ["Singh, I.", "Shoichet, B.K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37354015", - title: - "Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.", - journal: "Protein Sci. 32: e4712-e4712 (2023), 1469-896X", - doi: "https://doi.org/10.1002/pro.4712", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37354015", - pubDate: "2023", - abstract: "", - authors: [ - "Fink, E.A.", - "Bardine, C.", - "Gahbauer, S.", - "Singh, I.", - "Detomasi, T.", - "White, K.", - "Gu, S.", - "Wan, X.", - "Chen, J.", - "Ary, B.", - "Glenn, I.", - "O'Connell, J.", - "O'Donnell, H.", - "Fajtova, P.", - "Lyu, J.", - "Vigneron, S.", - "Young, N.J.", - "Kondratov, I.S.", - "Alisoltani, A.", - "Simons, L.M.", - "Lorenzo-Redondo, R.", - "Ozer, E.A.", - "Hultquist, J.F.", - "O'Donoghue, A.J.", - "Moroz, Y.", - "Taunton, J.", - "Renslo, A.R.", - "Irwin, J.J.", - "Garcia-Sastre, A.", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Craik, C.S.", - "Detomasi, T.C.", - "Moroz, Y.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dii_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dii", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 main protease in its apo-form", - emdb: null, - pdb: { - dbId: "7UU7", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7UU7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uu7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uu7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36629751", - title: - "A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.", - journal: "Acs Chem.Biol. 18: 449-455 (2023), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.2c00695", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36629751", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, K.S.", - "Blankenship, L.R.", - "Kuo, S.A.", - "Sheng, Y.J.", - "Li, P.", - "Fierke, C.A.", - "Russell, D.H.", - "Yan, X.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uu7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uu7", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC25.106 isolated from a vaccinated COVID-19 convalescent", - emdb: null, - pdb: { - dbId: "8DGU", - method: "X-RAY DIFFRACTION", - keywords: - "broadly neutralizing antibody, pan-betacoronavirus, S2 stem helix, spike, SARS-CoV-2, MERS-CoV, HCoV-HKU1, sarbecovirus, cross-reactive, cross-neutralizing, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8DGU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dgu_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dgu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Antibody CC25.106 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Antibody CC25.106 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Liu, H.", "Wilson, I.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36889306", - title: - "Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease.", - journal: "Immunity 56: 669-686.e7 (2023), 1074-7613", - doi: "https://doi.org/10.1016/j.immuni.2023.02.005", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36889306", - pubDate: "2023", - abstract: "", - authors: [ - "Zhou, P.", - "Song, G.", - "Liu, H.", - "Yuan, M.", - "He, W.T.", - "Beutler, N.", - "Zhu, X.", - "Tse, L.V.", - "Martinez, D.R.", - "Schafer, A.", - "Anzanello, F.", - "Yong, P.", - "Peng, L.", - "Dueker, K.", - "Musharrafieh, R.", - "Callaghan, S.", - "Capozzola, T.", - "Limbo, O.", - "Parren, M.", - "Garcia, E.", - "Rawlings, S.A.", - "Smith, D.M.", - "Nemazee, D.", - "Jardine, J.G.", - "Safonova, Y.", - "Briney, B.", - "Rogers, T.F.", - "Wilson, I.A.", - "Baric, R.S.", - "Gralinski, L.E.", - "Burton, D.R.", - "Andrabi, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dgu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dgu", - }, - }, - { - title: - "SARS-CoV-2 non-structural protein-1 (nsp1) in complex with (S)-1-(4-chlorophenyl)ethan-1-amine", - emdb: null, - pdb: { - dbId: "8AYW", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, non-structural protein-1, fragment hit, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8AYW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ayw_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ayw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Host translation inhibitor nsp1", - details: "", - altNames: "Leader protein,Non-structural protein 1,nsp1", - 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(0000-0002-9560-5082)", - "Damfo, S.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Kozielski, F. (0000-0001-6096-9102)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36293303", - title: - "Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening.", - journal: "Int J Mol Sci 23 (2022), 1422-0067", - doi: "https://doi.org/10.1021/ci200227u", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36293303", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S. (0000-0002-2070-7770)", - "Lou, J.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Haider, S. (0000-0003-2650-2925)", - "Kozielski, F. (0000-0001-6096-9102)", - "Ma, S.", - "Mykhaylyk, V. (0000-0003-0106-2724)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ayw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ayw", - }, - }, - { - title: - "Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp6-nsp7 (C6) cut site sequence (form 2)", - emdb: null, - pdb: { - dbId: "8DRT", - method: "X-RAY DIFFRACTION", - keywords: "Viral protease, SARS-CoV-2, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8DRT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8drt_final.pdb", - externalLink: "https://pdb-redo.eu/db/8drt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lee, J. (0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. (0000-0002-7408-5487)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8drt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8drt", - }, - }, - { - title: "Fab arm of antibody 10G4 bound to CoV-2 receptor binding domain (RBD)", - emdb: null, - pdb: { - dbId: "8CWI", - method: "X-RAY DIFFRACTION", - keywords: - "antibody, CoV-2, receptor binding domain, class 5 epitope, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CWI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cwi_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cwi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of Fab arm of antibody 10G4", - details: "Heavy chain of Fab arm of antibody 10G4", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of Fab arm of antibody 10G4", - details: "Light chain of Fab arm of antibody 10G4", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JLVVSXFLKOJNIY-UHFFFAOYSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Langley, D.B. (0000-0003-2752-0041)", - "Christ, D. (0000-0002-7313-3977)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Neutralization of CoV-2 omicron lineages by affinity-matured class 5 antibodies", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Langley, D.B.", "Christ, D."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cwi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cwi", - }, - }, - { - title: - "Structure of SARS-CoV-2 Mpro in complex with nsp12-nsp13 (C12) cut site sequence", - emdb: null, - pdb: { - dbId: "8DS1", - method: "X-RAY DIFFRACTION", - keywords: "Viral protease, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DS1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ds1_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ds1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N", "MTHSVFCYNBDYFN-UHFFFAOYSA-N"], - dbauthors: [ - "Lee, J. (0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. (0000-0002-7408-5487)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ds1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ds1", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI37", - emdb: null, - pdb: { - dbId: "7S73", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S73", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s73_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s73", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QPINBLRCPHAOCS-XLAORIBOSA-N"], - dbauthors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Sankaran, B. (0000-0002-3266-8131)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35839690", - title: - "A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114596-114596 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839690", - pubDate: "2022", - abstract: "", - authors: [ - "Alugubelli, Y.R.", - "Geng, Z.Z.", - "Yang, K.S.", - "Shaabani, N.", - "Khatua, K.", - "Ma, X.R.", - "Vatansever, E.C.", - "Cho, C.C.", - "Ma, Y.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s73_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s73", - }, - }, - { - title: - "SARS-CoV-2 3CLPro in complex with N-(4-(1H-imidazol-4-yl)phenyl)-N-(3-chloro-5-fluorobenzyl)-2-(isoquinolin-4-yl)acetamide", - emdb: null, - pdb: { - dbId: "7TEL", - method: "X-RAY DIFFRACTION", - keywords: - "Inhibitor, Complex, Protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TEL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tel_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tel", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["HMZYKUVJCFLOFI-UHFFFAOYSA-N"], - dbauthors: [ - "Goins, C.M. (0000-0002-6617-4877)", - "Stauffer, S.R. (0000-0002-6332-1827)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 3CL-protease inhibitors derived from ML300: investigation of P1 and replacements of the 1,2,3-benzotriazole", - journal: "Med.Chem.Res. (2023), 1054-2523", - doi: "https://doi.org/10.1007/s00044-023-03108-9", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Hooper, A.", - "Macdonald, J.D.", - "Reilly, B.", - "Maw, J.", - "Wirrick, A.P.", - "Han, S.H.", - "Lindsey, A.A.", - "Rico, E.G.", - "Romigh, T.", - "Goins, C.M.", - "Wang, N.S.", - "Stauffer, S.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tel_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tel", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl sulfonyl benzene inhibitor", - emdb: null, - pdb: { - dbId: "8E5Z", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, Viral protein-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8E5Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e5z_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e5z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ATVOVJHWVGHVRU-JLEJFLCFSA-N", "ATVOVJHWVGHVRU-FUOQNJDISA-N"], - dbauthors: [ - "Lovell, S. (0000-0002-3215-4472)", - "Liu, L. (0000-0003-0514-281X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Groutas, W.C. (0000-0001-5248-7912)", - "Miller, M.J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e5z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e5z", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CL protease in complex with a p-chlorophenylethanol based inhibitor", - emdb: null, - pdb: { - dbId: "8E6A", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, Viral protein-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8E6A", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e6a_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e6a", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "HSKHDUVNVQYLID-GRIKLCOCSA-N", - "ZBIMUYMJHGTCAY-BNVIUNNUSA-N", - ], - dbauthors: [ - "Lovell, S. (0000-0002-3215-4472)", - "Liu, L. (0000-0003-0514-281X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S. (0000-0002-8199-2376)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e6a_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e6a", - }, - }, - { - title: "SARS-CoV-2 RBD bound to neutralizing antibody Fab ICO-hu23", - emdb: null, - pdb: { - dbId: "8EL2", - method: "X-RAY DIFFRACTION", - keywords: - "Fab, SARS-CoV-2, receptor-binding domain, neutralizing antibody, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8EL2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8el2_final.pdb", - externalLink: "https://pdb-redo.eu/db/8el2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Fab ICO-hu23 Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab ICO-hu23 Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: [ - "Besaw, J.E. (0000-0002-7571-7132)", - "Kuo, A. (0000-0002-4234-6320)", - "Morizumi, T. (0000-0002-2785-209X)", - "Ernst, O.P. (0000-0002-8863-9444)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37531329", - title: - "Broadly neutralizing humanized SARS-CoV-2 antibody binds to a conserved epitope on Spike and provides antiviral protection through inhalation-based delivery in non-human primates.", - journal: "Plos Pathog. 19: e1011532-e1011532 (2023), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1011532", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37531329", - pubDate: "2023", - abstract: "", - authors: [ - "Hermet, P. (0000-0002-5642-2101)", - "Delache, B.", - "Herate, C.", - "Wolf, E.", - "Kivi, G.", - "Juronen, E.", - "Mumm, K.", - "Zusinaite, E.", - "Kainov, D.", - "Sankovski, E.", - "Virumae, K.", - "Planken, A.", - "Merits, A.", - "Besaw, J.E.", - "Yee, A.W.", - "Morizumi, T.", - "Kim, K.", - "Kuo, A.", - "Berriche, A.", - "Dereuddre-Bosquet, N.", - "Sconosciuti, Q.", - "Naninck, T.", - "Relouzat, F.", - "Cavarelli, M.", - "Ustav, M.", - "Wilson, D.", - "Ernst, O.P.", - "Mannik, A.", - "LeGrand, R.", - "Ustav Jr., M. (0000-0002-7804-3989)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8el2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8el2", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI29", - emdb: null, - pdb: { - dbId: "7S6W", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S6W", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s6w_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s6w", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BKEPDWNBCUBDEN-KOUJMVCDSA-N"], - dbauthors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Sankaran, B. (0000-0002-3266-8131)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35839690", - title: - "A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114596-114596 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839690", - pubDate: "2022", - abstract: "", - authors: [ - "Alugubelli, Y.R.", - "Geng, Z.Z.", - "Yang, K.S.", - "Shaabani, N.", - "Khatua, K.", - "Ma, X.R.", - "Vatansever, E.C.", - "Cho, C.C.", - "Ma, Y.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s6w_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s6w", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI36", - emdb: null, - pdb: { - dbId: "7S72", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S72", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s72_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s72", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WFDSDFTYLISRSE-ADSPCUKESA-N"], - dbauthors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Sankaran, B. (0000-0002-3266-8131)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35839690", - title: - "A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114596-114596 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839690", - pubDate: "2022", - abstract: "", - authors: [ - "Alugubelli, Y.R.", - "Geng, Z.Z.", - "Yang, K.S.", - "Shaabani, N.", - "Khatua, K.", - "Ma, X.R.", - "Vatansever, E.C.", - "Cho, C.C.", - "Ma, Y.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s72_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s72", - }, - }, - { - title: - "The Crystal structure of deuterated S-217622 (Ensitrelvir) bound to the main protease (3CLpro/Mpro) of SARS-CoV-2", - emdb: null, - pdb: { - dbId: "8HEF", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-COV-2, main protease, 3CLpro, inhibitor, deuterated compound, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8HEF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hef_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hef", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QMPBBNUOBOFBFS-UHFFFAOYSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Yan, M.", "Zhang, H. (0000-0003-4356-3615)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36997073", - title: - "Synthesis of deuterated S-217622 (Ensitrelvir) with antiviral activity against coronaviruses including SARS-CoV-2.", - journal: "Antiviral Res. 213: 105586-105586 (2023), 0166-3542", - doi: "https://doi.org/10.1016/j.antiviral.2023.105586", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36997073", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, Y.", - "Cao, L.", - "Yan, M.", - "Zhou, J.", - "Yang, S.", - "Xu, T.", - "Huang, S.", - "Li, K.", - "Zhou, Q.", - "Li, G.", - "Zhu, Y.", - "Cong, F.", - "Zhang, H.", - "Guo, D.", - "Li, Y.", - "Zhang, X.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hef_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hef", - }, - }, - { - title: - "Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp14-nsp15 (C14) cut site sequence (form 2)", - emdb: null, - pdb: { - dbId: "8DS0", - method: "X-RAY DIFFRACTION", - keywords: "Viral protease, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DS0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ds0_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ds0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MTHSVFCYNBDYFN-UHFFFAOYSA-N"], - dbauthors: [ - "Lee, J. (0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. 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(0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. (0000-0002-7408-5487)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dru_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dru", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 main protease in its apo-form", - emdb: null, - pdb: { - dbId: "7UU6", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7UU6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uu6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uu6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36629751", - title: - "A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.", - journal: "Acs Chem.Biol. 18: 449-455 (2023), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.2c00695", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36629751", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, K.S.", - "Blankenship, L.R.", - "Kuo, S.A.", - "Sheng, Y.J.", - "Li, P.", - "Fierke, C.A.", - "Russell, D.H.", - "Yan, X.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uu6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uu6", - }, - }, - { - title: - "Virtual screening for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors", - emdb: null, - pdb: { - dbId: "8DIH", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, MPro, nsp7, COVID-19, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DIH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dih_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dih", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "BYRXZERFENWTMH-HXUWFJFHSA-N"], - dbauthors: ["Singh, I.", "Shoichet, B.K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37354015", - title: - "Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.", - journal: "Protein Sci. 32: e4712-e4712 (2023), 1469-896X", - doi: "https://doi.org/10.1002/pro.4712", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37354015", - pubDate: "2023", - abstract: "", - authors: [ - "Fink, E.A.", - "Bardine, C.", - "Gahbauer, S.", - "Singh, I.", - "Detomasi, T.", - "White, K.", - "Gu, S.", - "Wan, X.", - "Chen, J.", - "Ary, B.", - "Glenn, I.", - "O'Connell, J.", - "O'Donnell, H.", - "Fajtova, P.", - "Lyu, J.", - "Vigneron, S.", - "Young, N.J.", - "Kondratov, I.S.", - "Alisoltani, A.", - "Simons, L.M.", - "Lorenzo-Redondo, R.", - "Ozer, E.A.", - "Hultquist, J.F.", - "O'Donoghue, A.J.", - "Moroz, Y.", - "Taunton, J.", - "Renslo, A.R.", - "Irwin, J.J.", - "Garcia-Sastre, A.", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Craik, C.S.", - "Detomasi, T.C.", - "Moroz, Y.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dih_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dih", - }, - }, - { - title: - "Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp3 epitope (orf1ab)1350-1364", - emdb: null, - pdb: { - dbId: "8CMF", - method: "X-RAY DIFFRACTION", - keywords: - "HLA-II, HLA-DR, HLA-DR1, human leukocyte antigen, major histocompatibility complex, major histocompatibility complex class 2, SARS-CoV-2, coronavirus, COVID-19, nsp3, orf1ab, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CMF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cmf_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cmf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01903", - organism: "9606", - name: "HLA class II histocompatibility antigen, DR alpha chain", - details: "", - altNames: "MHC class II antigen DRA", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", "KDYFGRWQOYBRFD-UHFFFAOYSA-N"], - dbauthors: [ - "MacLachlan, B.J. (0000-0002-2685-2733)", - "Mason, G.H. (0000-0002-7844-7190)", - "Sourfield, D.O. (0000-0002-0836-7718)", - "Godkin, A.J. (0000-0002-1910-7567)", - "Rizkallah, P.J. (0000-0002-9290-0369)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37471227", - title: - "Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.", - journal: "Cell Rep 42: 112827-112827 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112827", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37471227", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, Y.", - "Mason, G.H.", - "Scourfield, D.O.", - "Greenshields-Watson, A.", - "Haigh, T.A.", - "Sewell, A.K.", - "Long, H.M.", - "Gallimore, A.M.", - "Rizkallah, P.", - "MacLachlan, B.J.", - "Godkin, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cmf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cmf", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-245", - emdb: null, - pdb: { - dbId: "8DOX", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 main protease, 3C-like proteinase, VIRAL PROTEIN, SARS-CoV-2, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DOX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dox_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dox", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["HZJVVPOOURAASY-SWSSSNQJSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Bulut, H. (0000-0003-0262-6296)", - "Hayashi, H.", - "Tsuji, K.", - "Kuwata, N.", - "Das, D.", - "Tamamura, H.", - "Mitsuya, H. (0000-0001-9274-3853)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "A small molecule compound inhibits the main protease of SARS-CoV-2 and blocks virus replication.", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Bulut, H. (0000-0003-0262-6296)", - "Hayashi, H.", - "Tsuji, K.", - "Higashi-Kuwata, N. (0000-0002-9404-3532)", - "Das, D. (0000-0001-9943-5888)", - "Tamamura, H.", - "Mitsuya, H. (0000-0001-9274-3853)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dox_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dox", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV30-14", - emdb: null, - pdb: { - dbId: "8DTR", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, coronavirus, antibody, stem helix, neutralizing antibody, COVID-19, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8DTR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dtr_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dtr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "COV30-14 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COV30-14 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2' stem helix peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wilson, I.A. (0000-0002-6469-2419)", - "Lee, C.C.D. (0000-0002-5470-2484)", - "Lin, T.H. (0000-0002-0937-9972)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Mus musculus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36347257", - title: - "Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses.", - journal: "Cell Host Microbe 31 (2023), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2022.10.010", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36347257", - pubDate: "2023", - abstract: "", - authors: [ - "Dacon, C.", - "Peng, L.", - "Lin, T.H.", - "Tucker, C.", - "Lee, C.D.", - "Cong, Y.", - "Wang, L.", - "Purser, L.", - "Cooper, A.J.R.", - "Williams, J.K.", - "Pyo, C.W.", - "Yuan, M.", - "Kosik, I.", - "Hu, Z.", - "Zhao, M.", - "Mohan, D.", - "Peterson, M.", - "Skinner, J.", - "Dixit, S.", - "Kollins, E.", - "Huzella, L.", - "Perry, D.", - "Byrum, R.", - "Lembirik, S.", - "Murphy, M.", - "Zhang, Y.", - "Yang, E.S.", - "Chen, M.", - "Leung, K.", - "Weinberg, R.S.", - "Pegu, A.", - "Geraghty, D.E.", - "Davidson, E.", - "Doranz, B.J.", - "Douagi, I.", - "Moir, S.", - "Yewdell, J.W.", - "Schmaljohn, C.", - "Crompton, P.D.", - "Mascola, J.R.", - "Holbrook, M.R.", - "Nemazee, D.", - "Wilson, I.A.", - "Tan, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dtr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dtr", - }, - }, - { - title: "Crystal Structure of C77G12 Fab in complex with SARS-CoV-2 S fusion peptide", - emdb: null, - pdb: { - dbId: "7U0A", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 spike, COVID-19, fusion peptide, Fab, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7U0A", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u0a_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u0a", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "SARS-CoV-2 S fusion peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain Fab C77G12", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain Fab C77G12", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: ["Veesler, D.", "Tortorici, M.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35857703", - title: - "ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.", - journal: "Science 377: 735-742 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abq2679", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35857703", - pubDate: "2022", - abstract: "", - authors: [ - "Low, J.S.", - "Jerak, J.", - "Tortorici, M.A.", - "McCallum, M.", - "Pinto, D.", - "Cassotta, A.", - "Foglierini, M.", - "Mele, F.", - "Abdelnabi, R.", - "Weynand, B.", - "Noack, J.", - "Montiel-Ruiz, M.", - "Bianchi, S.", - "Benigni, F.", - "Sprugasci, N.", - "Joshi, A.", - "Bowen, J.E.", - "Stewart, C.", - "Rexhepaj, M.", - "Walls, A.C.", - "Jarrossay, D.", - "Morone, D.", - "Paparoditis, P.", - "Garzoni, C.", - "Ferrari, P.", - "Ceschi, A.", - "Neyts, J.", - "Purcell, L.A.", - "Snell, G.", - "Corti, D.", - "Lanzavecchia, A.", - "Veesler, D.", - "Sallusto, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7u0a_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7u0a", - }, - }, - { - title: - "Crystal structure of F2F-2020185-01X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.", - emdb: null, - pdb: { - dbId: "8OKL", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8OKL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8okl_final.pdb", - externalLink: "https://pdb-redo.eu/db/8okl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "AUPBHARHTRTBTF-ATIWLJMLSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "SVTOYMIYCMHPIV-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37043904", - title: - "Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination.", - journal: "Eur.J.Med.Chem. 253: 115311-115311 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115311", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37043904", - pubDate: "2023", - abstract: "", - authors: [ - "Stefanelli, I.", - "Corona, A.", - "Cerchia, C.", - "Cassese, E.", - "Improta, S.", - "Costanzi, E.", - "Pelliccia, S.", - "Morasso, S.", - "Esposito, F.", - "Paulis, A.", - "Scognamiglio, S.", - "Di Leva, F.S.", - "Storici, P.", - "Brindisi, M.", - "Tramontano, E.", - "Cannalire, R.", - "Summa, V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8okl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8okl", - }, - }, - { - title: - "SARS-CoV-2 Spike-derived peptide S1185-1193 K1191N mutant (RLNEVANNL) presented by HLA-A*02:01", - emdb: null, - pdb: { - dbId: "7U1R", - method: "X-RAY DIFFRACTION", - keywords: - "human leukocyte antigen, major histocompatibility complex, HLA-A2, HLA-A*02:01, SARS-CoV-2, Spike, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7U1R", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u1r_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u1r", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q53Z42", - organism: "9606", - name: "HLA class I antigen", - details: "", - altNames: - "HLA class I histocompatibility antigen,HLA class I histocompatibility antigen A alpha chain,A alpha chain,MHC class I antigen,MHC class I protein,MHC class I protein (HLA-A)", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2' peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "WLZRMCYVCSSEQC-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: ["Szeto, C. (0000-0003-3784-5210)", "Gras, S. (0000-0001-7416-038X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Spike-derived peptide S1185-1193 K1191N mutant (RLNEVANNL) presented by HLA-A*02:01", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Szeto, C. (0000-0003-3784-5210)", - "Gras, S. (0000-0001-7416-038X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7u1r_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7u1r", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM129", - emdb: null, - pdb: { - dbId: "7MAW", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MAW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7maw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7maw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JMWBRPAKKKBHFQ-NQRMBFEXSA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM129", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7maw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7maw", - }, - }, - { - title: - "Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304, in complex with nirmatrelvir (NMV)", - emdb: null, - pdb: { - dbId: "8GFU", - method: "X-RAY DIFFRACTION", - keywords: - "viral cysteine protease, inactive C145A mutant, homodimer, inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8GFU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gfu_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gfu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "LIENCHBZNNMNKG-OJFNHCPVSA-N"], - dbauthors: ["Coates, L.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37271339", - title: - "Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.", - journal: "J.Biol.Chem. 299: 104886-104886 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.104886", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37271339", - pubDate: "2023", - abstract: "", - authors: [ - "Kovalevsky, A.", - "Aniana, A.", - "Coates, L.", - "Bonnesen, P.V.", - "Nashed, N.T.", - "Louis, J.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gfu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gfu", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) T135I Mutant", - emdb: null, - pdb: { - dbId: "8EHK", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8EHK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ehk_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ehk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) T135I Mutant", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - "Chen, Y. (0000-0002-5115-3600)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ehk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ehk", - }, - }, - { - title: - "Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to Sinefungin", - emdb: null, - pdb: { - dbId: "7TW9", - method: "X-RAY DIFFRACTION", - keywords: "N7-guanine methyl transferase, SARS-CoV-2, nsp14, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TW9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tw9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tw9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P41212", - organism: "2697049", - name: - "Transcription factor ETV6,Proofreading exoribonuclease nsp14 chimera", - details: - "Fusion protein containing TELSAM (uniprot P41212) and SARS-CoV-2 nsp14 N7-Methyl Transferase domain (P0DTD1)", - altNames: - "ETS translocation variant 6,ETS-related protein Tel1,Tel,ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LMXOHSDXUQEUSF-YECHIGJVSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "LFQSCWFLJHTTHZ-UHFFFAOYSA-N", - "OKKJLVBELUTLKV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kottur, J. (0000-0002-8075-3883)", - "Aggarwal, A.K. (0000-0003-4389-0173)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36075969", - title: - "High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development.", - journal: "Nat.Struct.Mol.Biol. 29: 850-853 (2022), 1545-9985", - doi: "https://doi.org/10.1038/s41594-022-00828-1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36075969", - pubDate: "2022", - abstract: "", - authors: [ - "Kottur, J.", - "Rechkoblit, O.", - "Quintana-Feliciano, R.", - "Sciaky, D.", - "Aggarwal, A.K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tw9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tw9", - }, - }, - { - title: "SARS-CoV-2 Delta-RBD complexed with BA.2-10 and EY6A Fabs", - emdb: null, - pdb: { - dbId: "8BBN", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, BA.2 mAb, RBD, BA.2-36, BA.2-10, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8BBN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8bbn_final.pdb", - externalLink: "https://pdb-redo.eu/db/8bbn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BA.2-10 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BA.2-10 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36995936", - title: - "Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.", - journal: "Cell Rep 42: 112271-112271 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112271", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36995936", - pubDate: "2023", - abstract: "", - authors: [ - "Dijokaite-Guraliuc, A.", - "Das, R.", - "Zhou, D.", - "Ginn, H.M.", - "Liu, C.", - "Duyvesteyn, H.M.E.", - "Huo, J.", - "Nutalai, R.", - "Supasa, P.", - "Selvaraj, M.", - "de Silva, T.I.", - "Plowright, M.", - "Newman, T.A.H.", - "Hornsby, H.", - "Mentzer, A.J.", - "Skelly, D.", - "Ritter, T.G.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Roemer, C.", - "Peacock, T.P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8bbn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8bbn", - }, - }, - { - title: "SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab", - emdb: null, - pdb: { - dbId: "8BBO", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, BA.2 mAb, RBD, BA.2-36, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8BBO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8bbo_final.pdb", - externalLink: "https://pdb-redo.eu/db/8bbo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q6GMX6", - organism: "9606", - name: "IGH@ protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DOX7", - organism: "9606", - name: "Immunoglobulin kappa light chain", - details: "", - altNames: "Immunoglobulin kappa light chain EU", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36995936", - title: - "Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.", - journal: "Cell Rep 42: 112271-112271 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112271", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36995936", - pubDate: "2023", - abstract: "", - authors: [ - "Dijokaite-Guraliuc, A.", - "Das, R.", - "Zhou, D.", - "Ginn, H.M.", - "Liu, C.", - "Duyvesteyn, H.M.E.", - "Huo, J.", - "Nutalai, R.", - "Supasa, P.", - "Selvaraj, M.", - "de Silva, T.I.", - "Plowright, M.", - "Newman, T.A.H.", - "Hornsby, H.", - "Mentzer, A.J.", - "Skelly, D.", - "Ritter, T.G.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Roemer, C.", - "Peacock, T.P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8bbo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8bbo", - }, - }, - { - title: "Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SAH", - emdb: null, - pdb: { - dbId: "7TW8", - method: "X-RAY DIFFRACTION", - keywords: "N7-guanine methyl transferase, SARS-CoV-2, nsp14, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TW8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tw8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tw8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P41212", - organism: "2697049", - name: - "Transcription factor ETV6,Proofreading exoribonuclease nsp14 chimera", - details: - "Fusion protein containing TELSAM (uniprot P41212) and SARS-CoV-2 nsp14 N7-Methyl Transferase domain (P0DTD1)", - altNames: - "ETS translocation variant 6,ETS-related protein Tel1,Tel,ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZJUKTBDSGOFHSH-WFMPWKQPSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Kottur, J. (0000-0002-8075-3883)", - "Aggarwal, A.K. (0000-0003-4389-0173)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36075969", - title: - "High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development.", - journal: "Nat.Struct.Mol.Biol. 29: 850-853 (2022), 1545-9985", - doi: "https://doi.org/10.1038/s41594-022-00828-1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36075969", - pubDate: "2022", - abstract: "", - authors: [ - "Kottur, J.", - "Rechkoblit, O.", - "Quintana-Feliciano, R.", - "Sciaky, D.", - "Aggarwal, A.K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tw8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tw8", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with PF07321332", - emdb: null, - pdb: { - dbId: "7XB4", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7XB4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xb4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xb4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Replicase polyprotein 1a", - details: "", - altNames: "pp1a,ORF1a polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Zhang, J.", "Li, J.", "Hu, X.H."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with PF07321332", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Hu, X.H.", "Li, J.", "Zhang, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xb4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xb4", - }, - }, - { - title: - "Crystal structure of Omicron BA.4/5 RBD in complex with a neutralizing antibody scFv", - emdb: null, - pdb: { - dbId: "8GPY", - method: "X-RAY DIFFRACTION", - keywords: "Omicron, crystal strcture, neutralizing antibody, scFV, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8GPY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gpy_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gpy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "scFv heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "scFv light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Guo, Y. (0000-0002-8109-7515)", - "Gao, Y.X.", - "Song, Z.D.", - "Wang, W.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37322000", - title: - "Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection.", - journal: "Nat Commun 14: 3537-3537 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-39267-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37322000", - pubDate: "2023", - abstract: "", - authors: [ - "Guo, Y. (0000-0002-8109-7515)", - "Zhang, G.", - "Yang, Q. (0009-0009-1648-4189)", - "Xie, X.", - "Lu, Y.", - "Cheng, X.", - "Wang, H.", - "Liang, J.", - "Tang, J. (0000-0002-4398-2927)", - "Gao, Y.", - "Shang, H.", - "Dai, J.", - "Shi, Y.", - "Zhou, J. (0000-0003-2835-7178)", - "Zhou, J. (0000-0001-7858-8260)", - "Guo, H. (0000-0001-5213-9600)", - "Yang, H. (0000-0002-1875-3268)", - "Qi, J.", - "Liu, L.", - "Ma, S.", - "Zhang, B.", - "Huo, Q.", - "Xie, Y. (0000-0002-5672-3158)", - "Wu, J. (0000-0002-4556-7727)", - "Dong, F.", - "Zhang, S.", - "Lou, Z. (0000-0003-2728-881X)", - "Gao, Y. (0000-0002-0364-6427)", - "Song, Z.", - "Wang, W.", - "Sun, Z.", - "Yang, X. (0000-0002-2598-4355)", - "Xiong, D.", - "Liu, F. (0000-0002-9400-308X)", - "Chen, X.", - "Zhu, P. (0000-0002-4521-7524)", - "Wang, X.", - "Cheng, T. (0000-0003-4395-1095)", - "Rao, Z. (0000-0001-9866-2384)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gpy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gpy", - }, - }, - { - title: "TRIM7 in complex with C-terminal peptide of NSP12", - emdb: null, - pdb: { - dbId: "7X6Z", - method: "X-RAY DIFFRACTION", - keywords: "ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7X6Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x6z_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x6z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9C029", - organism: "9606", - name: "E3 ubiquitin-protein ligase TRIM7", - details: "", - altNames: - "Glycogenin-interacting protein,RING finger protein 90,Tripartite motif-containing protein 7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, H.", "Liang, X.", "Li, X.Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35982226", - title: - "A C-terminal glutamine recognition mechanism revealed by E3 ligase TRIM7 structures.", - journal: "Nat.Chem.Biol. 18: 1214-1223 (2022), 1552-4469", - doi: "https://doi.org/10.1038/s41589-022-01128-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35982226", - pubDate: "2022", - abstract: "", - authors: [ - "Liang, X.", - "Xiao, J.", - "Li, X.", - "Liu, Y.", - "Lu, Y.", - "Wen, Y.", - "Li, Z.", - "Che, X.", - "Ma, Y.", - "Zhang, X.", - "Zhang, Y.", - "Jian, D.", - "Wang, P.", - "Xuan, C.", - "Yu, G.", - "Li, L.", - "Zhang, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x6z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x6z", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H172Q Mutant", - emdb: null, - pdb: { - dbId: "8EHJ", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8EHJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ehj_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ehj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H172Q Mutant", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - "Chen, Y. (0000-0002-5115-3600)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ehj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ehj", - }, - }, - { - title: - "Epitope-based selection of SARS-CoV-2 neutralizing antibodies from convalescent patients", - emdb: null, - pdb: { - dbId: "7T72", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, antibody, receptor binding domain, neutralizing, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7T72", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t72_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t72", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "10090", - name: "Antibody light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "Antibody heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Langley, D.B. (0000-0003-2752-0041)", - "Christ, D. (0000-0002-7313-3977)", - "Rouet, R. (0000-0003-4210-9613)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36755042", - title: - "Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients.", - journal: "Nat Commun 14: 687-687 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-36295-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36755042", - pubDate: "2023", - abstract: "", - authors: [ - "Rouet, R.", - "Henry, J.Y. (0000-0003-0435-3308)", - "Johansen, M.D. (0000-0001-5553-5270)", - "Sobti, M.", - "Balachandran, H.", - "Langley, D.B.", - "Walker, G.J.", - "Lenthall, H.", - "Jackson, J.", - "Ubiparipovic, S.", - "Mazigi, O.", - "Schofield, P.", - "Burnett, D.L. (0000-0002-5642-3315)", - "Brown, S.H.J. (0000-0003-3997-4614)", - "Martinello, M.", - "Hudson, B.", - "Gilroy, N.", - "Post, J.J. (0000-0003-1475-9272)", - "Kelleher, A. (0000-0002-0009-3337)", - "Jack, H.M.", - "Goodnow, C.C. (0000-0001-5296-6155)", - "Turville, S.G. (0000-0003-1918-5343)", - "Rawlinson, W.D. (0000-0003-0988-7827)", - "Bull, R.A. (0000-0002-9844-3744)", - "Stewart, A.G. (0000-0002-2070-6030)", - "Hansbro, P.M.", - "Christ, D. (0000-0002-7313-3977)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t72_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t72", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFCit-yne", - emdb: null, - pdb: { - dbId: "7MAV", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MAV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mav_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mav", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "VYPOUUBVMAOAGP-VJGNERBWSA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFCit-yne", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mav_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mav", - }, - }, - { - title: - "PanDDA analysis -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z4718398507 - (R,S) isomer", - emdb: null, - pdb: { - dbId: "8ERS", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8ERS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ers_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ers", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DWGIEIVAFVJIQU-ZFWWWQNUSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ers_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ers", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main protease G143S mutant in complex with Nirmatrelvir", - emdb: null, - pdb: { - dbId: "8DZ9", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, 3cl, covid, sars-cov-2 ensitrelvir, nirmatrelvir, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DZ9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dz9_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dz9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Noske, G.D.", "Oliva, G.", "Godoy, A.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36775130", - title: - "Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.", - journal: "J.Biol.Chem. 299: 103004-103004 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36775130", - pubDate: "2023", - abstract: "", - authors: [ - "Noske, G.D.", - "de Souza Silva, E.", - "de Godoy, M.O.", - "Dolci, I.", - "Fernandes, R.S.", - "Guido, R.V.C.", - "Sjo, P.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dz9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dz9", - }, - }, - { - title: - "Crystal structure of F2F-2020197-00X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.", - emdb: null, - pdb: { - dbId: "8OKM", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8OKM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8okm_final.pdb", - externalLink: "https://pdb-redo.eu/db/8okm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MFQBHMWPFDDNFU-RABCQHRBSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "CPELXLSAUQHCOX-UHFFFAOYSA-M", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "SVTOYMIYCMHPIV-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37043904", - title: - "Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination.", - journal: "Eur.J.Med.Chem. 253: 115311-115311 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115311", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37043904", - pubDate: "2023", - abstract: "", - authors: [ - "Stefanelli, I.", - "Corona, A.", - "Cerchia, C.", - "Cassese, E.", - "Improta, S.", - "Costanzi, E.", - "Pelliccia, S.", - "Morasso, S.", - "Esposito, F.", - "Paulis, A.", - "Scognamiglio, S.", - "Di Leva, F.S.", - "Storici, P.", - "Brindisi, M.", - "Tramontano, E.", - "Cannalire, R.", - "Summa, V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8okm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8okm", - }, - }, - { - title: "Sars-Cov2 Main Protease in complex with CDD-1733", - emdb: null, - pdb: { - dbId: "7URB", - method: "X-RAY DIFFRACTION", - keywords: - "Sars-Cov2, Main Protease, Inhibitor, covalent, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7URB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7urb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7urb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "FOWCQWSLGBHNCT-WWGLSMKPSA-N"], - dbauthors: ["Lu, S.", "Palzkill, T.", "Matzuk, M.M.", "Judge, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37542196", - title: - "DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors.", - journal: "Commun Chem 6: 164-164 (2023), 2399-3669", - doi: "https://doi.org/10.1038/s42004-023-00961-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37542196", - pubDate: "2023", - abstract: "", - authors: [ - "Jimmidi, R.", - "Chamakuri, S. (0000-0002-7586-4992)", - "Lu, S.", - "Ucisik, M.N.", - "Chen, P.J.", - "Bohren, K.M. (0000-0002-3183-4118)", - "Moghadasi, S.A.", - "Versteeg, L.", - "Nnabuife, C. (0000-0001-9907-0508)", - "Li, J.Y.", - "Qin, X. (0000-0003-3728-5911)", - "Chen, Y.C.", - "Faver, J.C.", - "Nyshadham, P.", - "Sharma, K.L.", - "Sankaran, B. (0000-0002-3266-8131)", - "Judge, A. (0000-0003-4289-1748)", - "Yu, Z.", - "Li, F. (0000-0002-9680-4614)", - "Pollet, J. (0000-0003-1420-4015)", - "Harris, R.S.", - "Matzuk, M.M.", - "Palzkill, T. (0000-0002-5267-0001)", - "Young, D.W. (0000-0002-1595-9658)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7urb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7urb", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-198", - emdb: null, - pdb: { - dbId: "8DOY", - method: "X-RAY DIFFRACTION", - keywords: - "3C-like proteinase, VIRAL PROTEIN, SARS-CoV-2, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DOY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8doy_final.pdb", - externalLink: "https://pdb-redo.eu/db/8doy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "JLFNLZLINWHATN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "SBASXUCJHJRPEV-UHFFFAOYSA-N", - "UCQMGGDLMJSQEJ-LHXIGDLBSA-N", - ], - dbauthors: [ - "Bulut, H. (0000-0003-0262-6296)", - "Hayashi, H.", - "Tsuji, K.", - "Kuwata, N.", - "Das, D.", - "Tamamura, H.", - "Mitsuya, H. (0000-0001-9274-3853)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36338434", - title: - "Potent and biostable inhibitors of the main protease of SARS-CoV-2.", - journal: "Iscience 25: 105365-105365 (2022), 2589-0042", - doi: "https://doi.org/10.1016/j.isci.2022.105365", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36338434", - pubDate: "2022", - abstract: "", - authors: [ - "Tsuji, K.", - "Ishii, T.", - "Kobayakawa, T.", - "Higashi-Kuwata, N.", - "Azuma, C.", - "Nakayama, M.", - "Onishi, T.", - "Nakano, H.", - "Wada, N.", - "Hori, M.", - "Shinohara, K.", - "Miura, Y.", - "Kawada, T.", - "Hayashi, H.", - "Hattori, S.I.", - "Bulut, H.", - "Das, D.", - "Takamune, N.", - "Kishimoto, N.", - "Saruwatari, J.", - "Okamura, T.", - "Nakano, K.", - "Misumi, S.", - "Mitsuya, H.", - "Tamamura, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8doy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8doy", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z2799209083", - emdb: null, - pdb: { - dbId: "8DLB", - method: "X-RAY DIFFRACTION", - keywords: "viral cysteine protease, homodimer, enzyme-inhibitor complex, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8DLB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dlb_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dlb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "FOIXJKJVLPARQZ-KRWDZBQOSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A.Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36808989", - title: - "AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2.", - journal: "J.Chem.Inf.Model. 63: 1438-1453 (2023), 1549-960X", - doi: "https://doi.org/10.1021/acs.jcim.2c01377", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36808989", - pubDate: "2023", - abstract: "", - authors: [ - "Joshi, R.P.", - "Schultz, K.J.", - "Wilson, J.W. (0000-0002-2304-2540)", - "Kruel, A. (0000-0002-5571-7418)", - "Varikoti, R.A. (0000-0002-2355-1484)", - "Kombala, C.J.", - "Kneller, D.W. (0000-0002-5416-5789)", - "Galanie, S. (0000-0001-5712-2568)", - "Phillips, G.", - "Zhang, Q.", - "Coates, L. (0000-0003-2342-049X)", - "Parvathareddy, J.", - "Surendranathan, S.", - "Kong, Y.", - "Clyde, A.", - "Ramanathan, A. (0000-0002-1622-5488)", - "Jonsson, C.B. (0000-0002-2640-7672)", - "Brandvold, K.R. (0000-0001-5970-879X)", - "Zhou, M. (0000-0003-3575-3224)", - "Head, M.S.", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Kumar, N. (0000-0001-6713-2129)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dlb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dlb", - }, - }, - { - title: - "SARS-CoV-2 non-structural protein-1 (nsp1) in complex with N-methyl-1-(4-(thiophen-2-yl)phenyl)methanamine", - emdb: null, - pdb: { - dbId: "8ASQ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, non-structural protein-1, fragment hit, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8ASQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8asq_final.pdb", - externalLink: "https://pdb-redo.eu/db/8asq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Host translation inhibitor nsp1", - details: "", - altNames: "Leader protein,Non-structural protein 1,nsp1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DRDAOZOONYPMPX-UHFFFAOYSA-N"], - dbauthors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Kozielski, F. (0000-0001-6096-9102)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36293303", - title: - "Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening.", - journal: "Int J Mol Sci 23 (2022), 1422-0067", - doi: "https://doi.org/10.1021/ci200227u", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36293303", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S. (0000-0002-2070-7770)", - "Lou, J.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Haider, S. (0000-0003-2650-2925)", - "Kozielski, F. (0000-0001-6096-9102)", - "Ma, S.", - "Mykhaylyk, V. (0000-0003-0106-2724)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8asq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8asq", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound ZZ4461624291", - emdb: null, - pdb: { - dbId: "8DMD", - method: "X-RAY DIFFRACTION", - keywords: - "viral cysteine protease, homodimer, enzyme-inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DMD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dmd_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dmd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "NQWZHKWPOKKPNU-QGZVFWFLSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36808989", - title: - "AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2.", - journal: "J.Chem.Inf.Model. 63: 1438-1453 (2023), 1549-960X", - doi: "https://doi.org/10.1021/acs.jcim.2c01377", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36808989", - pubDate: "2023", - abstract: "", - authors: [ - "Joshi, R.P.", - "Schultz, K.J.", - "Wilson, J.W. (0000-0002-2304-2540)", - "Kruel, A. (0000-0002-5571-7418)", - "Varikoti, R.A. (0000-0002-2355-1484)", - "Kombala, C.J.", - "Kneller, D.W. (0000-0002-5416-5789)", - "Galanie, S. (0000-0001-5712-2568)", - "Phillips, G.", - "Zhang, Q.", - "Coates, L. (0000-0003-2342-049X)", - "Parvathareddy, J.", - "Surendranathan, S.", - "Kong, Y.", - "Clyde, A.", - "Ramanathan, A. (0000-0002-1622-5488)", - "Jonsson, C.B. (0000-0002-2640-7672)", - "Brandvold, K.R. (0000-0001-5970-879X)", - "Zhou, M. (0000-0003-3575-3224)", - "Head, M.S.", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Kumar, N. (0000-0001-6713-2129)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dmd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dmd", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with S217622", - emdb: null, - pdb: { - dbId: "8HUX", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX, P132H mutant, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8HUX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hux_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hux", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QMPBBNUOBOFBFS-UHFFFAOYSA-N"], - dbauthors: ["Zhang, J.", "Li, J.", "Li, W.W."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with S217622", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Li, W.W.", "Li, J.", "Zhang, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hux_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hux", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFR", - emdb: null, - pdb: { - dbId: "7MAT", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MAT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mat_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mat", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "QAOWNCQODCNURD-UHFFFAOYSA-L", "PJFSUJMJVYGASC-HKBOAZHASA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFR", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mat_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mat", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2", - emdb: null, - pdb: { - dbId: "7XWA", - method: "X-RAY DIFFRACTION", - keywords: "Spike protein, Receptor, Coronavirus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7XWA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xwa_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xwa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Processed angiotensin-converting enzyme 2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Hashiguchi, T. (0000-0001-7578-7571)", - "Suzuki, T. (0000-0002-6946-3850)", - "Kimura, K. (0000-0003-4913-7502)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36198317", - title: - "Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5.", - journal: "Cell 185 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.09.018", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36198317", - pubDate: "2022", - abstract: "", - authors: [ - "Kimura, I.", - "Yamasoba, D.", - "Tamura, T.", - "Nao, N.", - "Suzuki, T.", - "Oda, Y.", - "Mitoma, S.", - "Ito, J.", - "Nasser, H.", - "Zahradnik, J.", - "Uriu, K.", - "Fujita, S.", - "Kosugi, Y.", - "Wang, L.", - "Tsuda, M.", - "Kishimoto, M.", - "Ito, H.", - "Suzuki, R.", - "Shimizu, R.", - "Begum, M.M.", - "Yoshimatsu, K.", - "Kimura, K.T.", - "Sasaki, J.", - "Sasaki-Tabata, K.", - "Yamamoto, Y.", - "Nagamoto, T.", - "Kanamune, J.", - "Kobiyama, K.", - "Asakura, H.", - "Nagashima, M.", - "Sadamasu, K.", - "Yoshimura, K.", - "Shirakawa, K.", - "Takaori-Kondo, A.", - "Kuramochi, J.", - "Schreiber, G.", - "Ishii, K.J.", - "Hashiguchi, T.", - "Ikeda, T.", - "Saito, A.", - "Fukuhara, T.", - "Tanaka, S.", - "Matsuno, K.", - "Sato, K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xwa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xwa", - }, - }, - { - title: "Structure of SARS-CoV-2 ORF8", - emdb: null, - pdb: { - dbId: "7XMN", - method: "X-RAY DIFFRACTION", - keywords: "ORF8, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "A0A376KDN7", - organism: "562", - name: "Maltodextrin-binding protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC8", - organism: "2697049", - name: "ORF8 protein", - details: "", - altNames: "ORF8, Non-structural protein 8, ns8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "KOBHCUDVWOTEKO-VKHMYHEASA-N", - ], - dbauthors: ["Chen, X. (0000-0002-5580-6090)", "Xu, W. (0000-0002-3135-5010)"], - details: [ - { - sample: { - name: "", - exprSystem: "Mammalia", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure of SARS-CoV-2 ORF8 reveals its glycosylated,lipid-binding, and immune-related signatures", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Chen, X.", "Xu, W."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xmn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xmn", - }, - }, - { - title: "TRIM7 in complex with C-terminal peptide of NSP5", - emdb: null, - pdb: { - dbId: "7X6Y", - method: "X-RAY DIFFRACTION", - keywords: "ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7X6Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x6y_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x6y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9C029", - organism: "9606", - name: "E3 ubiquitin-protein ligase TRIM7", - details: "", - altNames: - "Glycogenin-interacting protein,RING finger protein 90,Tripartite motif-containing protein 7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, H.", "Liang, X.", "Li, X.Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35982226", - title: - "A C-terminal glutamine recognition mechanism revealed by E3 ligase TRIM7 structures.", - journal: "Nat.Chem.Biol. 18: 1214-1223 (2022), 1552-4469", - doi: "https://doi.org/10.1038/s41589-022-01128-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35982226", - pubDate: "2022", - abstract: "", - authors: [ - "Liang, X.", - "Xiao, J.", - "Li, X.", - "Liu, Y.", - "Lu, Y.", - "Wen, Y.", - "Li, Z.", - "Che, X.", - "Ma, Y.", - "Zhang, X.", - "Zhang, Y.", - "Jian, D.", - "Wang, P.", - "Xuan, C.", - "Yu, G.", - "Li, L.", - "Zhang, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x6y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x6y", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 NSP3 Macrodomain 3 (SARS-unique domain-M)", - emdb: null, - pdb: { - dbId: "7XC3", - method: "X-RAY DIFFRACTION", - keywords: "G-quadruplex-binding macrodomain, SARS-unique domain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7XC3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xc3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xc3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Li, J. (0000-0003-1466-9189)", "Gao, J. (0000-0001-9377-7553)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36356292", - title: - "Two Binding Sites of SARS-CoV-2 Macrodomain 3 Probed by Oxaprozin and Meclomen.", - journal: "J.Med.Chem. 65: 15227-15237 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c01168", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36356292", - pubDate: "2022", - abstract: "", - authors: [ - "Li, J.", - "Zhong, F.", - "Li, M.", - "Liu, Y.", - "Wang, L.", - "Liu, M.", - "Li, F.", - "Zhang, J.", - "Wu, J.", - "Shi, Y.", - "Zhang, Z.", - "Tu, X.", - "Ruan, K.", - "Gao, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xc3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xc3", - }, - }, - { - title: - "Crystallographic structure of two neutralizing nanobodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)", - emdb: null, - pdb: { - dbId: "7FH0", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, RBD, Spike, nanobodies, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FH0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fh0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fh0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1,Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "nanobodies aRBD-2-7", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: ["Zheng, P.", "Jin, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35906408", - title: - "Hetero-bivalent nanobodies provide broad-spectrum protection against SARS-CoV-2 variants of concern including Omicron.", - journal: "Cell Res. 32: 831-842 (2022), 1001-0602", - doi: "https://doi.org/10.1038/s41422-022-00700-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35906408", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, H.", - "Zhang, X.", - "Zheng, P.", - "Dube, P.H.", - "Zeng, W.", - "Chen, S.", - "Cheng, Q.", - "Yang, Y.", - "Wu, Y.", - "Zhou, J.", - "Hu, X.", - "Xiang, Y.", - "Zhang, H.", - "Chiu, S.", - "Jin, T.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fh0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fh0", - }, - }, - { - title: - "Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates", - emdb: null, - pdb: { - dbId: "8EJ7", - method: "X-RAY DIFFRACTION", - keywords: - "viral protein, HYDROLASE-HYDROLASE INHIBITOR complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8EJ7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ej7_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ej7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lu, J. (0000-0002-4090-5176)", - "Khan, M.B. (0000-0002-4164-9573)", - "Young, H.S. (0000-0002-5990-8422)", - "Lemieux, M.J. (0000-0003-4745-9153)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Mpro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals", - journal: "Acs Cent.Sci. 9: 696-708 (2023), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.3c00054", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, S.A.", - "Arutyunova, E.", - "Lu, J.", - "Khan, M.B.", - "Rut, W.", - "Zmudzinski, M.", - "Shahbaz, S.", - "Iyyathurai, J.", - "Moussa, E.W.", - "Turner, Z.", - "Bai, B.", - "Lamer, T.", - "Nieman, J.A.", - "Vederas, J.C.", - "Julien, O.", - "Drag, M.", - "Elahi, S.", - "Young, H.S.", - "Lemieux, M.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ej7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ej7", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with ML101", - emdb: null, - pdb: { - dbId: "7SFB", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, SARS-CoV-2, coronavirus, Main Protease, Protease, Mpro, 3C-like proteinase, CL3pro, Inhibitor, Complex, Covalent, Adduct, ML101, Ketoamide, Peptidomimetic, Viral Protein", - refModels: [ - { - emdbId: null, - pdbId: "7SFB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sfb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sfb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QQHOBZCFMWFGGP-KOUJMVCDSA-N", - "ZIBGPFATKBEMQZ-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fernandez, D. (0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sfb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sfb", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFR-yne", - emdb: null, - pdb: { - dbId: "7MAU", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MAU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mau_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mau", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "", - "RYHBNJHYFVUHQT-UHFFFAOYSA-N", - "JNSZEVHYEISGKR-VJGNERBWSA-N", - ], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFR-yne", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mau_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mau", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 Mpro in complex with cyclic peptide GM4 including unnatural amino acids.", - emdb: null, - pdb: { - dbId: "7Z4S", - method: "X-RAY DIFFRACTION", - keywords: "protease, UNKNOWN FUNCTION", - refModels: [ - { - emdbId: null, - pdbId: "7Z4S", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7z4s_final.pdb", - externalLink: "https://pdb-redo.eu/db/7z4s", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Macrocyclic peptide inhibitor", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "ZIBGPFATKBEMQZ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Owen, C.D. (0000-0001-5774-8202)", - "Miura, T.", - "Malla, T. (0000-0003-4989-6410)", - "Lukacik, L. (0000-0002-3179-7273)", - "Strain-Damerell, C.M. (0000-0003-4964-2090)", - "Tumber, A. (0000-0003-1958-8353)", - "Brewitz, L.", - "McDonough, M.A.", - "Salah, E.", - "Terasaka, N.", - "Katoh, T.", - "Kawamura, A. (0000-0003-1169-5082)", - "Schofield, C.J. (0000-0002-0290-6565)", - "Suga, H.", - "Walsh, M.A. (0000-0001-5683-1151)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37217786", - title: - "In vitro selection of macrocyclic peptide inhibitors containing cyclic gamma 2,4 -amino acids targeting the SARS-CoV-2 main protease.", - journal: "Nat.Chem. 15: 998-1005 (2023), 1755-4349", - doi: "https://doi.org/10.1038/s41557-023-01205-1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37217786", - pubDate: "2023", - abstract: "", - authors: [ - "Miura, T.", - "Malla, T.R.", - "Owen, C.D.", - "Tumber, A.", - "Brewitz, L.", - "McDonough, M.A.", - "Salah, E.", - "Terasaka, N.", - "Katoh, T.", - "Lukacik, P.", - "Strain-Damerell, C.", - "Mikolajek, H.", - "Walsh, M.A.", - "Kawamura, A.", - "Schofield, C.J.", - "Suga, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z4s_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z4s", - }, - }, - { - title: - "Crystal structure of F2F-2020198-00X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.", - emdb: null, - pdb: { - dbId: "8OKN", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8OKN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8okn_final.pdb", - externalLink: "https://pdb-redo.eu/db/8okn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FREYRXXGOYXVLM-BCYZHJNNSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "SVTOYMIYCMHPIV-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37043904", - title: - "Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination.", - journal: "Eur.J.Med.Chem. 253: 115311-115311 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115311", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37043904", - pubDate: "2023", - abstract: "", - authors: [ - "Stefanelli, I.", - "Corona, A.", - "Cerchia, C.", - "Cassese, E.", - "Improta, S.", - "Costanzi, E.", - "Pelliccia, S.", - "Morasso, S.", - "Esposito, F.", - "Paulis, A.", - "Scognamiglio, S.", - "Di Leva, F.S.", - "Storici, P.", - "Brindisi, M.", - "Tramontano, E.", - "Cannalire, R.", - "Summa, V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8okn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8okn", - }, - }, - { - title: - "Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-196) in complex with GC-376", - emdb: null, - pdb: { - dbId: "7UJG", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, catalytic domain, viral enzyme, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7UJG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ujg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ujg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36114420", - title: - "Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain.", - journal: "Commun Biol 5: 976-976 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03910-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36114420", - pubDate: "2022", - abstract: "", - authors: [ - "Nashed, N.T.", - "Kneller, D.W.", - "Coates, L. (0000-0003-2342-049X)", - "Ghirlando, R. (0000-0003-4880-4959)", - "Aniana, A.", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Louis, J.M. (0000-0002-0052-1899)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ujg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ujg", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 soluble dimeric ORF9b", - emdb: null, - pdb: { - dbId: "7YE7", - method: "X-RAY DIFFRACTION", - keywords: - "ORF9b, SARS-CoV-2, immune escape, viral antagonist, membrane association, fold switch, lipid binding, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7YE7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ye7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ye7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD2", - organism: "2697049", - name: "ORF9b protein", - details: "", - altNames: "ORF9b,Accessory protein 9b,ORF-9b,Protein 9b", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BKIMMITUMNQMOS-UHFFFAOYSA-N", "TVMXDCGIABBOFY-UHFFFAOYSA-N"], - dbauthors: ["Qi, J.", "Chai, Y.", "Gao, G.F.", "Song, H.", "Jin, X."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36184694", - title: - "Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism.", - journal: "Sci China Life Sci 66: 152-164 (2023), 1869-1889", - doi: "https://doi.org/10.1007/s11427-022-2168-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36184694", - pubDate: "2023", - abstract: "", - authors: [ - "Jin, X.", - "Sun, X.", - "Chai, Y.", - "Bai, Y.", - "Li, Y.", - "Hao, T.", - "Qi, J.", - "Song, H.", - "Wong, C.C.L.", - "Gao, G.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ye7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ye7", - }, - }, - { - title: - "Crystal structure of neutralizing antibody D29 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)", - emdb: null, - pdb: { - dbId: "8DW9", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SarbecoVirus, WIV1 RBD, Viral protein, Spike glycoprotein, Receptor Binding Protein, Neutralizing antibody, potent, 10-40, Fab, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8DW9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dw9_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dw9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "D29 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "D29 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Reddem, E.R. (0000-0003-3054-5506)", - "Shapiro, L. (0000-0001-9943-8819)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36354024", - title: - "Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2.", - journal: - "Emerg Microbes Infect 12: 2146538-2146538 (2023), 2222-1751", - doi: "https://doi.org/10.1080/22221751.2022.2146538", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36354024", - pubDate: "2023", - abstract: "", - authors: [ - "Luo, M.", - "Zhou, B.", - "Reddem, E.R.", - "Tang, B.", - "Chen, B.", - "Zhou, R.", - "Liu, H.", - "Liu, L.", - "Katsamba, P.S.", - "Au, K.K.", - "Man, H.O.", - "To, K.K.", - "Yuen, K.Y.", - "Shapiro, L.", - "Dang, S.", - "Ho, D.D.", - "Chen, Z.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dw9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dw9", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV93-03", - emdb: null, - pdb: { - dbId: "8DTT", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, coronavirus, antibody, stem helix, neutralizing antibody, COVID-19, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8DTT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dtt_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dtt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "COV93-03 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COV93-03 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2' stem helix peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wilson, I.A. (0000-0002-6469-2419)", - "Lee, C.C.D. (0000-0002-5470-2484)", - "Lin, T.H. (0000-0002-0937-9972)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Mus musculus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36347257", - title: - "Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses.", - journal: "Cell Host Microbe 31 (2023), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2022.10.010", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36347257", - pubDate: "2023", - abstract: "", - authors: [ - "Dacon, C.", - "Peng, L.", - "Lin, T.H.", - "Tucker, C.", - "Lee, C.D.", - "Cong, Y.", - "Wang, L.", - "Purser, L.", - "Cooper, A.J.R.", - "Williams, J.K.", - "Pyo, C.W.", - "Yuan, M.", - "Kosik, I.", - "Hu, Z.", - "Zhao, M.", - "Mohan, D.", - "Peterson, M.", - "Skinner, J.", - "Dixit, S.", - "Kollins, E.", - "Huzella, L.", - "Perry, D.", - "Byrum, R.", - "Lembirik, S.", - "Murphy, M.", - "Zhang, Y.", - "Yang, E.S.", - "Chen, M.", - "Leung, K.", - "Weinberg, R.S.", - "Pegu, A.", - "Geraghty, D.E.", - "Davidson, E.", - "Doranz, B.J.", - "Douagi, I.", - "Moir, S.", - "Yewdell, J.W.", - "Schmaljohn, C.", - "Crompton, P.D.", - "Mascola, J.R.", - "Holbrook, M.R.", - "Nemazee, D.", - "Wilson, I.A.", - "Tan, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dtt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dtt", - }, - }, - { - title: "Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD", - emdb: null, - pdb: { - dbId: "8HN6", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, RBD, monoclonal antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8HN6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hn6_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hn6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of monoclonal antibody 3G10", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of monoclonal antibody 3G10", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Chen, Y.", "Qi, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37234155", - title: - "Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.", - journal: "Front Immunol 14: 1160283-1160283 (2023), 1664-3224", - doi: "https://doi.org/10.3389/fimmu.2023.1160283", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37234155", - pubDate: "2023", - abstract: "", - authors: [ - "Wang, Z.", - "Li, D.", - "Chen, Y.", - "Sun, Y.", - "Jin, C.", - "Hu, C.", - "Feng, Y.", - "Su, J.", - "Ren, L.", - "Hao, Y.", - "Wang, S.", - "Zhu, M.", - "Liu, Y.", - "Qi, J.", - "Zhu, B.", - "Shao, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hn6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hn6", - }, - }, - { - title: "Crystal structure of apo SARS-CoV-2 main protease", - emdb: null, - pdb: { - dbId: "8IGO", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, NSP5, main protease, coronavirus, protease inhibitor, alpha-ketoamide inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8IGO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8igo_final.pdb", - externalLink: "https://pdb-redo.eu/db/8igo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhou, B.", - "Xiong, X. (0000-0002-4632-9122)", - "Huang, X.", - "Xu, J.", - "Yang, Z. (0000-0002-2681-4171)", - "Zhong, N. (0000-0003-2274-1427)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Inhibition mechanism and antiviral activity of an alpha-ketoamide based SARS-CoV-2 main protease inhibitor", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Huang, X.", - "Zhou, B.", - "Xiong, X. (0000-0002-4632-9122)", - "Yang, Z. (0000-0002-2681-4171)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8igo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8igo", - }, - }, - { - title: "SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented by HLA-A*29:02", - emdb: null, - pdb: { - dbId: "7TLT", - method: "X-RAY DIFFRACTION", - keywords: - "human leukocyte antigen, major histocompatibility complex, HLA-A29, HLA-A*29:02, SARS-CoV-2, Spike, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7TLT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tlt_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tlt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q861F7", - organism: "9606", - name: "HLA class I histocompatibility antigen, A alpha chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S1 peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Szeto, C. (0000-0003-3784-5210)", - "Gras, S. (0000-0001-7416-038X)", - "Murdolo, L.D. (0000-0001-5222-9585)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented by HLA-A*29:02", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Murdolo, L.D. (0000-0001-5222-9585)", - "Szeto, C. (0000-0003-3784-5210)", - "Gras, S. (0000-0001-7416-038X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tlt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tlt", - }, - }, - { - title: "Crystal structure of SARS-Cov-2 main protease D48N mutant", - emdb: null, - pdb: { - dbId: "7XB3", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7XB3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xb3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xb3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Replicase polyprotein 1a", - details: "", - altNames: "pp1a,ORF1a polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, J.", "Li, J.", "Hu, X.H."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Crystal structure of SARS-Cov-2 main protease D48N mutant", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Hu, X.H.", "Li, J.", "Zhang, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xb3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xb3", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) S144F Mutant", - emdb: null, - pdb: { - dbId: "8EHM", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8EHM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ehm_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ehm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) S144F Mutant", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - "Chen, Y. (0000-0002-5115-3600)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ehm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ehm", - }, - }, - { - title: "Crystal structure of SARS Cov-2 main protease in complex with an inhibitor 4", - emdb: null, - pdb: { - dbId: "7ZV5", - method: "X-RAY DIFFRACTION", - keywords: "SARS Cov-2, 3CL, main protease, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZV5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zv5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zv5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "inhibitor TRIP5", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Rahimova, R. (0000-0002-4992-842X)", - "Di Micco, S. (0000-0002-4688-1080)", - "Marquez, J.A. (0000-0002-3453-9261)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36332548", - title: - "Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARS-CoV-2.", - journal: "Eur.J.Med.Chem. 244: 114857-114857 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114857", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36332548", - pubDate: "2022", - abstract: "", - authors: [ - "Di Micco, S.", - "Rahimova, R.", - "Sala, M.", - "Scala, M.C.", - "Vivenzio, G.", - "Musella, S.", - "Andrei, G.", - "Remans, K.", - "Mammri, L.", - "Snoeck, R.", - "Bifulco, G.", - "Di Matteo, F.", - "Vestuto, V.", - "Campiglia, P.", - "Marquez, J.A.", - "Fasano, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zv5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zv5", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) S144M Mutant", - emdb: null, - pdb: { - dbId: "8EHL", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8EHL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ehl_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ehl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) S144M Mutant", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - "Chen, Y. (0000-0002-5115-3600)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ehl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ehl", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing antibody ADI-62113 Fab", - emdb: null, - pdb: { - dbId: "7T7B", - method: "X-RAY DIFFRACTION", - keywords: - "cross-neutralizing antibody; YYDRxG; SARS-CoV-2; ADI-62113; Sarbecovirus; pattern search; IGHD3-22, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7T7B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t7b_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t7b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "ADI-62113 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "ADI-62113 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Liu, H. (0000-0002-2412-7853)", "Wilson, I.A. (0000-0002-6469-2419)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35906394", - title: - "Human antibodies to SARS-CoV-2 with a recurring YYDRxG motif retain binding and neutralization to variants of concern including Omicron.", - journal: "Commun Biol 5: 766-766 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03700-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35906394", - pubDate: "2022", - abstract: "", - authors: [ - "Liu, H. (0000-0002-2412-7853)", - "Kaku, C.I. (0000-0002-9854-8351)", - "Song, G.", - "Yuan, M. (0000-0001-9754-4503)", - "Andrabi, R. (0000-0001-8837-7520)", - "Burton, D.R. (0000-0001-6711-9864)", - "Walker, L.M.", - "Wilson, I.A. (0000-0002-6469-2419)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t7b_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t7b", - }, - }, - { - title: - "Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304, in complex with NBH2", - emdb: null, - pdb: { - dbId: "8GFR", - method: "X-RAY DIFFRACTION", - keywords: - "viral cysteine protease, inactive C145A mutant, homodimer, inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8GFR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gfr_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gfr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "BSSSIUKIEUQFQH-QXMOZHRRSA-N"], - dbauthors: ["Coates, L.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37271339", - title: - "Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.", - journal: "J.Biol.Chem. 299: 104886-104886 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.104886", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37271339", - pubDate: "2023", - abstract: "", - authors: [ - "Kovalevsky, A.", - "Aniana, A.", - "Coates, L.", - "Bonnesen, P.V.", - "Nashed, N.T.", - "Louis, J.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gfr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gfr", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with ML1001", - emdb: null, - pdb: { - dbId: "7SF1", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, SARS-CoV-2, coronavirus, Main Protease, Protease, Mpro, 3C-like proteinase, CL3pro, Inhibitor, Complex, Covalent, Adduct, ML1001, Ketoamide, Peptidomimetic, Viral Protein", - refModels: [ - { - emdbId: null, - pdbId: "7SF1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sf1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sf1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AQCHRJCCMXXILC-CMBJTQIYSA-N"], - dbauthors: [ - "Fernandez, D. (0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. 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(0000-0002-4632-9122)", - "Huang, X.", - "Xu, J.", - "Yang, Z. (0000-0002-2681-4171)", - "Zhong, N. (0000-0003-2274-1427)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Inhibition mechanism and antiviral activity of an alpha-ketoamide based SARS-CoV-2 main protease inhibitor", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Huang, X.", - "Zhou, B.", - "Xiong, X. (0000-0002-4632-9122)", - "Yang, Z. 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(0000-0002-9358-4732)"], - details: [ - { - sample: { - name: "", - exprSystem: "Mammalian expression vector BsrGI-MCS-pcDNA3.1", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37234155", - title: - "Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.", - journal: "Front Immunol 14: 1160283-1160283 (2023), 1664-3224", - doi: "https://doi.org/10.3389/fimmu.2023.1160283", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37234155", - pubDate: "2023", - abstract: "", - authors: [ - "Wang, Z.", - "Li, D.", - "Chen, Y.", - "Sun, Y.", - "Jin, C.", - "Hu, C.", - "Feng, Y.", - "Su, J.", - "Ren, L.", - "Hao, Y.", - "Wang, S.", - "Zhu, M.", - "Liu, Y.", - "Qi, J.", - "Zhu, B.", - "Shao, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hn7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hn7", - }, - }, - { - title: - "Crystal structure of F2F-2020184-00X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.", - emdb: null, - pdb: { - dbId: "8OKK", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8OKK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8okk_final.pdb", - externalLink: "https://pdb-redo.eu/db/8okk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "CUINDADQQONHSA-ATIWLJMLSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "SVTOYMIYCMHPIV-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37043904", - title: - "Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination.", - journal: "Eur.J.Med.Chem. 253: 115311-115311 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115311", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37043904", - pubDate: "2023", - abstract: "", - authors: [ - "Stefanelli, I.", - "Corona, A.", - "Cerchia, C.", - "Cassese, E.", - "Improta, S.", - "Costanzi, E.", - "Pelliccia, S.", - "Morasso, S.", - "Esposito, F.", - "Paulis, A.", - "Scognamiglio, S.", - "Di Leva, F.S.", - "Storici, P.", - "Brindisi, M.", - "Tramontano, E.", - "Cannalire, R.", - "Summa, V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8okk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8okk", - }, - }, - { - title: - "Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-196) in complex with nirmatrelvir", - emdb: null, - pdb: { - dbId: "7UJU", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, catalytic domain, viral enzyme, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7UJU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uju_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uju", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36114420", - title: - "Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain.", - journal: "Commun Biol 5: 976-976 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03910-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36114420", - pubDate: "2022", - abstract: "", - authors: [ - "Nashed, N.T.", - "Kneller, D.W.", - "Coates, L. (0000-0003-2342-049X)", - "Ghirlando, R. (0000-0003-4880-4959)", - "Aniana, A.", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Louis, J.M. 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(0000-0002-0421-3543)", - "Soprano, A.S. (0000-0001-7117-927X)", - "Tonoli, C.C.C. (0000-0003-2580-5588)", - "Prado, P.F.V. (0000-0002-3427-2229)", - "da Silva, J.C. (0000-0001-5970-561X)", - "Franchini, K.G. (0000-0002-0190-6635)", - "Trivella, D.B.B. (0000-0002-7505-2345)", - "Benedetti, C.E. (0000-0002-4602-0256)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 papain-like protease C111S mutant", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Bezerra, E.H.S. (0000-0002-0421-3543)", - "Soprano, A.S. (0000-0001-7117-927X)", - "Tonoli, C.C.C. (0000-0003-2580-5588)", - "Prado, P.F.V. (0000-0002-3427-2229)", - "da Silva, J.C. (0000-0001-5970-561X)", - "Franchini, K.G. (0000-0002-0190-6635)", - "Trivella, D.B.B. (0000-0002-7505-2345)", - "Benedetti, C.E. (0000-0002-4602-0256)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8fwn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8fwn", - }, - }, - { - title: "Sars-Cov2 Main Protease in complex with CDD-1819", - emdb: null, - pdb: { - dbId: "7US4", - method: "X-RAY DIFFRACTION", - keywords: - "Sars-Cov2 Main protease, no-covalent, inhibitor, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7US4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7us4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7us4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "YXZCMQAWBHCPMS-HTFLBPPUSA-N"], - dbauthors: [ - "Lu, S.", - "Palzkill, T.", - "Matzuk, M.M.", - "Judge, A. (0000-0003-4289-1748)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37542196", - title: - "DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors.", - journal: "Commun Chem 6: 164-164 (2023), 2399-3669", - doi: "https://doi.org/10.1038/s42004-023-00961-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37542196", - pubDate: "2023", - abstract: "", - authors: [ - "Jimmidi, R.", - "Chamakuri, S. (0000-0002-7586-4992)", - "Lu, S.", - "Ucisik, M.N.", - "Chen, P.J.", - "Bohren, K.M. (0000-0002-3183-4118)", - "Moghadasi, S.A.", - "Versteeg, L.", - "Nnabuife, C. (0000-0001-9907-0508)", - "Li, J.Y.", - "Qin, X. (0000-0003-3728-5911)", - "Chen, Y.C.", - "Faver, J.C.", - "Nyshadham, P.", - "Sharma, K.L.", - "Sankaran, B. (0000-0002-3266-8131)", - "Judge, A. (0000-0003-4289-1748)", - "Yu, Z.", - "Li, F. (0000-0002-9680-4614)", - "Pollet, J. (0000-0003-1420-4015)", - "Harris, R.S.", - "Matzuk, M.M.", - "Palzkill, T. (0000-0002-5267-0001)", - "Young, D.W. (0000-0002-1595-9658)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7us4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7us4", - }, - }, - { - title: - "Crystal structure of neutralizing antibody 80 in complex with SARS-CoV-2 receptor binding domain", - emdb: null, - pdb: { - dbId: "8DNN", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, ANTIBODY, VIRAL GLYCOPROTEIN, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "8DNN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dnn_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dnn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "80 FAB HEAVY CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "80 FAB LIGHT CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Muthuraman, K. (0000-0003-0361-772X)", - "Kucharska, I. (0000-0001-6150-3419)", - "Ivanochko, D. (0000-0002-2826-8100)", - "Julien, J.P. (0000-0001-7602-3995)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "hexameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of neutralizing antibody 80 in complex with SARS-CoV-2 receptor binding domain", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Muthuraman, K. (0000-0003-0361-772X)", - "Kucharska, I. (0000-0001-6150-3419)", - "Ivanochko, D. (0000-0002-2826-8100)", - "Julien, J.P. (0000-0001-7602-3995)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dnn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dnn", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with ATP", - emdb: null, - pdb: { - dbId: "8OSX", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, methyltransferase, complex, inhibitor", - refModels: [ - { - emdbId: null, - pdbId: "8OSX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8osx_final.pdb", - externalLink: "https://pdb-redo.eu/db/8osx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ZKHQWZAMYRWXGA-KQYNXXCUSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - "Kiene, A.", - "Galchenkova, M. (0000-0001-8676-0091)", - "Garcia, Y. (0000-0002-9592-2141)", - "Ehr, C. (0000-0003-1428-0042)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8osx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8osx", - }, - }, - { - title: "Structure of SARS-CoV-2 Omicron BA.2.75 RBD in complex with human ACE2", - emdb: null, - pdb: { - dbId: "8H5C", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Omicron BA.2.75, hACE2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8H5C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8h5c_final.pdb", - externalLink: "https://pdb-redo.eu/db/8h5c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Processed angiotensin-converting enzyme 2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Zhao, Z.N.", "Qi, J.X.", "Gao, G.F.", "Bai, B.", "Liu, K.F."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37479708", - title: - "Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.", - journal: "Nat Commun 14: 4405-4405 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-39942-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37479708", - pubDate: "2023", - abstract: "", - authors: [ - "Zhao, Z.", - "Xie, Y. (0000-0001-9602-0003)", - "Bai, B.", - "Luo, C.", - "Zhou, J.", - "Li, W.", - "Meng, Y.", - "Li, L.", - "Li, D.", - "Li, X.", - "Wang, X.", - "Sun, J.", - "Xu, Z.", - "Sun, Y. (0000-0001-9977-9103)", - "Zhang, W.", - "Fan, Z.", - "Zhao, X. (0000-0002-2001-1343)", - "Wu, L.", - "Ma, J.", - "Li, O.Y.", - "Shang, G.", - "Chai, Y.", - "Liu, K. (0000-0001-9076-2647)", - "Wang, P. (0000-0001-7737-181X)", - "Gao, G.F. (0000-0002-3869-615X)", - "Qi, J. (0000-0002-9358-4732)", - "Xie, Y.", - "Sun, Y.", - "Zhao, X.", - "Liu, K.", - "Wang, P.", - "Gao, G.F.", - "Qi, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8h5c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8h5c", - }, - }, - { - title: "Fab arm of antibody GAR12 bound to the receptor binding domain of SARS-CoV-2.", - emdb: null, - pdb: { - dbId: "8DXT", - method: "X-RAY DIFFRACTION", - keywords: - "anti-CoV-2, antibodies, convalescent patients, receptor binding domain., ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DXT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dxt_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dxt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of Fab arm of antibody GAR12", - details: "Light chain of Fab arm of antibody GAR12", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of Fab arm of antibody GAR12", - details: - "Heavy chain of Fab arm of antibody GAR12, with a 6His tag at the C-terminus", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Langley, D.B.", "Christ, D.", "Henry, J.Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36755042", - title: - "Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients.", - journal: "Nat Commun 14: 687-687 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-36295-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36755042", - pubDate: "2023", - abstract: "", - authors: [ - "Rouet, R.", - "Henry, J.Y. (0000-0003-0435-3308)", - "Johansen, M.D. (0000-0001-5553-5270)", - "Sobti, M.", - "Balachandran, H.", - "Langley, D.B.", - "Walker, G.J.", - "Lenthall, H.", - "Jackson, J.", - "Ubiparipovic, S.", - "Mazigi, O.", - "Schofield, P.", - "Burnett, D.L. (0000-0002-5642-3315)", - "Brown, S.H.J. (0000-0003-3997-4614)", - "Martinello, M.", - "Hudson, B.", - "Gilroy, N.", - "Post, J.J. (0000-0003-1475-9272)", - "Kelleher, A. (0000-0002-0009-3337)", - "Jack, H.M.", - "Goodnow, C.C. (0000-0001-5296-6155)", - "Turville, S.G. (0000-0003-1918-5343)", - "Rawlinson, W.D. (0000-0003-0988-7827)", - "Bull, R.A. (0000-0002-9844-3744)", - "Stewart, A.G. (0000-0002-2070-6030)", - "Hansbro, P.M.", - "Christ, D. (0000-0002-7313-3977)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dxt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dxt", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI88", - emdb: null, - pdb: { - dbId: "7SH8", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7SH8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sh8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sh8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LQGMWKMFHKDJKF-FBZFJNBBSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure of the SARS-CoV-2 main protease in complex with inhibitors", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Yang, K.S.", - "Liu, W.R.", - "Sankaran, B.", - "Blankenship, L.B. (0000-0002-1714-4399)", - "Liu, W.R. (0000-0002-7078-6534)", - "Blankenship, L.B.", - "Kang, Y.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sh8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sh8", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z1367095370", - emdb: null, - pdb: { - dbId: "7FR9", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FR9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fr9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fr9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CSGYXQGPYNFEFB-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fr9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fr9", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with ML1006m", - emdb: null, - pdb: { - dbId: "7SF3", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, SARS-CoV-2, coronavirus, Main Protease, Protease, Mpro, 3C-like proteinase, CL3pro, Inhibitor, Complex, Covalent, Adduct, ML1006m, Ketoamide, Peptidomimetic, Viral Protein", - refModels: [ - { - emdbId: null, - pdbId: "7SF3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sf3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sf3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QDKCXRMRZLIIFP-OGEQHFGCSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Fernandez, D. (0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sf3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sf3", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 NSP3 Macrodomain 3 (SARS-unique domain-M) in complex with Oxaprozin", - emdb: null, - pdb: { - dbId: "7XC4", - method: "X-RAY DIFFRACTION", - keywords: "G-quadruplex-binding, Viral protein", - refModels: [ - { - emdbId: null, - pdbId: "7XC4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xc4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xc4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OFPXSFXSNFPTHF-UHFFFAOYSA-N"], - dbauthors: ["Liu, Y.", "Li, J. (0000-0003-1466-9189)", "Ruan, K.", "Gao, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36356292", - title: - "Two Binding Sites of SARS-CoV-2 Macrodomain 3 Probed by Oxaprozin and Meclomen.", - journal: "J.Med.Chem. 65: 15227-15237 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c01168", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36356292", - pubDate: "2022", - abstract: "", - authors: [ - "Li, J.", - "Zhong, F.", - "Li, M.", - "Liu, Y.", - "Wang, L.", - "Liu, M.", - "Li, F.", - "Zhang, J.", - "Wu, J.", - "Shi, Y.", - "Zhang, Z.", - "Tu, X.", - "Ruan, K.", - "Gao, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xc4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xc4", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with halicin", - emdb: null, - pdb: { - dbId: "7TUU", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TUU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tuu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tuu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VVVCJCRUFSIVHI-UHFFFAOYSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35815070", - title: - "Repurposing Halicin as a potent covalent inhibitor for the SARS-CoV-2 main protease.", - journal: "Curr Res Chem Biol 2: 100025-100025 (2022), 2666-2469", - doi: "https://doi.org/10.1016/j.crchbi.2022.100025", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35815070", - pubDate: "2022", - abstract: "", - authors: [ - "Yang, K.S.", - "Alex Kuo, S.T.", - "Blankenship, L.R.", - "Geng, Z.Z.", - "Li, S.G.", - "Russell, D.H.", - "Yan, X.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tuu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tuu", - }, - }, - { - title: "Crystal structure of SARS Cov-2 main protease in complex with an inhibitor 57", - emdb: null, - pdb: { - dbId: "7ZV7", - method: "X-RAY DIFFRACTION", - keywords: "SARS Cov-2, 3CL, main protease, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZV7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zv7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zv7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "inhibitor 57", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Rahimova, R. (0000-0002-4992-842X)", - "Di Micco, S. (0000-0002-4688-1080)", - "Marquez, J.A. (0000-0002-3453-9261)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36332548", - title: - "Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARS-CoV-2.", - journal: "Eur.J.Med.Chem. 244: 114857-114857 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114857", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36332548", - pubDate: "2022", - abstract: "", - authors: [ - "Di Micco, S.", - "Rahimova, R.", - "Sala, M.", - "Scala, M.C.", - "Vivenzio, G.", - "Musella, S.", - "Andrei, G.", - "Remans, K.", - "Mammri, L.", - "Snoeck, R.", - "Bifulco, G.", - "Di Matteo, F.", - "Vestuto, V.", - "Campiglia, P.", - "Marquez, J.A.", - "Fasano, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zv7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zv7", - }, - }, - { - title: "SARS-CoV-2 RBD in complex with Omicron-neutralizing antibody 2A10", - emdb: null, - pdb: { - dbId: "8E1G", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Omicron, antibody, neutralizing, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8E1G", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e1g_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e1g", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "2A10 Fab, heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "2A10 Fab, light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Hastie, K.M. (0000-0002-3406-1210)", - "Saphire, E.O. (0000-0002-1206-7451)", - "Wasserman, H. (0000-0003-2826-9020)", - "Buck, T.K. (0000-0002-4792-1312)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37083327", - title: - "Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence.", - journal: "Cell Rep 42: 112421-112421 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112421", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37083327", - pubDate: "2023", - abstract: "", - authors: [ - "Hastie, K.M.", - "Yu, X.", - "Ana-Sosa-Batiz, F.", - "Zyla, D.S.", - "Harkins, S.S.", - "Hariharan, C.", - "Wasserman, H.", - "Zandonatti, M.A.", - "Miller, R.", - "Maule, E.", - "Kim, K.", - "Valentine, K.M.", - "Shresta, S.", - "Saphire, E.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e1g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e1g", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 Main Protease in complex with covalently bound GC376", - emdb: null, - pdb: { - dbId: "7QKA", - method: "X-RAY DIFFRACTION", - keywords: - "main protease, MPro, cystein protease, drug development, drug target, peptide-like inhibitor, SARS-CoV-2, COVID-19, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7QKA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qka_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qka", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "JUCVXDDMQHPCKT-BZSNNMDCSA-N"], - dbauthors: [ - "Falke, S. (0000-0003-3409-1791)", - "Reinke, P.Y.A. (0000-0002-7354-0839)", - "Lieske, J. (0000-0002-5439-5082)", - "Ewert, W. (0000-0001-8626-4864)", - "Loboda, J. (0000-0002-9601-3484)", - "Rahmani Mashhour, A. (0000-0001-9177-5589)", - "Hauser, M.", - "Karnicar, K. (0000-0002-7033-9224)", - "Usenik, A. (0000-0003-2366-2886)", - "Lindic, N. (0000-0001-7681-3436)", - "Lach, M.", - "Boehler, H.", - "Beck, T.", - "Cox, R.", - "Chapman, H.N. (0000-0002-4655-1743)", - "Hinrichs, W. (0000-0002-0435-4565)", - "Turk, D. (0000-0003-0205-6609)", - "Guenther, S. (0000-0002-7329-6653)", - "Meents, A. 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(0000-0002-1714-4399)", - "Liu, W.R. 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(0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Wang, J. (0000-0002-4845-4621)", - "Kohaal, N. (0000-0002-4462-6158)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164I Mutant", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Kohaal, N. (0000-0002-4462-6158)", - "Wang, J. (0000-0002-4845-4621)", - "Chen, Y. (0000-0002-5115-3600)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8sxo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8sxo", - }, - }, - { - title: "Crystal Structure of C13C9 Fab in complex with SARS-CoV-2 S fusion peptide", - emdb: null, - pdb: { - dbId: "7U0E", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 spike, COVID-19, fusion peptide, Fab, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7U0E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u0e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u0e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain Fab C13C9", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain Fab C13C9", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "SARS-CoV-2 S fusion peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Veesler, D.", "Tortorici, M.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35857703", - title: - "ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.", - journal: "Science 377: 735-742 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abq2679", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35857703", - pubDate: "2022", - abstract: "", - authors: [ - "Low, J.S.", - "Jerak, J.", - "Tortorici, M.A.", - "McCallum, M.", - "Pinto, D.", - "Cassotta, A.", - "Foglierini, M.", - "Mele, F.", - "Abdelnabi, R.", - "Weynand, B.", - "Noack, J.", - "Montiel-Ruiz, M.", - "Bianchi, S.", - "Benigni, F.", - "Sprugasci, N.", - "Joshi, A.", - "Bowen, J.E.", - "Stewart, C.", - "Rexhepaj, M.", - "Walls, A.C.", - "Jarrossay, D.", - "Morone, D.", - "Paparoditis, P.", - "Garzoni, C.", - "Ferrari, P.", - "Ceschi, A.", - "Neyts, J.", - "Purcell, L.A.", - "Snell, G.", - "Corti, D.", - "Lanzavecchia, A.", - "Veesler, D.", - "Sallusto, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7u0e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7u0e", - }, - }, - { - title: - "Fab arms of antibodies GAR03 and 10G4 bound to the receptor binding domain of SARS-CoV-2 in a 1:1:1 complex.", - emdb: null, - pdb: { - dbId: "8DXU", - method: "X-RAY DIFFRACTION", - keywords: - "anti-CoV-2, antibodies, convalescent patients, receptor binding domain., ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DXU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dxu_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dxu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of Fab arm of antibody 10G4", - details: "Heavy chain of Fab arm of antibody 10G4", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of Fab arm of antibody 10G4", - details: "Light chain of Fab arm of antibody 10G4", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of Fab arm of antibody GAR03", - details: "Heavy chain of Fab arm of antibody GAR03", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of Fab arm of antibody GAR03", - details: "Light chain of Fab arm of antibody GAR03", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: ["Langley, D.B.", "Christ, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36755042", - title: - "Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients.", - journal: "Nat Commun 14: 687-687 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-36295-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36755042", - pubDate: "2023", - abstract: "", - authors: [ - "Rouet, R.", - "Henry, J.Y. (0000-0003-0435-3308)", - "Johansen, M.D. (0000-0001-5553-5270)", - "Sobti, M.", - "Balachandran, H.", - "Langley, D.B.", - "Walker, G.J.", - "Lenthall, H.", - "Jackson, J.", - "Ubiparipovic, S.", - "Mazigi, O.", - "Schofield, P.", - "Burnett, D.L. (0000-0002-5642-3315)", - "Brown, S.H.J. (0000-0003-3997-4614)", - "Martinello, M.", - "Hudson, B.", - "Gilroy, N.", - "Post, J.J. (0000-0003-1475-9272)", - "Kelleher, A. (0000-0002-0009-3337)", - "Jack, H.M.", - "Goodnow, C.C. (0000-0001-5296-6155)", - "Turville, S.G. (0000-0003-1918-5343)", - "Rawlinson, W.D. (0000-0003-0988-7827)", - "Bull, R.A. (0000-0002-9844-3744)", - "Stewart, A.G. (0000-0002-2070-6030)", - "Hansbro, P.M.", - "Christ, D. 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(0000-0002-1551-0359)", - "Zarganes-Tzitzikas, T.", - "Bennett, J.", - "De Cesco, S. (0000-0003-4443-4217)", - "Fearon, D. (0000-0003-3529-7863)", - "von Delft, F. (0000-0003-0378-0017)", - "Fedorov, O.", - "Brennan, P.E.", - "Ahel, I.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8c1a_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8c1a", - }, - }, - { - title: - "SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01", - emdb: null, - pdb: { - dbId: "7UR1", - method: "X-RAY DIFFRACTION", - keywords: - "human leukocyte antigen, major histocompatibility complex, HLA-A2, HLA-A*02:01, SARS-CoV-2, Spike, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7UR1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ur1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ur1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q53Z42", - organism: "9606", - name: "HLA class I antigen", - details: "", - altNames: - "HLA class I histocompatibility antigen,HLA class I histocompatibility antigen A alpha chain,A alpha chain,MHC class I antigen,MHC class I protein,MHC class I protein (HLA-A)", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Szeto, C. (0000-0003-3784-5210)", - "Gras, S. (0000-0001-7416-038X)", - "Ahn, Y.M. (0000-0002-9008-9867)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Szeto, C. (0000-0003-3784-5210)", - "Ahn, Y.M. (0000-0002-9008-9867)", - "Gras, S. (0000-0001-7416-038X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ur1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ur1", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 refolded dimeric ORF9b", - emdb: null, - pdb: { - dbId: "7YE8", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, ORF9b, immune escape, viral antagonist, membrane association, fold switch, lipid binding, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7YE8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ye8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ye8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD2", - organism: "2697049", - name: "ORF9b protein", - details: "", - altNames: "ORF9b,Accessory protein 9b,ORF-9b,Protein 9b", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["TVMXDCGIABBOFY-UHFFFAOYSA-N"], - dbauthors: ["Qi, J.", "Chai, Y.", "Gao, G.F.", "Song, H.", "Jin, X."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36184694", - title: - "Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism.", - journal: "Sci China Life Sci 66: 152-164 (2023), 1869-1889", - doi: "https://doi.org/10.1007/s11427-022-2168-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36184694", - pubDate: "2023", - abstract: "", - authors: [ - "Jin, X.", - "Sun, X.", - "Chai, Y.", - "Bai, Y.", - "Li, Y.", - "Hao, T.", - "Qi, J.", - "Song, H.", - "Wong, C.C.L.", - "Gao, G.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ye8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ye8", - }, - }, - { - title: - "Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain", - emdb: null, - pdb: { - dbId: "8SMT", - method: "X-RAY DIFFRACTION", - keywords: - "viral protein, antibody, sars-cov-2, immune system, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8SMT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8smt_final.pdb", - externalLink: "https://pdb-redo.eu/db/8smt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2134 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2134 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Sankhala, R.S.", "Jensen, J.L.", "Joyce, M.G."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Sankhala, R.S.", "Jensen, J.L.", "Joyce, M.G."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8smt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8smt", - }, - }, - { - title: - "Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates", - emdb: null, - pdb: { - dbId: "8DMN", - method: "X-RAY DIFFRACTION", - keywords: - "viral protein, HYDROLASE-HYDROLASE INHIBITOR complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DMN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dmn_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dmn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lu, J. (0000-0002-4090-5176)", - "Khan, M.B. (0000-0002-4164-9573)", - "Young, H.S. (0000-0002-5990-8422)", - "Lemieux, M.J. (0000-0003-4745-9153)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Mpro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals", - journal: "Acs Cent.Sci. 9: 696-708 (2023), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.3c00054", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, S.A.", - "Arutyunova, E.", - "Lu, J.", - "Khan, M.B.", - "Rut, W.", - "Zmudzinski, M.", - "Shahbaz, S.", - "Iyyathurai, J.", - "Moussa, E.W.", - "Turner, Z.", - "Bai, B.", - "Lamer, T.", - "Nieman, J.A.", - "Vederas, J.C.", - "Julien, O.", - "Drag, M.", - "Elahi, S.", - "Young, H.S.", - "Lemieux, M.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dmn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dmn", - }, - }, - { - title: "Crystal structure of SARS-Cov-2 main protease in complex with S217622", - emdb: null, - pdb: { - dbId: "8HUR", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8HUR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hur_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hur", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QMPBBNUOBOFBFS-UHFFFAOYSA-N"], - dbauthors: ["Zhang, J.", "Li, J.", "Zhou, X.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 main protease in complex with S217622", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zhou, X.L.", "Zhang, J.", "Li, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hur_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hur", - }, - }, - { - title: - "Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (1.58 angstrom resolution)", - emdb: null, - pdb: { - dbId: "8HBL", - method: "X-RAY DIFFRACTION", - keywords: "NSP3, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8HBL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hbl_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hbl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "HBBGRARXTFLTSG-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: ["Li, Z.", "Qin, B.", "Aumonier, S.", "Wang, M.", "Cui, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Structure of a coronavirus G4-binding protein", - journal: "Nat Commun 2023, 2041-1723", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Qin, B.", - "Li, Z.", - "Aumonier, S.", - "Wang, M.", - "Cui, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hbl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hbl", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main protease mutant M49I in complex with Ensitrelvir", - emdb: null, - pdb: { - dbId: "8DZ1", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, 3cl, covid, sars-cov-2 ensitrelvir, nirmatrelvir, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DZ1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dz1_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dz1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "QMPBBNUOBOFBFS-UHFFFAOYSA-N"], - dbauthors: ["Noske, G.D.", "Oliva, G.", "Godoy, A.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36775130", - title: - "Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.", - journal: "J.Biol.Chem. 299: 103004-103004 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36775130", - pubDate: "2023", - abstract: "", - authors: [ - "Noske, G.D.", - "de Souza Silva, E.", - "de Godoy, M.O.", - "Dolci, I.", - "Fernandes, R.S.", - "Guido, R.V.C.", - "Sjo, P.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dz1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dz1", - }, - }, - { - title: "Reduced form of SARS-CoV-2 Main Protease determined by XFEL radiation", - emdb: null, - pdb: { - dbId: "7PXZ", - method: "X-RAY DIFFRACTION", - keywords: - "3C-like protease, Main-Protease, Viral replication, Polyprotein maturation, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7PXZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7pxz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7pxz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Kim, Y.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Murillo, G.E.P.", - "Kim, C.", - "Bean, R.", - "Turk, D.", - "Hinrichs, W.", - "Middendorf, P.", - "Round, A.", - "Schmidt, C.", - "Mills, G.", - "Kirkwood, H.", - "Han, H.", - "Koliyadu, J.", - "Bielecki, J.", - "Gelisio, L.", - "Sikorski, M.", - "Kloos, M.", - "Vakilii, M.", - "Yefanov, O.N.", - "Vagovic, P.", - "de-Wijn, R.", - "Letrun, R.", - "Guenther, S.", - "White, T.A.", - "Sato, T.", - "Srinivasan, V.", - "Chretien, A.", - "Han, S.", - "Brognaro, H.", - "Maracke, J.", - "Knoska, J.", - "Seychell, B.C.", - "Brings, L.", - "Norton-Baker, B.", - "Geng, T.", - "Dore, A.S.", - "Uetrecht, C.", - "Redecke, L.", - "Lorenzen, K.", - "Betzel, C.", - "Mancuso, A.P.", - "Bajt, S.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Reduced form of SARS-CoV-2 Main Protease determined by XFEL radiation", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Murillo, G.", - "Kim, C.", - "Bean, R.", - "Turk, D.", - "Hinrichs, W.", - "Middendorf, P.", - "Round, A.", - "Schmidt, C.", - "Mills, G.", - "Kirkwood, H.", - "Han, H.", - "Koliyadu, J.", - "Bielecki, J.", - "Gelisio, L.", - "Sikorski, M.", - "Kloos, M.", - "Vakilii, M.", - "Yefanov, O.", - "Vagovic, P.", - "de-Wijn, R.", - "Letrun, R.", - "Guenther, S.", - "White, T.", - "Sato, T.", - "Srinivasan, V.", - "Kim, Y.", - "Chretien, A.", - "Han, S.", - "Brognaro, H.", - "Maracke, J.", - "Knoska, J.", - "Seychell, B.", - "Brings, L.", - "Norton-Baker, B.", - "Geng, T.", - "Dore, A.", - "Uetrecht, C.", - "Redecke, L.", - "Beck, T.", - "Lorenzen, K.", - "Betzel, C.", - "Mancuso, A.", - "Bajt, S.", - "Chapman, H.", - "Meents, A.", - "Lane, T.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7pxz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7pxz", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2890189003", - emdb: null, - pdb: { - dbId: "7FR5", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FR5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fr5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fr5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JAOVHLJGWXTEMD-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fr5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fr5", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with PTERA_A05 - (R) isomer", - emdb: null, - pdb: { - dbId: "7FRC", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FRC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7frc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7frc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["HCXYCGJASBHJRP-CQSZACIVSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7frc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7frc", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM145", - emdb: null, - pdb: { - dbId: "7MB3", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MB3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mb3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mb3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DFVBMNVNJFHZTI-KJHMZRPRSA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM145", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mb3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mb3", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BQ.1.1 variant spike protein in complex with its receptor ACE2", - emdb: null, - pdb: { - dbId: "8IF2", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Spike protein, RBD, ACE2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8IF2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8if2_final.pdb", - externalLink: "https://pdb-redo.eu/db/8if2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Processed angiotensin-converting enzyme 2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Hashiguchi, T.", "Suzuki, T.", "Kimura, K."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37169744", - title: - "Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.", - journal: "Nat Commun 14: 2671-2671 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-38188-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37169744", - pubDate: "2023", - abstract: "", - authors: [ - "Ito, J.", - "Suzuki, R.", - "Uriu, K.", - "Itakura, Y.", - "Zahradnik, J.", - "Kimura, K.T.", - "Deguchi, S.", - "Wang, L.", - "Lytras, S.", - "Tamura, T.", - "Kida, I.", - "Nasser, H.", - "Shofa, M.", - "Begum, M.M.", - "Tsuda, M.", - "Oda, Y.", - "Suzuki, T.", - "Sasaki, J.", - "Sasaki-Tabata, K.", - "Fujita, S.", - "Yoshimatsu, K.", - "Ito, H.", - "Nao, N.", - "Asakura, H.", - "Nagashima, M.", - "Sadamasu, K.", - "Yoshimura, K.", - "Yamamoto, Y.", - "Nagamoto, T.", - "Kuramochi, J.", - "Schreiber, G.", - "Saito, A.", - "Matsuno, K.", - "Takayama, K.", - "Hashiguchi, T.", - "Tanaka, S.", - "Fukuhara, T.", - "Ikeda, T.", - "Sato, K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8if2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8if2", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with ML104", - emdb: null, - pdb: { - dbId: "7SFI", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, SARS-CoV-2, coronavirus, Main Protease, Protease, Mpro, 3C-like proteinase, CL3pro, Inhibitor, Complex, Covalent, Adduct, ML104, Ketoamide, Peptidomimetic, Viral Protein", - refModels: [ - { - emdbId: null, - pdbId: "7SFI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sfi_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sfi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "YNUIIZLFVOREIR-NZIQIWATSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "BHPQYMZQTOCNFJ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fernandez, D. (0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sfi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sfi", - }, - }, - { - title: - "Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304", - emdb: null, - pdb: { - dbId: "8GFK", - method: "X-RAY DIFFRACTION", - keywords: "viral cysteine protease, inactive C145A mutant, homodimer, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8GFK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gfk_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gfk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Coates, L.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37271339", - title: - "Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.", - journal: "J.Biol.Chem. 299: 104886-104886 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.104886", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37271339", - pubDate: "2023", - abstract: "", - authors: [ - "Kovalevsky, A.", - "Aniana, A.", - "Coates, L.", - "Bonnesen, P.V.", - "Nashed, N.T.", - "Louis, J.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gfk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gfk", - }, - }, - { - title: "A human neutralizing antibody targeting SARS-CoV-2 RBD", - emdb: null, - pdb: { - dbId: "7VZT", - method: "X-RAY DIFFRACTION", - keywords: - "antibody, antigen, glycosylation, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7VZT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vzt_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vzt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "GH12-Heavy", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "GH12-LIGHT", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wang, F.Z. (0000-0002-8347-8004)", - "Wang, Y. (0000-0001-6946-2666)", - "Tan, X.W.", - "Shi, R.", - "Yan, J.H.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Eukaryota sp.", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "GH12, glycosylation function", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Wang, F.Z.", "Tan, X.W.", "Shi, R."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vzt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vzt", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with adenosine", - emdb: null, - pdb: { - dbId: "8BZV", - method: "X-RAY DIFFRACTION", - keywords: "Methyltransferase, Complex, Inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8BZV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8bzv_final.pdb", - externalLink: "https://pdb-redo.eu/db/8bzv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OIRDTQYFTABQOQ-KQYNXXCUSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - "Kiene, A.", - "Galchenkova, M. (0000-0001-8676-0091)", - "Garcia, Y. (0000-0002-9592-2141)", - "Ehr, C. (0000-0003-1428-0042)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8bzv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8bzv", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI49", - emdb: null, - pdb: { - dbId: "7SDA", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7SDA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sda_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sda", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["TTZNYKDOBZQMLD-DOXZYTNZSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure of the SARS-CoV-2 main protease in complex with inhibitors", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Yang, K.S.", - "Liu, W.R.", - "Sankaran, B.", - "Blankenship, L.B. (0000-0002-1714-4399)", - "Liu, W.R. (0000-0002-7078-6534)", - "Blankenship, L.B.", - "Kang, Y.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sda_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sda", - }, - }, - { - title: "SARS-CoV-2-Beta-RBD and BD-236-GWP/P-VK antibody complex", - emdb: null, - pdb: { - dbId: "7X63", - method: "X-RAY DIFFRACTION", - keywords: "COVID-19, antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7X63", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x63_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x63", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "BD-236 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-236 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wang, Y.", - "Wu, Z.", - "Shi, R.", - "Han, X. (0000-0003-4751-1740)", - "Yan, J. (0000-0001-7140-5548)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2-Beta-RBD and BD-236-GWP/P-VK antibody complex", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Shi, R.", - "Wang, Y.", - "Wu, Z.", - "Han, X. (0000-0003-4751-1740)", - "Yan, J. (0000-0001-7140-5548)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x63_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x63", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 nucleocapsid N-terminal domain (NTD) protein,pH8.0", - emdb: null, - pdb: { - dbId: "7VBD", - method: "X-RAY DIFFRACTION", - keywords: "SARS-Cov-2, nucleocapsid, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VBD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vbd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vbd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, J.", "Li, J.", "Zhou, X.L.", "Zeng, P.", "Zhong, F.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 nucleocapsid N-terminal domain (NTD) protein,pH8.0", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Zeng, P.", - "Zhou, X.L.", - "Zhong, F.L.", - "Li, J.", - "Zhang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vbd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vbd", - }, - }, - { - title: - "Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (1.35 angstrom resolution)", - emdb: null, - pdb: { - dbId: "8GQC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, NSP3, SUD domain, G4-binding, virus replication, drug target, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8GQC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gqc_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gqc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Li, Z.", "Qin, B.", "Aumonier, S.", "Wang, M.", "Cui, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Structure of a coronavirus G4-binding protein", - journal: "Nat Commun 2023, 2041-1723", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Qin, B.", - "Li, Z.", - "Aumonier, S.", - "Wang, M.", - "Cui, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gqc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gqc", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with ML102", - emdb: null, - pdb: { - dbId: "7SFH", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, SARS-CoV-2, coronavirus, Main Protease, Protease, Mpro, 3C-like proteinase, CL3pro, Inhibitor, Complex, Covalent, Adduct, ML102, Ketoamide, Peptidomimetic, Viral Protein", - refModels: [ - { - emdbId: null, - pdbId: "7SFH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sfh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sfh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RGRBMZCTKPAORA-RZCQQDKOSA-N", "BHPQYMZQTOCNFJ-UHFFFAOYSA-N"], - dbauthors: [ - "Fernandez, D. (0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sfh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sfh", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5551426009 - (S) isomer", - emdb: null, - pdb: { - dbId: "7FRB", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FRB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7frb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7frb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RZITUVZKCFWKQP-LLVKDONJSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7frb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7frb", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144", - emdb: null, - pdb: { - dbId: "7MB2", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MB2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mb2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mb2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AMUUPQIKCDYOIG-XQVPNCLKSA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mb2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mb2", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with PTERA_A26A - (S) isomer", - emdb: null, - pdb: { - dbId: "7FR4", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FR4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fr4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fr4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "DESZZRQUGKNYDX-ZDUSSCGKSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fr4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fr4", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Main protease in complex with Ensitrelvir", - emdb: null, - pdb: { - dbId: "8DZ0", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, 3cl, covid, sars-cov-2 ensitrelvir, nirmatrelvir, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DZ0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dz0_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dz0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "QMPBBNUOBOFBFS-UHFFFAOYSA-N"], - dbauthors: ["Noske, G.D.", "Oliva, G.", "Godoy, A.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36775130", - title: - "Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.", - journal: "J.Biol.Chem. 299: 103004-103004 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36775130", - pubDate: "2023", - abstract: "", - authors: [ - "Noske, G.D.", - "de Souza Silva, E.", - "de Godoy, M.O.", - "Dolci, I.", - "Fernandes, R.S.", - "Guido, R.V.C.", - "Sjo, P.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dz0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dz0", - }, - }, - { - title: - "Crystal structure of neutralizing antibody P1D9 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)", - emdb: null, - pdb: { - dbId: "8DWA", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, Viral protein, Spike glycoprotein, Receptor Binding Protein, RBD, Neutralizing antibody, 10-28, Fab, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8DWA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dwa_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dwa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P1D9 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P1D9 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Reddem, E.R. (0000-0003-3054-5506)", - "Shapiro, L. (0000-0001-9943-8819)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36354024", - title: - "Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2.", - journal: - "Emerg Microbes Infect 12: 2146538-2146538 (2023), 2222-1751", - doi: "https://doi.org/10.1080/22221751.2022.2146538", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36354024", - pubDate: "2023", - abstract: "", - authors: [ - "Luo, M.", - "Zhou, B.", - "Reddem, E.R.", - "Tang, B.", - "Chen, B.", - "Zhou, R.", - "Liu, H.", - "Liu, L.", - "Katsamba, P.S.", - "Au, K.K.", - "Man, H.O.", - "To, K.K.", - "Yuen, K.Y.", - "Shapiro, L.", - "Dang, S.", - "Ho, D.D.", - "Chen, Z.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dwa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dwa", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10-90-3-C1", - emdb: null, - pdb: { - dbId: "8D4P", - method: "X-RAY DIFFRACTION", - keywords: - "Inhibitor, protease, SARS-CoV-2, MPro, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8D4P", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8d4p_final.pdb", - externalLink: "https://pdb-redo.eu/db/8d4p", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "QPUDXWFOZNQTRA-HXUWFJFHSA-N"], - dbauthors: ["Wang, J.", "Chen, Y.", "Butler, S.G."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10-90-3-C1", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Butler, S.G.", "Chen, Y.", "Wang, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8d4p_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8d4p", - }, - }, - { - title: "Crystal structure of S43 bound to SARS-CoV-2 RBD", - emdb: null, - pdb: { - dbId: "7WD2", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, RBD, S43, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WD2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wd2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wd2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "Anti-RON nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Wang, Q.H.", - "Qi, J.X.", - "Gao, G.F.", - "Su, C.", - "Liu, H.H.", - "Wu, L.L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36702124", - title: - "Two pan-SARS-CoV-2 nanobodies and their multivalent derivatives effectively prevent Omicron infections in mice.", - journal: "Cell Rep Med 4: 100918-100918 (2023), 2666-3791", - doi: "https://doi.org/10.1016/j.xcrm.2023.100918", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36702124", - pubDate: "2023", - abstract: "", - authors: [ - "Liu, H.", - "Wu, L.", - "Liu, B.", - "Xu, K.", - "Lei, W.", - "Deng, J.", - "Rong, X.", - "Du, P.", - "Wang, L.", - "Wang, D.", - "Zhang, X.", - "Su, C.", - "Bi, Y.", - "Chen, H.", - "Liu, W.J.", - "Qi, J.", - "Cui, Q.", - "Qi, S.", - "Fan, R.", - "Jiang, J.", - "Wu, G.", - "Gao, G.F.", - "Wang, Q.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wd2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wd2", - }, - }, - { - title: "SARS-CoV-2 specific T cell receptor", - emdb: null, - pdb: { - dbId: "8DNT", - method: "X-RAY DIFFRACTION", - keywords: "TCR complex, MHC, HLA, SARS-CoV-2, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8DNT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dnt_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dnt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "T-cell receptor alpha chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "T-cell receptor beta chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "C6ZK69", - organism: "9685", - name: "MHC class I antigen alpha chain", - details: "", - altNames: "FLA class I histocompatibility antigen, alpha chain", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wu, D.", - "Pierce, B.G.", - "Mariuzza, R.A.", - "Gallagher, D.T.", - "Gowthaman, R.", - "Weng, N.P.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2 specific T cell receptor", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Wu, D.", - "Gallagher, D.T.", - "Gowthaman, R.", - "Pierce, B.G.", - "Mariuzza, R.A.", - "Weng, N.P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dnt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dnt", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV91-27", - emdb: null, - pdb: { - dbId: "8D6Z", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, coronavirus, antibody, fusion peptide, neutralizing antibody, COVID-19, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8D6Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8d6z_final.pdb", - externalLink: "https://pdb-redo.eu/db/8d6z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Neutralizing antibody COV91-27 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Neutralizing antibody COV91-27 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2 fusion peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wilson, I.A. (0000-0002-6469-2419)", - "Yuan, M. (0000-0001-9754-4503)", - "Lee, C.C.D. (0000-0002-5470-2484)", - "Lin, T.H. (0000-0002-0937-9972)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Mus musculus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35857439", - title: - "Broadly neutralizing antibodies target the coronavirus fusion peptide.", - journal: "Science 377: 728-735 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abq3773", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35857439", - pubDate: "2022", - abstract: "", - authors: [ - "Dacon, C.", - "Tucker, C.", - "Peng, L.", - "Lee, C.D.", - "Lin, T.H.", - "Yuan, M.", - "Cong, Y.", - "Wang, L.", - "Purser, L.", - "Williams, J.K.", - "Pyo, C.W.", - "Kosik, I.", - "Hu, Z.", - "Zhao, M.", - "Mohan, D.", - "Cooper, A.J.R.", - "Peterson, M.", - "Skinner, J.", - "Dixit, S.", - "Kollins, E.", - "Huzella, L.", - "Perry, D.", - "Byrum, R.", - "Lembirik, S.", - "Drawbaugh, D.", - "Eaton, B.", - "Zhang, Y.", - "Yang, E.S.", - "Chen, M.", - "Leung, K.", - "Weinberg, R.S.", - "Pegu, A.", - "Geraghty, D.E.", - "Davidson, E.", - "Douagi, I.", - "Moir, S.", - "Yewdell, J.W.", - "Schmaljohn, C.", - "Crompton, P.D.", - "Holbrook, M.R.", - "Nemazee, D.", - "Mascola, J.R.", - "Wilson, I.A.", - "Tan, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8d6z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8d6z", - }, - }, - { - title: - "SARS-CoV-2 NSP3 macrodomain in complex with 1-methyl-4-[5-(morpholin-4-ylcarbonyl)-2-furyl]-1H-pyrrolo[2,3-b]pyridine", - emdb: null, - pdb: { - dbId: "8C19", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, viral protein", - refModels: [ - { - emdbId: null, - pdbId: "8C19", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8c19_final.pdb", - externalLink: "https://pdb-redo.eu/db/8c19", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", "GADYVYMUQFVEQZ-UHFFFAOYSA-N"], - dbauthors: ["Schuller, M.", "Ahel, I."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36839595", - title: - "Discovery and Development Strategies for SARS-CoV-2 NSP3 Macrodomain Inhibitors.", - journal: "Pathogens 12 (2023), 2076-0817", - doi: "https://doi.org/10.3390/pathogens12020324", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36839595", - pubDate: "2023", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Zarganes-Tzitzikas, T.", - "Bennett, J.", - "De Cesco, S. (0000-0003-4443-4217)", - "Fearon, D. (0000-0003-3529-7863)", - "von Delft, F. (0000-0003-0378-0017)", - "Fedorov, O.", - "Brennan, P.E.", - "Ahel, I.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8c19_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8c19", - }, - }, - { - title: - "Room-temperature X-ray structure of SARS-CoV-2 main protease in complex with GC-376", - emdb: null, - pdb: { - dbId: "7UKK", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, catalytic domain, viral enzyme, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7UKK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ukk_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ukk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36114420", - title: - "Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain.", - journal: "Commun Biol 5: 976-976 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03910-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36114420", - pubDate: "2022", - abstract: "", - authors: [ - "Nashed, N.T.", - "Kneller, D.W.", - "Coates, L. (0000-0003-2342-049X)", - "Ghirlando, R. (0000-0003-4880-4959)", - "Aniana, A.", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Louis, J.M. (0000-0002-0052-1899)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ukk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ukk", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV89-22", - emdb: null, - pdb: { - dbId: "8DTX", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, coronavirus, antibody, stem helix, neutralizing antibody, COVID-19, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8DTX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dtx_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dtx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "COV89-22 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COV89-22 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2' stem helix peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wilson, I.A. (0000-0002-6469-2419)", - "Lee, C.C.D. (0000-0002-5470-2484)", - "Lin, T.H. (0000-0002-0937-9972)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Mus musculus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36347257", - title: - "Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses.", - journal: "Cell Host Microbe 31 (2023), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2022.10.010", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36347257", - pubDate: "2023", - abstract: "", - authors: [ - "Dacon, C.", - "Peng, L.", - "Lin, T.H.", - "Tucker, C.", - "Lee, C.D.", - "Cong, Y.", - "Wang, L.", - "Purser, L.", - "Cooper, A.J.R.", - "Williams, J.K.", - "Pyo, C.W.", - "Yuan, M.", - "Kosik, I.", - "Hu, Z.", - "Zhao, M.", - "Mohan, D.", - "Peterson, M.", - "Skinner, J.", - "Dixit, S.", - "Kollins, E.", - "Huzella, L.", - "Perry, D.", - "Byrum, R.", - "Lembirik, S.", - "Murphy, M.", - "Zhang, Y.", - "Yang, E.S.", - "Chen, M.", - "Leung, K.", - "Weinberg, R.S.", - "Pegu, A.", - "Geraghty, D.E.", - "Davidson, E.", - "Doranz, B.J.", - "Douagi, I.", - "Moir, S.", - "Yewdell, J.W.", - "Schmaljohn, C.", - "Crompton, P.D.", - "Mascola, J.R.", - "Holbrook, M.R.", - "Nemazee, D.", - "Wilson, I.A.", - "Tan, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dtx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dtx", - }, - }, - { - title: - "Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-199)", - emdb: null, - pdb: { - dbId: "7UJ9", - method: "X-RAY DIFFRACTION", - keywords: "cysteine protease, catalytic domain, viral enzyme, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7UJ9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uj9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uj9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36114420", - title: - "Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain.", - journal: "Commun Biol 5: 976-976 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03910-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36114420", - pubDate: "2022", - abstract: "", - authors: [ - "Nashed, N.T.", - "Kneller, D.W.", - "Coates, L. (0000-0003-2342-049X)", - "Ghirlando, R. (0000-0003-4880-4959)", - "Aniana, A.", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Louis, J.M. (0000-0002-0052-1899)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uj9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uj9", - }, - }, - { - title: - "Crystal structure of chimeric omicron RBD (strain BA.2) complexed with chimeric mouse ACE2", - emdb: null, - pdb: { - dbId: "7UFL", - method: "X-RAY DIFFRACTION", - keywords: "RBD, ACE2, VIRAL PROTEIN-HYDROLASE complex", - refModels: [ - { - emdbId: null, - pdbId: "7UFL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ufl_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ufl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, W.", - "Shi, K. (0000-0003-4175-3714)", - "Geng, Q.", - "Ye, G.", - "Aihara, H. (0000-0001-7508-6230)", - "Li, F. (0000-0002-1958-366X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36256797", - title: - "Structural basis for mouse receptor recognition by SARS-CoV-2 omicron variant.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2206509119-e2206509119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2206509119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36256797", - pubDate: "2022", - abstract: "", - authors: [ - "Zhang, W. (0000-0003-3938-1245)", - "Shi, K. (0000-0003-4175-3714)", - "Geng, Q. (0000-0003-4872-2400)", - "Ye, G. (0000-0001-6034-2174)", - "Aihara, H. (0000-0001-7508-6230)", - "Li, F. (0000-0002-1958-366X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ufl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ufl", - }, - }, - { - title: "Oxidized form of SARS-CoV-2 Main Protease determined by XFEL radiation", - emdb: null, - pdb: { - dbId: "7PZQ", - method: "X-RAY DIFFRACTION", - keywords: - "3C-like protease, Main-Protease, Viral replication, Polyprotein maturation, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7PZQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7pzq_final.pdb", - externalLink: "https://pdb-redo.eu/db/7pzq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Murillo, G.E.P.", - "Kim, C.", - "Bean, R.", - "Turk, D.", - "Hinrichs, W.", - "Middendorf, P.", - "Round, A.", - "Schmidt, C.", - "Mills, G.", - "Kirkwood, H.", - "Han, H.", - "Koliyadu, J.", - "Bielecki, J.", - "Gelisio, L.", - "Sikorski, M.", - "Kloos, M.", - "Vakilii, M.", - "Yefanov, O.N.", - "Vagovic, P.", - "de-Wijn, R.", - "Letrun, R.", - "Guenther, S.", - "White, T.A.", - "Sato, T.", - "Srinivasan, V.", - "Chretien, A.", - "Han, S.", - "Brognaro, H.", - "Maracke, J.", - "Knoska, J.", - "Seychell, B.C.", - "Brings, L.", - "Norton-Baker, B.", - "Geng, T.", - "Dore, A.S.", - "Uetrecht, C.", - "Redecke, L.", - "Lorenzen, K.", - "Betzel, C.", - "Mancuso, A.P.", - "Bajt, S.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Oxidized form of SARS-CoV-2 Main Protease determined by XFEL radiation", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Murillo, G.E.P.", - "Kim, C.", - "Bean, R.", - "Turk, D.", - "Hinrichs, W.", - "Middendorf, P.", - "Round, A.", - "Schmidt, C.", - "Mills, G.", - "Kirkwood, H.", - "Han, H.", - "Koliyadu, J.", - "Bielecki, J.", - "Gelisio, L.", - "Sikorski, M.", - "Kloos, M.", - "Vakilii, M.", - "Yefanov, O.N.", - "Vagovic, P.", - "de-Wijn, R.", - "Letrun, R.", - "Guenther, S.", - "White, T.A.", - "Sato, T.", - "Srinivasan, V.", - "Kim, Y.", - "Chretien, A.", - "Han, S.", - "Brognaro, H.", - "Maracke, J.", - "Knoska, J.", - "Seychell, B.C.", - "Brings, L.", - "Norton-Baker, B.", - "Geng, T.", - "Dore, A.S.", - "Uetrecht, C.", - "Redecke, L.", - "Beck, T.", - "Lorenzen, K.", - "Betzel, C.", - "Mancuso, A.P.", - "Bajt, S.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7pzq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7pzq", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Main protease in complex with Nirmatrelvir", - emdb: null, - pdb: { - dbId: "8DZ2", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, 3cl, covid, sars-cov-2 ensitrelvir, nirmatrelvir, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DZ2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dz2_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dz2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Noske, G.D.", "Oliva, G.", "Godoy, A.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36775130", - title: - "Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.", - journal: "J.Biol.Chem. 299: 103004-103004 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36775130", - pubDate: "2023", - abstract: "", - authors: [ - "Noske, G.D.", - "de Souza Silva, E.", - "de Godoy, M.O.", - "Dolci, I.", - "Fernandes, R.S.", - "Guido, R.V.C.", - "Sjo, P.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dz2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dz2", - }, - }, - { - title: "SARS-CoV-2 Main Protease complexed with N-(pyridin-3-ylmethyl)thioformamide", - emdb: null, - pdb: { - dbId: "8AEB", - method: "X-RAY DIFFRACTION", - keywords: - "3C-like proteinase, cysteine protease, complex, inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8AEB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8aeb_final.pdb", - externalLink: "https://pdb-redo.eu/db/8aeb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "HIZAQBZIUYYGKR-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Hanoulle, X. (0000-0002-3755-2680)", - "Charton, J. (0000-0001-6895-276X)", - "Deprez, B. 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(0000-0002-1279-5432)", - "Li, X.M.", - "Li, Y.F. (0000-0002-7936-7555)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36317101", - title: - "Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.", - journal: "Sci Bull (Beijing) 67: 2327-2335 (2022), 2095-9273", - doi: "https://doi.org/10.1016/j.scib.2022.10.021", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36317101", - pubDate: "2022", - abstract: "", - authors: [ - "Luan, X.", - "Li, X.", - "Li, Y.", - "Su, G.", - "Yin, W.", - "Jiang, Y.", - "Xu, N.", - "Wang, F.", - "Cheng, W.", - "Jin, Y.", - "Zhang, L.", - "Xu, H.E.", - "Xue, Y.", - "Zhang, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xx1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xx1", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM141", - emdb: null, - pdb: { - dbId: "7MB0", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MB0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mb0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mb0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OCJALNNRTNBTPO-LIONHTAISA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM141", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mb0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mb0", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide", - emdb: null, - pdb: { - dbId: "7Z8O", - method: "X-RAY DIFFRACTION", - keywords: "sRBD, Stapled peptide, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7Z8O", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7z8o_final.pdb", - externalLink: "https://pdb-redo.eu/db/7z8o", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Stapled peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "", "RICRAVHJCLFPFF-UHFFFAOYSA-N"], - dbauthors: [ - "Brear, P. (0000-0002-4045-0474)", - "Chen, L. (0000-0003-1776-3146)", - "Gaynor, K. (0000-0003-0461-810X)", - "Harman, M. (0000-0002-3667-5929)", - "Dods, R. (0000-0003-4014-7499)", - "Hyvonen, M. (0000-0001-8683-4070)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37328472", - title: - "Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2.", - journal: "Nat Commun 14: 3583-3583 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-39158-1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37328472", - pubDate: "2023", - abstract: "", - authors: [ - "Gaynor, K.U. (0000-0003-0461-810X)", - "Vaysburd, M.", - "Harman, M.A.J. (0000-0002-3667-5929)", - "Albecka, A.", - "Jeffrey, P.", - "Beswick, P.", - "Papa, G. (0000-0002-5215-0014)", - "Chen, L. (0000-0003-1776-3146)", - "Mallery, D. (0000-0003-2713-5215)", - "McGuinness, B.", - "Van Rietschoten, K.", - "Stanway, S.", - "Brear, P. (0000-0002-4045-0474)", - "Lulla, A.", - "Ciazynska, K. (0000-0002-9899-2428)", - "Chang, V.T. (0000-0001-7047-9019)", - "Sharp, J. (0000-0001-8482-5736)", - "Neary, M.", - "Box, H.", - "Herriott, J.", - "Kijak, E.", - "Tatham, L.", - "Bentley, E.G.", - "Sharma, P.", - "Kirby, A.", - "Han, X.", - "Stewart, J.P. (0000-0002-8928-2037)", - "Owen, A. (0000-0002-9819-7651)", - "Briggs, J.A.G. (0000-0003-3990-6910)", - "Hyvonen, M. (0000-0001-8683-4070)", - "Skynner, M.J. (0000-0001-6586-9055)", - "James, L.C. (0000-0003-2131-0334)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z8o_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z8o", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 RBD in complex with aRBD5", - emdb: null, - pdb: { - dbId: "7VOA", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-ANTIVIRAL PROTEIN COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7VOA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7voa_final.pdb", - externalLink: "https://pdb-redo.eu/db/7voa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "30538", - name: "alpaca nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Ma, H. (0000-0002-4668-0107)", - "Zeng, W.H. (0000-0003-3853-3630)", - "Jin, T.C. (0000-0002-1395-188X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35906408", - title: - "Hetero-bivalent nanobodies provide broad-spectrum protection against SARS-CoV-2 variants of concern including Omicron.", - journal: "Cell Res. 32: 831-842 (2022), 1001-0602", - doi: "https://doi.org/10.1038/s41422-022-00700-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35906408", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, H.", - "Zhang, X.", - "Zheng, P.", - "Dube, P.H.", - "Zeng, W.", - "Chen, S.", - "Cheng, Q.", - "Yang, Y.", - "Wu, Y.", - "Zhou, J.", - "Hu, X.", - "Xiang, Y.", - "Zhang, H.", - "Chiu, S.", - "Jin, T.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7voa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7voa", - }, - }, - { - title: - "Crystal structure of 3C-like protease from SARS-CoV-2 in complex with covalent inhibitor", - emdb: null, - pdb: { - dbId: "7XAR", - method: "X-RAY DIFFRACTION", - keywords: - "3C-like proteinase, Main protease, SARS-CoV-2, Chlorofluoroacetamides, Targeted covalent inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7XAR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xar_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xar", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEQPNABPJHWNSG-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "MRCDFPNCOHGYQJ-GUYCJALGSA-N", - ], - dbauthors: [ - "Caaveiro, J.M.M.", - "Ochi, J.", - "Takahashi, D.", - "Ueda, T.", - "Ojida, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36229406", - title: - "Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease.", - journal: "J.Med.Chem. 65: 13852-13865 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c01081", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36229406", - pubDate: "2022", - abstract: "", - authors: [ - "Hirose, Y.", - "Shindo, N. (0000-0002-2374-9896)", - "Mori, M.", - "Onitsuka, S.", - "Isogai, H.", - "Hamada, R.", - "Hiramoto, T.", - "Ochi, J.", - "Takahashi, D.", - "Ueda, T.", - "Caaveiro, J.M.M. (0000-0001-5568-2369)", - "Yoshida, Y.", - "Ohdo, S.", - "Matsunaga, N.", - "Toba, S.", - "Sasaki, M.", - "Orba, Y.", - "Sawa, H.", - "Sato, A.", - "Kawanishi, E.", - "Ojida, A. (0000-0002-9440-8167)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xar_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xar", - }, - }, - { - title: "Crystal structure of SARS Cov-2 main protease in complex with an inhibitor 58", - emdb: null, - pdb: { - dbId: "7ZV8", - method: "X-RAY DIFFRACTION", - keywords: "SARS Cov-2, 3CL, main protease, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZV8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zv8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zv8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "inhibitor 58", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "WWZKQHOCKIZLMA-UHFFFAOYSA-N"], - dbauthors: [ - "Rahimova, R. (0000-0002-4992-842X)", - "Di Micco, S. (0000-0002-4688-1080)", - "Marquez, J.A. (0000-0002-3453-9261)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36332548", - title: - "Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARS-CoV-2.", - journal: "Eur.J.Med.Chem. 244: 114857-114857 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114857", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36332548", - pubDate: "2022", - abstract: "", - authors: [ - "Di Micco, S.", - "Rahimova, R.", - "Sala, M.", - "Scala, M.C.", - "Vivenzio, G.", - "Musella, S.", - "Andrei, G.", - "Remans, K.", - "Mammri, L.", - "Snoeck, R.", - "Bifulco, G.", - "Di Matteo, F.", - "Vestuto, V.", - "Campiglia, P.", - "Marquez, J.A.", - "Fasano, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zv8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zv8", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MI-09", - emdb: null, - pdb: { - dbId: "7SDC", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7SDC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sdc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sdc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OINAVIUBZFOBLX-VMBFOHBNSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure of the SARS-CoV-2 main protease in complex with inhibitors", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Yang, K.S.", - "Liu, W.R.", - "Sankaran, B.", - "Blankenship, L.B. 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(0000-0002-7078-6534)", - "Blankenship, L.B.", - "Kang, Y.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sdc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sdc", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143", - emdb: null, - pdb: { - dbId: "7MB1", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MB1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mb1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mb1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NURFMZSCLLICCV-QVQNZMNRSA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM143", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mb1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mb1", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z1343520564", - emdb: null, - pdb: { - dbId: "7FRA", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FRA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fra_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fra", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LLNQFWFHQRNMTN-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fra_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fra", - }, - }, - { - title: "SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented by HLA-A*02:01", - emdb: null, - pdb: { - dbId: "7SIS", - method: "X-RAY DIFFRACTION", - keywords: - "human leukocyte antigen, major histocompatibility complex, HLA-A2, HLA-A*02:01, SARS-CoV-2, Spike, VLNDILSRL, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7SIS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sis_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sis", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q861F7", - organism: "9606", - name: "HLA class I histocompatibility antigen, A-2 alpha chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2' peptide VLNDILSRL", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "WLZRMCYVCSSEQC-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: ["Szeto, C. (0000-0003-3784-5210)", "Gras, S. (0000-0001-7416-038X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented by HLA-A*02:01", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Szeto, C. (0000-0003-3784-5210)", - "Gras, S. (0000-0001-7416-038X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sis_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sis", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z431872694", - emdb: null, - pdb: { - dbId: "7FR7", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FR7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fr7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fr7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CEJLELZDXLZHDJ-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fr7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fr7", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79", - emdb: null, - pdb: { - dbId: "8DAO", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, coronavirus, antibody, fusion peptide, neutralizing antibody, COVID-19, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8DAO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dao_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dao", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "COV44-79 heavy chain variable domain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COV44-79 light chain variable domain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DOX5", - organism: "9606", - name: "COV44-79 heavy chain constant domain", - details: "", - altNames: - "Immunoglobulin gamma-1 heavy chain, Immunoglobulin gamma-1 heavy chain NIE", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P01834", - organism: "9606", - name: "COV44-79 light chain constant domain", - details: "", - altNames: - "Immunoglobulin kappa constant, Ig kappa chain C region,Ig kappa chain C region AG,Ig kappa chain C region CUM,Ig kappa chain C region EU,Ig kappa chain C region OU,Ig kappa chain C region ROY,Ig kappa chain C region TI", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2 fusion peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wilson, I.A. (0000-0002-6469-2419)", - "Yuan, M. (0000-0001-9754-4503)", - "Lee, C.C.D. (0000-0002-5470-2484)", - "Lin, T.H. (0000-0002-0937-9972)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Mus musculus", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35857439", - title: - "Broadly neutralizing antibodies target the coronavirus fusion peptide.", - journal: "Science 377: 728-735 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abq3773", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35857439", - pubDate: "2022", - abstract: "", - authors: [ - "Dacon, C.", - "Tucker, C.", - "Peng, L.", - "Lee, C.D.", - "Lin, T.H.", - "Yuan, M.", - "Cong, Y.", - "Wang, L.", - "Purser, L.", - "Williams, J.K.", - "Pyo, C.W.", - "Kosik, I.", - "Hu, Z.", - "Zhao, M.", - "Mohan, D.", - "Cooper, A.J.R.", - "Peterson, M.", - "Skinner, J.", - "Dixit, S.", - "Kollins, E.", - "Huzella, L.", - "Perry, D.", - "Byrum, R.", - "Lembirik, S.", - "Drawbaugh, D.", - "Eaton, B.", - "Zhang, Y.", - "Yang, E.S.", - "Chen, M.", - "Leung, K.", - "Weinberg, R.S.", - "Pegu, A.", - "Geraghty, D.E.", - "Davidson, E.", - "Douagi, I.", - "Moir, S.", - "Yewdell, J.W.", - "Schmaljohn, C.", - "Crompton, P.D.", - "Holbrook, M.R.", - "Nemazee, D.", - "Mascola, J.R.", - "Wilson, I.A.", - "Tan, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dao_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dao", - }, - }, - { - title: "Crystal structure of R14 bound to SARS-CoV-2 RBD", - emdb: null, - pdb: { - dbId: "7WD1", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, RBD, nanobody, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WD1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wd1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wd1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "R14", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wang, Q.H.", - "Qi, J.X.", - "Gao, G.F.", - "Su, C.", - "Liu, H.H.", - "Wu, L.L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36702124", - title: - "Two pan-SARS-CoV-2 nanobodies and their multivalent derivatives effectively prevent Omicron infections in mice.", - journal: "Cell Rep Med 4: 100918-100918 (2023), 2666-3791", - doi: "https://doi.org/10.1016/j.xcrm.2023.100918", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36702124", - pubDate: "2023", - abstract: "", - authors: [ - "Liu, H.", - "Wu, L.", - "Liu, B.", - "Xu, K.", - "Lei, W.", - "Deng, J.", - "Rong, X.", - "Du, P.", - "Wang, L.", - "Wang, D.", - "Zhang, X.", - "Su, C.", - "Bi, Y.", - "Chen, H.", - "Liu, W.J.", - "Qi, J.", - "Cui, Q.", - "Qi, S.", - "Fan, R.", - "Jiang, J.", - "Wu, G.", - "Gao, G.F.", - "Wang, Q.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wd1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wd1", - }, - }, - { - title: "Crystal structure of BD55-1403 and SARS-CoV-2 Omicron RBD", - emdb: null, - pdb: { - dbId: "7Y0C", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Omicron variants, antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7Y0C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7y0c_final.pdb", - externalLink: "https://pdb-redo.eu/db/7y0c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "BD55-1403 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD55-1403 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, Z. (0000-0002-5690-9796)", "Xiao, J. (0000-0003-1822-1701)"], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36493787", - title: - "Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents.", - journal: "Cell Rep 41: 111845-111845 (2022), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2022.111845", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36493787", - pubDate: "2022", - abstract: "", - authors: [ - "Cao, Y.", - "Jian, F.", - "Zhang, Z.", - "Yisimayi, A.", - "Hao, X.", - "Bao, L.", - "Yuan, F.", - "Yu, Y.", - "Du, S.", - "Wang, J.", - "Xiao, T.", - "Song, W.", - "Zhang, Y.", - "Liu, P.", - "An, R.", - "Wang, P.", - "Wang, Y.", - "Yang, S.", - "Niu, X.", - "Gu, Q.", - "Shao, F.", - "Hu, Y.", - "Yin, W.", - "Zheng, A.", - "Qin, C.", - "Jin, R.", - "Xiao, J.", - "Xie, X.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7y0c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7y0c", - }, - }, - { - title: - "NMR structure of a peptide deriving from SARS-CoV-2 Lineage B.1.1.7 S RBD 482-506 fragment in HFIP/H2O", - emdb: null, - pdb: { - dbId: "7P5Q", - method: "SOLUTION NMR", - keywords: - "SARS-CoV-2, mimicking peptides, Spike, Receptor Binding Domain, COVID-19, Lineage B.1.1.7, N501Y, ANTIVIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Santoro, A.", "Buonocore, M.", "Grimaldi, M.", "D'Ursi, A.M."], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "36406731", - title: - "Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site.", - journal: "Heliyon 8: e11568-e11568 (2022), 2405-8440", - doi: "https://doi.org/10.1016/j.heliyon.2022.e11568", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36406731", - pubDate: "2022", - abstract: "", - authors: [ - "Buonocore, M.", - "Santoro, A.", - "Grimaldi, M.", - "Covelli, V.", - "Firoznezhad, M.", - "Rodriquez, M.", - "Santin, M.", - "D'Ursi, A.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7p5q_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7p5q", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main protease A193T mutant in complex with Nirmatrelvir", - emdb: null, - pdb: { - dbId: "8DZA", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, 3cl, covid, sars-cov-2 ensitrelvir, nirmatrelvir, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DZA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dza_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dza", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Noske, G.D.", "Oliva, G.", "Godoy, A.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36775130", - title: - "Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.", - journal: "J.Biol.Chem. 299: 103004-103004 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36775130", - pubDate: "2023", - abstract: "", - authors: [ - "Noske, G.D.", - "de Souza Silva, E.", - "de Godoy, M.O.", - "Dolci, I.", - "Fernandes, R.S.", - "Guido, R.V.C.", - "Sjo, P.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dza_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dza", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl phenyl sulfane inhibitor", - emdb: null, - pdb: { - dbId: "8F44", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, HYDROLASE-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8F44", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8f44_final.pdb", - externalLink: "https://pdb-redo.eu/db/8f44", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "AGWHKDXHVADVIY-FUOQNJDISA-N", - "AGWHKDXHVADVIY-JLEJFLCFSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Lovell, S. (0000-0002-3215-4472)", - "Liu, L. (0000-0003-0514-281X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S. (0000-0002-8199-2376)", - "Cooper, A. (0000-0002-1893-4149)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8f44_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8f44", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with PTERA_A01A - (S) isomer", - emdb: null, - pdb: { - dbId: "7FR3", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FR3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fr3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fr3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YUSKQHZYIKIRME-AWEZNQCLSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fr3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fr3", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM137", - emdb: null, - pdb: { - dbId: "7MAX", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MAX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7max_final.pdb", - externalLink: "https://pdb-redo.eu/db/7max", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OAHGUBRTPCCHJJ-QVQNZMNRSA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM137", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7max_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7max", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 N-NTD and dsRNA complex", - emdb: null, - pdb: { - dbId: "7XWZ", - method: "X-RAY DIFFRACTION", - keywords: - "structural protein, drug target, VIRAL PROTEIN, VIRAL PROTEIN-DNA complex", - refModels: [ - { - emdbId: null, - pdbId: "7XWZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xwz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xwz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "RNA (5'-R(*CP*AP*CP*UP*GP*AP*C)-3')", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "RNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3')", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Luan, X.D. (0000-0002-1279-5432)", - "Li, X.M.", - "Li, Y.F. (0000-0002-7936-7555)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36317101", - title: - "Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.", - journal: "Sci Bull (Beijing) 67: 2327-2335 (2022), 2095-9273", - doi: "https://doi.org/10.1016/j.scib.2022.10.021", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36317101", - pubDate: "2022", - abstract: "", - authors: [ - "Luan, X.", - "Li, X.", - "Li, Y.", - "Su, G.", - "Yin, W.", - "Jiang, Y.", - "Xu, N.", - "Wang, F.", - "Cheng, W.", - "Jin, Y.", - "Zhang, L.", - "Xu, H.E.", - "Xue, Y.", - "Zhang, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xwz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xwz", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with ML1000", - emdb: null, - pdb: { - dbId: "7SET", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, SARS-CoV-2, coronavirus, Main Protease, Protease, Mpro, 3C-like proteinase, CL3pro, Inhibitor, Complex, Covalent, Adduct, ML1000, Ketoamide, Peptidomimetic, Viral Protein", - refModels: [ - { - emdbId: null, - pdbId: "7SET", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7set_final.pdb", - externalLink: "https://pdb-redo.eu/db/7set", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PGHPGMLPXLZINT-UHFFFAOYSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Fernandez, D. (0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Covalent adduct between Cys145 of the SARSCoV2 Main Protease and the ketoamide-based peptidomimetic ML1000", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7set_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7set", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 Beta RBD complexed with P36-5D2 Fab", - emdb: null, - pdb: { - dbId: "7FJC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 variant of concern, Beta, RBD, Neutralization antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FJC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fjc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fjc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "P36-5D2 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P36-5D2 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, L.Q.", "Wang, X.Q.", "Shan, S.S.", "Lan, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 Beta RBD complexed with P36-5D2 Fab", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zhang, L.Q.", "Wang, X.Q.", "Shan, S.S.", "Lan, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fjc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fjc", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease N142S mutant in complex with Nirmatrelvir", - emdb: null, - pdb: { - dbId: "8E26", - method: "X-RAY DIFFRACTION", - keywords: "Main Protease, SARS-CoV-2, Nirmatrelvir, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8E26", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e26_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e26", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Noske, G.D.", "Oliva, G.", "Godoy, A.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36775130", - title: - "Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.", - journal: "J.Biol.Chem. 299: 103004-103004 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36775130", - pubDate: "2023", - abstract: "", - authors: [ - "Noske, G.D.", - "de Souza Silva, E.", - "de Godoy, M.O.", - "Dolci, I.", - "Fernandes, R.S.", - "Guido, R.V.C.", - "Sjo, P.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e26_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e26", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobody VHH-12", - emdb: null, - pdb: { - dbId: "7Q3Q", - method: "X-RAY DIFFRACTION", - keywords: "Coronavirus, nanobody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7Q3Q", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7q3q_final.pdb", - externalLink: "https://pdb-redo.eu/db/7q3q", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "30538", - name: "VHH-12", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: ["Fernandez, I.", "Pederzoli, R.", "Rey, F.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Fernandez, I.", "Rey, F.A."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7q3q_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7q3q", - }, - }, - { - title: "Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SAM", - emdb: null, - pdb: { - dbId: "7TW7", - method: "X-RAY DIFFRACTION", - keywords: "N7-guanine methyl transferase, SARS-CoV-2, nsp14, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TW7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tw7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tw7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P41212", - organism: "2697049", - name: - "Transcription factor ETV6,Proofreading exoribonuclease nsp14 chimera", - details: - "Fusion protein containing TELSAM (uniprot P41212) and SARS-CoV-2 nsp14 N7-Methyl Transferase domain (P0DTD1)", - altNames: - "ETS translocation variant 6,ETS-related protein Tel1,Tel,ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "MEFKEPWMEQBLKI-AIRLBKTGSA-N"], - dbauthors: [ - "Kottur, J. (0000-0002-8075-3883)", - "Aggarwal, A.K. (0000-0003-4389-0173)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36075969", - title: - "High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development.", - journal: "Nat.Struct.Mol.Biol. 29: 850-853 (2022), 1545-9985", - doi: "https://doi.org/10.1038/s41594-022-00828-1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36075969", - pubDate: "2022", - abstract: "", - authors: [ - "Kottur, J.", - "Rechkoblit, O.", - "Quintana-Feliciano, R.", - "Sciaky, D.", - "Aggarwal, A.K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tw7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tw7", - }, - }, - { - title: "TRIM7 in complex with C-terminal peptide of NSP8", - emdb: null, - pdb: { - dbId: "7X70", - method: "X-RAY DIFFRACTION", - keywords: "ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7X70", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x70_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x70", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9C029", - organism: "9606", - name: "E3 ubiquitin-protein ligase TRIM7", - details: "", - altNames: - "Glycogenin-interacting protein,RING finger protein 90,Tripartite motif-containing protein 7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, H.", "Liang, X.", "Li, X.Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35982226", - title: - "A C-terminal glutamine recognition mechanism revealed by E3 ligase TRIM7 structures.", - journal: "Nat.Chem.Biol. 18: 1214-1223 (2022), 1552-4469", - doi: "https://doi.org/10.1038/s41589-022-01128-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35982226", - pubDate: "2022", - abstract: "", - authors: [ - "Liang, X.", - "Xiao, J.", - "Li, X.", - "Liu, Y.", - "Lu, Y.", - "Wen, Y.", - "Li, Z.", - "Che, X.", - "Ma, Y.", - "Zhang, X.", - "Zhang, Y.", - "Jian, D.", - "Wang, P.", - "Xuan, C.", - "Yu, G.", - "Li, L.", - "Zhang, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x70_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x70", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor-binding domain in complex with intermediate horseshoe bat ACE2", - emdb: null, - pdb: { - dbId: "7XA7", - method: "X-RAY DIFFRACTION", - keywords: "complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7XA7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xa7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xa7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "G1TEF4", - organism: "9986", - name: "Angiotensin-converting enzyme", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Han, P.", "Qi, J.X.", "Zhang, D.", "Tang, L.F."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35874946", - title: - "Structural basis of SARS-CoV-2 and its variants binding to intermediate horseshoe bat ACE2.", - journal: "Int J Biol Sci 18: 4658-4668 (2022), 1449-2288", - doi: "https://doi.org/10.7150/ijbs.73640", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35874946", - pubDate: "2022", - abstract: "", - authors: [ - "Tang, L.", - "Zhang, D.", - "Han, P.", - "Kang, X.", - "Zheng, A.", - "Xu, Z.", - "Zhao, X.", - "Wang, V.Y.", - "Qi, J.", - "Wang, Q.", - "Liu, K.", - "Gao, G.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xa7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xa7", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5551425673 - (S) isomer", - emdb: null, - pdb: { - dbId: "7FR2", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FR2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fr2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fr2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YUSKQHZYIKIRME-AWEZNQCLSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fr2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fr2", - }, - }, - { - title: "Crystal structure of SARS-Cov-2 main protease in complex with PF07304814", - emdb: null, - pdb: { - dbId: "7VVP", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7VVP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vvp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vvp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FQKALOFOWPDTED-WBAXXEDZSA-N"], - dbauthors: [ - "Zhang, J.", - "Li, J.", - "Zhou, X.L.", - "Zeng, P.", - "Zhong, F.L.", - "Lin, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814", - journal: "J.Mol.Biol. 434 (2022), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2022.167706", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Li, J.", - "Lin, C.", - "Zhou, X.", - "Zhong, F.", - "Zeng, P.", - "McCormick, P.J.", - "Jiang, H.", - "Zhang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vvp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vvp", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with PTERA_A25A - (S) isomer", - emdb: null, - pdb: { - dbId: "7FRD", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FRD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7frd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7frd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CYMALXAWPAIOPB-AWEZNQCLSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7frd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7frd", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main protease mutant Q189K in complex with Nirmatrelvir", - emdb: null, - pdb: { - dbId: "8DZ6", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, 3cl, covid, sars-cov-2 ensitrelvir, nirmatrelvir, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DZ6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dz6_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dz6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Noske, G.D.", "Oliva, G.", "Godoy, A.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36775130", - title: - "Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.", - journal: "J.Biol.Chem. 299: 103004-103004 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36775130", - pubDate: "2023", - abstract: "", - authors: [ - "Noske, G.D.", - "de Souza Silva, E.", - "de Godoy, M.O.", - "Dolci, I.", - "Fernandes, R.S.", - "Guido, R.V.C.", - "Sjo, P.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dz6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dz6", - }, - }, - { - title: "Crystal Structure of C13B8 Fab in complex with SARS-CoV-2 S fusion peptide", - emdb: null, - pdb: { - dbId: "7U09", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 spike, COVID-19, fusion peptide, Fab, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7U09", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u09_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u09", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain Fab C13B8", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain Fab C13B8", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "SARS-CoV-2 S fusion peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Veesler, D.", "Tortorici, M.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35857703", - title: - "ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.", - journal: "Science 377: 735-742 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abq2679", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35857703", - pubDate: "2022", - abstract: "", - authors: [ - "Low, J.S.", - "Jerak, J.", - "Tortorici, M.A.", - "McCallum, M.", - "Pinto, D.", - "Cassotta, A.", - "Foglierini, M.", - "Mele, F.", - "Abdelnabi, R.", - "Weynand, B.", - "Noack, J.", - "Montiel-Ruiz, M.", - "Bianchi, S.", - "Benigni, F.", - "Sprugasci, N.", - "Joshi, A.", - "Bowen, J.E.", - "Stewart, C.", - "Rexhepaj, M.", - "Walls, A.C.", - "Jarrossay, D.", - "Morone, D.", - "Paparoditis, P.", - "Garzoni, C.", - "Ferrari, P.", - "Ceschi, A.", - "Neyts, J.", - "Purcell, L.A.", - "Snell, G.", - "Corti, D.", - "Lanzavecchia, A.", - "Veesler, D.", - "Sallusto, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7u09_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7u09", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 nsp10/nsp16 methyltransferase in complex with TO383", - emdb: null, - pdb: { - dbId: "8A23", - method: "X-RAY DIFFRACTION", - keywords: "viral, methyltransferase, inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8A23", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8a23_final.pdb", - externalLink: "https://pdb-redo.eu/db/8a23", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "ILUKGDRLISPDRN-WGQQHEPDSA-N", - ], - dbauthors: [ - "Hanigovsky, M. (0000-0002-4893-545X)", - "Krafcikova, P. (0000-0002-3363-2499)", - "Klima, M. (0000-0002-9083-509X)", - "Boura, E. (0000-0002-9652-4065)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 nsp10/nsp16 methyltransferase in\ncomplex with TO383", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Hanigovsky, M. (0000-0002-4893-545X)", - "Krafcikova, P. (0000-0002-3363-2499)", - "Klima, M. (0000-0002-9083-509X)", - "Boura, E. (0000-0002-9652-4065)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8a23_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8a23", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CL protease in complex with a phenyl dimethyl sulfane inhibitor (cyclopropyl ketoamide warhead)", - emdb: null, - pdb: { - dbId: "8F45", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, Viral Protein, HYDROLASE-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8F45", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8f45_final.pdb", - externalLink: "https://pdb-redo.eu/db/8f45", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MVHBODFTFWPKCE-ZYAAQSTJSA-N"], - dbauthors: [ - "Lovell, S. (0000-0002-3215-4472)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S. (0000-0002-8199-2376)", - "Cooper, A. (0000-0002-1893-4149)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8f45_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8f45", - }, - }, - { - title: - "NMR structure of a peptide deriving from SARS-CoV-2 S RBD 482-506 fragment in HFIP/H2O", - emdb: null, - pdb: { - dbId: "7P5G", - method: "SOLUTION NMR", - keywords: - "SARS-CoV-2, mimicking peptides, Spike, Receptor Binding Domain, Covid-19, ANTIVIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Santoro, A.", "Buonocore, M.", "Grimaldi, M.", "D'Ursi, A.M."], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "36406731", - title: - "Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site.", - journal: "Heliyon 8: e11568-e11568 (2022), 2405-8440", - doi: "https://doi.org/10.1016/j.heliyon.2022.e11568", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36406731", - pubDate: "2022", - abstract: "", - authors: [ - "Buonocore, M.", - "Santoro, A.", - "Grimaldi, M.", - "Covelli, V.", - "Firoznezhad, M.", - "Rodriquez, M.", - "Santin, M.", - "D'Ursi, A.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7p5g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7p5g", - }, - }, - { - title: "fp.006 Fab in complex with SARS-CoV-2 Fusion Peptide", - emdb: null, - pdb: { - dbId: "8D47", - method: "X-RAY DIFFRACTION", - keywords: - "antibody, fusion peptide, TMPRSS2 binding site, complex, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8D47", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8d47_final.pdb", - externalLink: "https://pdb-redo.eu/db/8d47", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "fp.006 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "fp.006 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "SARS-CoV-2 fusion peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: ["Abernathy, M.E.", "Barnes, C.O."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36701425", - title: - "Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein.", - journal: "Sci Immunol 8: eade0958-eade0958 (2023), 2470-9468", - doi: "https://doi.org/10.1126/sciimmunol.ade0958", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36701425", - pubDate: "2023", - abstract: "", - authors: [ - "Bianchini, F. (0000-0002-0746-7629)", - "Crivelli, V. (0000-0003-2494-7242)", - "Abernathy, M.E.", - "Guerra, C. (0000-0001-5597-6885)", - "Palus, M. (0000-0002-4279-7092)", - "Muri, J.", - "Marcotte, H. (0000-0002-7168-349X)", - "Piralla, A. (0000-0002-6062-2579)", - "Pedotti, M. (0000-0003-1370-9505)", - "De Gasparo, R. (0000-0002-7934-8290)", - "Simonelli, L.", - "Matkovic, M. (0000-0002-4872-1996)", - "Toscano, C. (0000-0002-0309-946X)", - "Biggiogero, M.", - "Calvaruso, V.", - "Svoboda, P. (0000-0002-2180-3174)", - "Cervantes Rincon, T. (0000-0002-6355-6781)", - "Fava, T. (0000-0003-2767-5641)", - "Podesvova, L. (0000-0003-1054-2252)", - "Shanbhag, A.A. (0000-0002-1676-2478)", - "Celoria, A. (0000-0002-6107-8296)", - "Sgrignani, J.", - "Stefanik, M. (0000-0003-4390-7780)", - "Honig, V. (0000-0003-0469-4604)", - "Pranclova, V. (0000-0003-1660-1372)", - "Michalcikova, T. (0000-0002-0172-2254)", - "Prochazka, J.", - "Guerrini, G. (0000-0002-1446-0556)", - "Mehn, D. (0000-0003-3482-2996)", - "Ciabattini, A. (0000-0002-4585-7783)", - "Abolhassani, H. (0000-0002-4838-0407)", - "Jarrossay, D. (0000-0002-0924-6395)", - "Uguccioni, M. (0000-0002-9570-7011)", - "Medaglini, D.", - "Pan-Hammarstrom, Q. (0000-0003-1990-8804)", - "Calzolai, L. (0000-0002-8474-7974)", - "Fernandez, D. (0000-0002-6221-152X)", - "Baldanti, F. (0000-0002-3358-8969)", - "Franzetti-Pellanda, A. (0000-0002-0769-2500)", - "Garzoni, C. (0000-0002-0832-2376)", - "Sedlacek, R. (0000-0002-3352-392X)", - "Ruzek, D. (0000-0003-4655-2380)", - "Varani, L. (0000-0002-0963-0987)", - "Cavalli, A. (0000-0003-4063-4502)", - "Barnes, C.O. (0000-0003-2754-5951)", - "Robbiani, D.F. (0000-0001-7379-3484)", - "Guerra, C.", - "Muri, J. (0000-0002-6476-3766)", - "Marcotte, H.", - "Piralla, A.", - "Gasparo, R.", - "Svoboda, P.", - "Rincon, T.C.", - "Fava, T.", - "Celoria, A.", - "Sgrignani, J. (0000-0002-8633-1032)", - "Prochazka, J. (0000-0003-4675-8995)", - "Guerrini, G.", - "Mehn, D.", - "Ciabattini, A.", - "Abolhassani, H.", - "Pan-Hammarstrom, Q.", - "Calzolai, L.", - "Fernandez, D.", - "Baldanti, F.", - "Franzetti-Pellanda, A.", - "Garzoni, C.", - "Barnes, C.O.", - ], - }, - { - pmID: "36482967", - title: - "Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.11.24.515932", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36482967", - pubDate: "2022", - abstract: "", - authors: [ - "Bianchini, F. (0000-0002-0746-7629)", - "Crivelli, V. (0000-0003-2494-7242)", - "Abernathy, M.E.", - "Guerra, C. (0000-0001-5597-6885)", - "Palus, M. (0000-0002-4279-7092)", - "Muri, J.", - "Marcotte, H. (0000-0002-7168-349X)", - "Piralla, A. (0000-0002-6062-2579)", - "Pedotti, M. (0000-0003-1370-9505)", - "De Gasparo, R. (0000-0002-7934-8290)", - "Simonelli, L.", - "Matkovic, M. (0000-0002-4872-1996)", - "Toscano, C. 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(0000-0002-0769-2500)", - "Garzoni, C. (0000-0002-0832-2376)", - "Sedlacek, R. (0000-0002-3352-392X)", - "Ruzek, D. (0000-0003-4655-2380)", - "Varani, L. (0000-0002-0963-0987)", - "Cavalli, A. (0000-0003-4063-4502)", - "Barnes, C.O. (0000-0003-2754-5951)", - "Robbiani, D.F. (0000-0001-7379-3484)", - "Guerra, C.", - "Muri, J. (0000-0002-6476-3766)", - "Marcotte, H.", - "Piralla, A.", - "Gasparo, R.", - "Svoboda, P.", - "Rincon, T.C.", - "Fava, T.", - "Celoria, A.", - "Sgrignani, J. (0000-0002-8633-1032)", - "Prochazka, J. (0000-0003-4675-8995)", - "Guerrini, G.", - "Mehn, D.", - "Ciabattini, A.", - "Abolhassani, H.", - "Pan-Hammarstrom, Q.", - "Calzolai, L.", - "Fernandez, D.", - "Baldanti, F.", - "Franzetti-Pellanda, A.", - "Garzoni, C.", - "Barnes, C.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8d47_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8d47", - }, - }, - { - title: "SARS-Cov2 Main protease in complex with inhibitor CDD-1845", - emdb: null, - pdb: { - dbId: "7UR9", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-Cov2, Main protease, inhibitor, Non-covalent, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7UR9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ur9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ur9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "CTPLSMAVLSTZPJ-QFIPXVFZSA-N"], - dbauthors: ["Lu, S.", "Palzkill, T."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37542196", - title: - "DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors.", - journal: "Commun Chem 6: 164-164 (2023), 2399-3669", - doi: "https://doi.org/10.1038/s42004-023-00961-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37542196", - pubDate: "2023", - abstract: "", - authors: [ - "Jimmidi, R.", - "Chamakuri, S. (0000-0002-7586-4992)", - "Lu, S.", - "Ucisik, M.N.", - "Chen, P.J.", - "Bohren, K.M. (0000-0002-3183-4118)", - "Moghadasi, S.A.", - "Versteeg, L.", - "Nnabuife, C. (0000-0001-9907-0508)", - "Li, J.Y.", - "Qin, X. (0000-0003-3728-5911)", - "Chen, Y.C.", - "Faver, J.C.", - "Nyshadham, P.", - "Sharma, K.L.", - "Sankaran, B. (0000-0002-3266-8131)", - "Judge, A. (0000-0003-4289-1748)", - "Yu, Z.", - "Li, F. (0000-0002-9680-4614)", - "Pollet, J. (0000-0003-1420-4015)", - "Harris, R.S.", - "Matzuk, M.M.", - "Palzkill, T. (0000-0002-5267-0001)", - "Young, D.W. (0000-0002-1595-9658)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ur9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ur9", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z199538122", - emdb: null, - pdb: { - dbId: "8DL9", - method: "X-RAY DIFFRACTION", - keywords: "viral cysteine protease, homodimer, enzyme-inhibitor complex, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8DL9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dl9_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dl9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OCMXSYZDVBVSSV-UHFFFAOYSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A.Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36808989", - title: - "AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2.", - journal: "J.Chem.Inf.Model. 63: 1438-1453 (2023), 1549-960X", - doi: "https://doi.org/10.1021/acs.jcim.2c01377", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36808989", - pubDate: "2023", - abstract: "", - authors: [ - "Joshi, R.P.", - "Schultz, K.J.", - "Wilson, J.W. (0000-0002-2304-2540)", - "Kruel, A. (0000-0002-5571-7418)", - "Varikoti, R.A. (0000-0002-2355-1484)", - "Kombala, C.J.", - "Kneller, D.W. (0000-0002-5416-5789)", - "Galanie, S. (0000-0001-5712-2568)", - "Phillips, G.", - "Zhang, Q.", - "Coates, L. (0000-0003-2342-049X)", - "Parvathareddy, J.", - "Surendranathan, S.", - "Kong, Y.", - "Clyde, A.", - "Ramanathan, A. (0000-0002-1622-5488)", - "Jonsson, C.B. (0000-0002-2640-7672)", - "Brandvold, K.R. (0000-0001-5970-879X)", - "Zhou, M. (0000-0003-3575-3224)", - "Head, M.S.", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Kumar, N. (0000-0001-6713-2129)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dl9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dl9", - }, - }, - { - title: "SARS-CoV-2 Delta-RBD complexed with BA.2-13 Fab and C1 nanobody", - emdb: null, - pdb: { - dbId: "8C3V", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, BA.2 mAb, RBD, BA.2-13, BA.2-36, VIRAL PROTEIN/Immune system, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8C3V", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8c3v_final.pdb", - externalLink: "https://pdb-redo.eu/db/8c3v", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "BA.2-13 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BA.2-13 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody C1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "SBASXUCJHJRPEV-UHFFFAOYSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36995936", - title: - "Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.", - journal: "Cell Rep 42: 112271-112271 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112271", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36995936", - pubDate: "2023", - abstract: "", - authors: [ - "Dijokaite-Guraliuc, A.", - "Das, R.", - "Zhou, D.", - "Ginn, H.M.", - "Liu, C.", - "Duyvesteyn, H.M.E.", - "Huo, J.", - "Nutalai, R.", - "Supasa, P.", - "Selvaraj, M.", - "de Silva, T.I.", - "Plowright, M.", - "Newman, T.A.H.", - "Hornsby, H.", - "Mentzer, A.J.", - "Skelly, D.", - "Ritter, T.G.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Roemer, C.", - "Peacock, T.P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8c3v_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8c3v", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with S217622", - emdb: null, - pdb: { - dbId: "8HUW", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX, K90R mutant, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8HUW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8huw_final.pdb", - externalLink: "https://pdb-redo.eu/db/8huw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QMPBBNUOBOFBFS-UHFFFAOYSA-N"], - dbauthors: ["Wang, J.", "Zhang, J.", "Li, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with S217622", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Wang, J.", "Zhang, J.", "Li, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8huw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8huw", - }, - }, - { - title: "SARS-CoV-2 main protease in complex with Z-VAD-FMK", - emdb: null, - pdb: { - dbId: "7WQA", - method: "X-RAY DIFFRACTION", - keywords: "main protease, 3C-like protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WQA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wqa_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wqa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Z-VAD(OMe)-FMK", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Chen, Y.", "Wang, Y.C.", "Yang, C.S.", "Hou, M.H.", "Tsai, C.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2 main protease in complex with Z-VAD-FMK", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Wang, Y.C.", - "Yang, C.S.", - "Hou, M.H.", - "Tsai, C.L.", - "Chen, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wqa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wqa", - }, - }, - { - title: - "Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD)", - emdb: null, - pdb: { - dbId: "7WQV", - method: "X-RAY DIFFRACTION", - keywords: - "Ab08, mAb, Coronavirus, Covid-19, Monoclonal antibody, nAb, Neutralizing antibody, RBD, Receptor-binding domain, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WQV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wqv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wqv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Ab08", - details: - "fusion protein of a pelB signal peptide (SKYLLPTAAAGLLLLAAQPAMA), a linker (GSSS), the variable domain of heavy chain (1-128), a GS linker (15 amino acids), the variable domain of light chain (numbered 1001-1110), Myc and hexahistidine tag", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SVTOYMIYCMHPIV-UHFFFAOYSA-N", - "BHPQYMZQTOCNFJ-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: ["Zhang, X.", "Zha, J.", "Meng, L.", "Li, D. (0000-0003-4729-4678)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36706160", - title: - "A Spike-destructing human antibody effectively neutralizes Omicron-included SARS-CoV-2 variants with therapeutic efficacy.", - journal: "Plos Pathog. 19: e1011085-e1011085 (2023), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1011085", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36706160", - pubDate: "2023", - abstract: "", - authors: [ - "Meng, L.", - "Zha, J.", - "Zhou, B.", - "Cao, L.", - "Jiang, C.", - "Zhu, Y.", - "Li, T.", - "Lu, L.", - "Zhang, J.", - "Yang, H.", - "Feng, J.", - "Gu, Z.", - "Tang, H.", - "Jiang, L.", - "Li, D.", - "Lavillette, D. (0000-0002-4706-1519)", - "Zhang, X. (0000-0001-6732-9132)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wqv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wqv", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor 11", - emdb: null, - pdb: { - dbId: "8DZB", - method: "X-RAY DIFFRACTION", - keywords: - "COVID, COVID19, COVID-19, SARS, SARS COV2, COV, NCOV 19, coronavirus, main protease, 3CL, MPRO, PRO, GC376, calpain inhibitor II, leupeptin, calpain, aldehyde, GC-376, 3cl-like, a-ketoamide, alpheketoamide, alpha, ketoamide, petidometic, protease, cysteine, HYDROLASE-HYDROLASE INHIBITOR complex, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DZB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dzb_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dzb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "CJHGCZGBAUVONS-TVLDRFKXSA-N"], - dbauthors: ["Chen, Y.", "Sacco, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36920943", - title: - "Development of the Safe and Broad-Spectrum Aldehyde and Ketoamide Mpro inhibitors Derived from the Constrained alpha , gamma-AA Peptide Scaffold.", - journal: "Chemistry 29: e202300476-e202300476 (2023), 0947-6539", - doi: "https://doi.org/10.1002/chem.202300476", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36920943", - pubDate: "2023", - abstract: "", - authors: [ - "Wang, L.", - "Ma, C.", - "Sacco, M.D.", - "Xue, S.", - "Mahmoud, M.", - "Calcul, L.", - "Chen, Y. (0000-0002-5115-3600)", - "Wang, J. (0000-0002-4845-4621)", - "Cai, J. (0000-0003-3106-3306)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dzb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dzb", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 (Covid-19) Nsp3 macrodomain in complex with TFMU-ADPr", - emdb: null, - pdb: { - dbId: "8GIA", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, SARS-CoV, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8GIA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gia_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gia", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "JNMHMJORTGCLAH-IPSZZCKZSA-N"], - dbauthors: [ - "Wallace, S.D. (0000-0002-7593-0427)", - "Bagde, S.R. (0000-0001-9800-9326)", - "Fromme, J.C. (0000-0002-8837-0473)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37126856", - title: - "A Fluorescence Polarization Assay for Macrodomains Facilitates the Identification of Potent Inhibitors of the SARS-CoV-2 Macrodomain.", - journal: "Acs Chem.Biol. 18: 1200-1207 (2023), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.3c00092", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37126856", - pubDate: "2023", - abstract: "", - authors: [ - "Anmangandla, A.", - "Jana, S.", - "Peng, K.", - "Wallace, S.D.", - "Bagde, S.R.", - "Drown, B.S.", - "Xu, J.", - "Hergenrother, P.J.", - "Fromme, J.C.", - "Lin, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gia_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gia", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2890182452", - emdb: null, - pdb: { - dbId: "7FR0", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FR0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fr0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fr0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YCKAXCQPMUENML-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fr0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fr0", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 neutralizing antibody WS6 in complex with spike S2 peptide", - emdb: null, - pdb: { - dbId: "7TCQ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, spike, antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7TCQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tcq_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tcq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "10090", - name: "Anti-SARS-CoV-2 antibody WS6 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "Anti-SARS-CoV-2 antibody WS6 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Pegylated spike S2 peptide", - details: "N-term acetylated and C-term pegylated", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QAOWNCQODCNURD-UHFFFAOYSA-L", "MTHSVFCYNBDYFN-UHFFFAOYSA-N"], - dbauthors: ["Zhou, T. (0000-0002-3935-4637)", "Kwong, P.D. (0000-0003-3560-232X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35841885", - title: - "Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability.", - journal: "Structure 30 (2022), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2022.06.004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35841885", - pubDate: "2022", - abstract: "", - authors: [ - "Shi, W.", - "Wang, L.", - "Zhou, T.", - "Sastry, M.", - "Yang, E.S.", - "Zhang, Y.", - "Chen, M.", - "Chen, X.", - "Choe, M.", - "Creanga, A.", - "Leung, K.", - "Olia, A.S.", - "Pegu, A.", - "Rawi, R.", - "Schon, A.", - "Shen, C.H.", - "Stancofski, E.D.", - "Talana, C.A.", - "Teng, I.T.", - "Wang, S.", - "Corbett, K.S.", - "Tsybovsky, Y.", - "Mascola, J.R.", - "Kwong, P.D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tcq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tcq", - }, - }, - { - title: - "Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304, in complex with BBH1", - emdb: null, - pdb: { - dbId: "8GFN", - method: "X-RAY DIFFRACTION", - keywords: - "viral cysteine protease, inactive C145A mutant, homodimer, inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8GFN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gfn_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gfn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "ZWFVHGRPHWFQQC-QLJGKSERSA-N"], - dbauthors: ["Coates, L.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37271339", - title: - "Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.", - journal: "J.Biol.Chem. 299: 104886-104886 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.104886", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37271339", - pubDate: "2023", - abstract: "", - authors: [ - "Kovalevsky, A.", - "Aniana, A.", - "Coates, L.", - "Bonnesen, P.V.", - "Nashed, N.T.", - "Louis, J.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gfn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gfn", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with ML124N", - emdb: null, - pdb: { - dbId: "7SGH", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, SARS-CoV-2, coronavirus, Main Protease, Protease, Mpro, 3C-like proteinase, CL3pro, Inhibitor, Complex, Covalent, Adduct, ML124N, Ketoamide, Peptidomimetic, Viral Protein", - refModels: [ - { - emdbId: null, - pdbId: "7SGH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sgh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sgh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZQILDLPZFYNMME-JDFRZJQESA-N"], - dbauthors: [ - "Fernandez, D. (0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sgh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sgh", - }, - }, - { - title: - "Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates", - emdb: null, - pdb: { - dbId: "8EJ9", - method: "X-RAY DIFFRACTION", - keywords: - "viral protein, HYDROLASE-HYDROLASE INHIBITOR complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8EJ9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ej9_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ej9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lu, J. (0000-0002-4090-5176)", - "Khan, M.B. (0000-0002-4164-9573)", - "Young, H.S. (0000-0002-5990-8422)", - "Lemieux, M.J. (0000-0003-4745-9153)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Mpro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals", - journal: "Acs Cent.Sci. 9: 696-708 (2023), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.3c00054", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, S.A.", - "Arutyunova, E.", - "Lu, J.", - "Khan, M.B.", - "Rut, W.", - "Zmudzinski, M.", - "Shahbaz, S.", - "Iyyathurai, J.", - "Moussa, E.W.", - "Turner, Z.", - "Bai, B.", - "Lamer, T.", - "Nieman, J.A.", - "Vederas, J.C.", - "Julien, O.", - "Drag, M.", - "Elahi, S.", - "Young, H.S.", - "Lemieux, M.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ej9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ej9", - }, - }, - { - title: "SARS-CoV-2-Omicron-RBD and BD-236-GWP/P-VK antibody complex", - emdb: null, - pdb: { - dbId: "7X66", - method: "X-RAY DIFFRACTION", - keywords: "COVID-19, antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7X66", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x66_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x66", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "BD-236 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-236 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wang, Y.", - "Wu, Z.", - "Shi, R.", - "Han, X. (0000-0003-4751-1740)", - "Yan, J. (0000-0001-7140-5548)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2-Omicron-RBD and BD-236-GWP/P-VK antibody complex", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Shi, R.", - "Wang, Y.", - "Wu, Z.", - "Han, X. (0000-0003-4751-1740)", - "Yan, J. (0000-0001-7140-5548)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x66_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x66", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobodies VHH-F04 and VHH-G09", - emdb: null, - pdb: { - dbId: "7Q3R", - method: "X-RAY DIFFRACTION", - keywords: "Coronavirus, nanobody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7Q3R", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7q3r_final.pdb", - externalLink: "https://pdb-redo.eu/db/7q3r", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "VHH-F04", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "VHH-G09", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: ["Fernandez, I.", "Pederzoli, R.", "Rey, F.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Fernandez, I.", "Rey, F.A."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7q3r_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7q3r", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease M49I mutant in complex with Nirmatrelvir", - emdb: null, - pdb: { - dbId: "8E25", - method: "X-RAY DIFFRACTION", - keywords: "Main Protease, SARS-CoV-2, Nirmatrelvir, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8E25", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e25_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e25", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Noske, G.D.", "Oliva, G.", "Godoy, A.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36775130", - title: - "Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.", - journal: "J.Biol.Chem. 299: 103004-103004 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36775130", - pubDate: "2023", - abstract: "", - authors: [ - "Noske, G.D.", - "de Souza Silva, E.", - "de Godoy, M.O.", - "Dolci, I.", - "Fernandes, R.S.", - "Guido, R.V.C.", - "Sjo, P.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e25_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e25", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main protease A193S mutant in complex with Nirmatrelvir", - emdb: null, - pdb: { - dbId: "8E1Y", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, 3cl, covid, sars-cov-2 ensitrelvir, nirmatrelvir, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8E1Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e1y_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e1y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Noske, G.D.", "Oliva, G.", "Godoy, A.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36775130", - title: - "Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.", - journal: "J.Biol.Chem. 299: 103004-103004 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.103004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36775130", - pubDate: "2023", - abstract: "", - authors: [ - "Noske, G.D.", - "de Souza Silva, E.", - "de Godoy, M.O.", - "Dolci, I.", - "Fernandes, R.S.", - "Guido, R.V.C.", - "Sjo, P.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e1y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e1y", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 ORF8 accessory protein", - emdb: null, - pdb: { - dbId: "7MX9", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, COVID19, ORF8, immunoglobulin fold, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7MX9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mx9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mx9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC8", - organism: "2697049", - name: "ORF8 protein", - details: "", - altNames: "ORF8, Non-structural protein 8, ns8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Bailey-Elkin, B.A. (0000-0001-6863-2643)", - "Stetefeld, J. (0000-0003-1478-3248)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The unique ORF8 protein of SARS-CoV-2 binds to human dendritic cells and induces a cytokine storm", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Hamdorf, M.", - "Imhof, T.", - "Theobald, S.J.", - "Simonis, A.", - "Di Cristanziano, V.", - "Gieselmann, L.", - "Dewald, F.", - "Lehmann, C.", - "Augustin, M.", - "Klein, F.", - "Alejandre Alcazar, M.A.", - "Rongisch, R.", - "Fabri, M.", - "Cursiefen, C.", - "Rybniker, J.", - "Bailey-Elkin, B.A.", - "Stetefeld, J.", - "Koch, M.", - "Bock, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mx9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mx9", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 N-CTD", - emdb: null, - pdb: { - dbId: "7XWX", - method: "X-RAY DIFFRACTION", - keywords: "structural protein, drug target, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7XWX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xwx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xwx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NBIIXXVUZAFLBC-UHFFFAOYSA-K"], - dbauthors: [ - "Luan, X.D. (0000-0002-1279-5432)", - "Li, X.M.", - "Li, Y.F. (0000-0002-7936-7555)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36317101", - title: - "Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.", - journal: "Sci Bull (Beijing) 67: 2327-2335 (2022), 2095-9273", - doi: "https://doi.org/10.1016/j.scib.2022.10.021", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36317101", - pubDate: "2022", - abstract: "", - authors: [ - "Luan, X.", - "Li, X.", - "Li, Y.", - "Su, G.", - "Yin, W.", - "Jiang, Y.", - "Xu, N.", - "Wang, F.", - "Cheng, W.", - "Jin, Y.", - "Zhang, L.", - "Xu, H.E.", - "Xue, Y.", - "Zhang, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xwx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xwx", - }, - }, - { - title: - "Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304, in complex with GC373", - emdb: null, - pdb: { - dbId: "8GFO", - method: "X-RAY DIFFRACTION", - keywords: - "viral cysteine protease, inactive C145A mutant, homodimer, inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8GFO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gfo_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gfo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "QYENXTYKACLCGO-BZSNNMDCSA-N"], - dbauthors: ["Coates, L.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37271339", - title: - "Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.", - journal: "J.Biol.Chem. 299: 104886-104886 (2023), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2023.104886", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37271339", - pubDate: "2023", - abstract: "", - authors: [ - "Kovalevsky, A.", - "Aniana, A.", - "Coates, L.", - "Bonnesen, P.V.", - "Nashed, N.T.", - "Louis, J.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gfo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gfo", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139", - emdb: null, - pdb: { - dbId: "7MAZ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COVALENT INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MAZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7maz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7maz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WOTTZMBQRDTTCI-KTJVCJKDSA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7maz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7maz", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z1423250928", - emdb: null, - pdb: { - dbId: "7FR1", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FR1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fr1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fr1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NBIADPZZLKISOX-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fr1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fr1", - }, - }, - { - title: - "Crystal structure of chimeric omicron RBD (strain BA.2) complexed with human ACE2", - emdb: null, - pdb: { - dbId: "7UFK", - method: "X-RAY DIFFRACTION", - keywords: "ACE2, RBD, VIRAL PROTEIN-HYDROLASE complex", - refModels: [ - { - emdbId: null, - pdbId: "7UFK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ufk_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ufk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, W.", - "Shi, K. (0000-0003-4175-3714)", - "Geng, Q.", - "Ye, G.", - "Aihara, H. (0000-0001-7508-6230)", - "Li, F. (0000-0002-1958-366X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36256797", - title: - "Structural basis for mouse receptor recognition by SARS-CoV-2 omicron variant.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2206509119-e2206509119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2206509119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36256797", - pubDate: "2022", - abstract: "", - authors: [ - "Zhang, W. (0000-0003-3938-1245)", - "Shi, K. (0000-0003-4175-3714)", - "Geng, Q. (0000-0003-4872-2400)", - "Ye, G. (0000-0001-6034-2174)", - "Aihara, H. (0000-0001-7508-6230)", - "Li, F. (0000-0002-1958-366X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ufk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ufk", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl phenyl sulfane inhibitor (cyano warhead)", - emdb: null, - pdb: { - dbId: "8F46", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, HYDROLASE-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8F46", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8f46_final.pdb", - externalLink: "https://pdb-redo.eu/db/8f46", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZIDTZUSIKUZLIR-BJLQDIEVSA-N", "UWHCKJMYHZGTIT-UHFFFAOYSA-N"], - dbauthors: [ - "Lovell, S. (0000-0002-3215-4472)", - "Liu, L. (0000-0003-0514-281X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S. (0000-0002-8199-2376)", - "Cooper, A. (0000-0002-1893-4149)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8f46_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8f46", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor 17", - emdb: null, - pdb: { - dbId: "8DZC", - method: "X-RAY DIFFRACTION", - keywords: - "COVID, COVID19, COVID-19, SARS, SARS COV2, COV, NCOV 19, coronavirus, main protease, 3CL, MPRO, PRO, GC376, calpain inhibitor II, leupeptin, calpain, aldehyde, GC-376, 3cl-like, a-ketoamide, alpheketoamide, alpha, ketoamide, petidometic, protease, cysteine, HYDROLASE-HYDROLASE INHIBITOR complex, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DZC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dzc_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dzc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NMYLRAOUIBCXHJ-PPCGFTSFSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Chen, Y.", "Sacco, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36920943", - title: - "Development of the Safe and Broad-Spectrum Aldehyde and Ketoamide Mpro inhibitors Derived from the Constrained alpha , gamma-AA Peptide Scaffold.", - journal: "Chemistry 29: e202300476-e202300476 (2023), 0947-6539", - doi: "https://doi.org/10.1002/chem.202300476", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36920943", - pubDate: "2023", - abstract: "", - authors: [ - "Wang, L.", - "Ma, C.", - "Sacco, M.D.", - "Xue, S.", - "Mahmoud, M.", - "Calcul, L.", - "Chen, Y. (0000-0002-5115-3600)", - "Wang, J. (0000-0002-4845-4621)", - "Cai, J. (0000-0003-3106-3306)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dzc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dzc", - }, - }, - { - title: - "NMR structure of a peptide deriving from SARS-CoV-2 Lineages P.1 and B.1.351 S RBD 482-506 fragment in HFIP/H2O", - emdb: null, - pdb: { - dbId: "7P5S", - method: "SOLUTION NMR", - keywords: - "SARS-CoV-2, mimicking peptides, Spike, Receptor Binding Domain, COVID-19, Lineage P.1, Lineage B.1.351, E484K, N501Y, ANTIVIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Santoro, A.", "Buonocore, M.", "Grimaldi, M.", "D'Ursi, A.M."], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "36406731", - title: - "Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site.", - journal: "Heliyon 8: e11568-e11568 (2022), 2405-8440", - doi: "https://doi.org/10.1016/j.heliyon.2022.e11568", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36406731", - pubDate: "2022", - abstract: "", - authors: [ - "Buonocore, M.", - "Santoro, A.", - "Grimaldi, M.", - "Covelli, V.", - "Firoznezhad, M.", - "Rodriquez, M.", - "Santin, M.", - "D'Ursi, A.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7p5s_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7p5s", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with S217622", - emdb: null, - pdb: { - dbId: "8HUV", - method: "X-RAY DIFFRACTION", - keywords: "INHIBITOR COMPLEX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8HUV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8huv_final.pdb", - externalLink: "https://pdb-redo.eu/db/8huv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QMPBBNUOBOFBFS-UHFFFAOYSA-N"], - dbauthors: ["Zhang, J.", "Li, J.", "Zeng, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 main protease\nG15S mutant in complex with S217622", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zeng, P.", "Zhang, J.", "Li, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8huv_deposited_chain_front_image-200x200.png", - 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genes: [], - }, - refdoc: [ - { - pmID: "36493787", - title: - "Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents.", - journal: "Cell Rep 41: 111845-111845 (2022), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2022.111845", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36493787", - pubDate: "2022", - abstract: "", - authors: [ - "Cao, Y.", - "Jian, F.", - "Zhang, Z.", - "Yisimayi, A.", - "Hao, X.", - "Bao, L.", - "Yuan, F.", - "Yu, Y.", - "Du, S.", - "Wang, J.", - "Xiao, T.", - "Song, W.", - "Zhang, Y.", - "Liu, P.", - "An, R.", - "Wang, P.", - "Wang, Y.", - "Yang, S.", - "Niu, X.", - "Gu, Q.", - "Shao, F.", - "Hu, Y.", - "Yin, W.", - "Zheng, A.", - "Qin, C.", - "Jin, R.", - "Xiao, J.", - "Xie, X.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7y0v_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7y0v", - }, - }, - { - title: - "Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates", - 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(0000-0002-9822-8251)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t2t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t2t", - }, - }, - { - title: "Crystal structure of SARS-Cov-2 main protease in complex with inhibitor YH-53", - emdb: null, - pdb: { - dbId: "7XRS", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7XRS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xrs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xrs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Replicase polyprotein 1a", - details: "", - altNames: "pp1a,ORF1a polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JBLLRCOZJMVOAE-HSQYWUDLSA-N"], - dbauthors: [ - "Zhang, J.", - "Li, J.", - "Zhou, X.L.", - "Zeng, P.", - "Zhong, F.L.", - "Lin, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36146880", - title: - "Structural Basis for the Inhibition of Coronaviral Main Proteases by a Benzothiazole-Based Inhibitor.", - journal: "Viruses 14 (2022), 1999-4915", - doi: "https://doi.org/10.3390/v14092075", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36146880", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, X.", - "Lin, C.", - "Xu, Q.", - "Zhou, X.", - "Zeng, P.", - "McCormick, P.J. (0000-0002-2225-5181)", - "Jiang, H. (0000-0002-1895-3040)", - "Li, J.", - "Zhang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xrs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xrs", - }, - }, - { - title: - "Room-temperature X-ray structure of SARS-CoV-2 main protease H41A miniprecursor mutant in complex with GC373", - emdb: null, - pdb: { - dbId: "8E4R", - method: "X-RAY DIFFRACTION", - keywords: - "homodimer, cysteine protease, precursor enzyme, H41A mutation, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8E4R", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8e4r_final.pdb", - externalLink: "https://pdb-redo.eu/db/8e4r", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36334779", - title: - "Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor.", - journal: "J.Mol.Biol. 434: 167876-167876 (2022), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2022.167876", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36334779", - pubDate: "2022", - abstract: "", - authors: [ - "Kovalevsky, A.", - "Coates, L.", - "Kneller, D.W.", - "Ghirlando, R.", - "Aniana, A.", - "Nashed, N.T.", - "Louis, J.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e4r_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e4r", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in complex with nirmatrelvir alkyne", - emdb: null, - pdb: { - dbId: "8B2T", - method: "X-RAY DIFFRACTION", - keywords: "inhibitor, complex, covalent, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8B2T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8b2t_final.pdb", - externalLink: "https://pdb-redo.eu/db/8b2t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["TWWPGJPLBPBRGX-FHULIHMCSA-N"], - dbauthors: [ - "Zhao, Y.", - "Owen, C.D.", - "Brewitz, L.", - "Salah, E.", - "Malla, T.R.", - "Strain-Damerell, C.", - "Walsh, M.A.", - "Schofield, C.J.", - "Crawshaw, A.D.", - "Warren, A.J.", - "Trincao, J.", - "Petra, L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36757959", - title: - "Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine.", - journal: "J.Med.Chem. 66: 2663-2680 (2023), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c01627", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36757959", - pubDate: "2023", - abstract: "", - authors: [ - "Brewitz, L.", - "Dumjahn, L.", - "Zhao, Y.", - "Owen, C.D.", - "Laidlaw, S.M.", - "Malla, T.R.", - "Nguyen, D.", - "Lukacik, P.", - "Salah, E.", - "Crawshaw, A.D.", - "Warren, A.J.", - "Trincao, J.", - "Strain-Damerell, C.", - "Carroll, M.W.", - "Walsh, M.A.", - "Schofield, C.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8b2t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8b2t", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 RBD with P2C-1F11 and P2B-1G5", - emdb: null, - pdb: { - dbId: "8GX9", - method: "X-RAY DIFFRACTION", - keywords: - "spike, receptor binding domain, antibody, viral protein, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8GX9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gx9_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gx9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "light chain of P2C-1F11", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "heavy chain of P2C-1F11", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "light chain of P2B-1G5", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "heavy chain of P2B-1G5", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Wang, X.", "Zhang, L.", "Ge, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "decameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Crystal structure of SARS-CoV-2 antibody P2C-1F11 and RBD", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Wang, X.", "Zhang, L.", "Ge, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gx9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gx9", - }, - }, - { - title: - "Crystal Structure of HLA-B*15:01 in complex with spike derived peptide NQKLIANQF from SARS-CoV-2 virus", - emdb: null, - pdb: { - dbId: "8ELH", - method: "X-RAY DIFFRACTION", - keywords: - "TCR, T cell, HLA-B*15:01, NQK, spike, SARS-CoV-2, COVID, immune response, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8ELH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8elh_final.pdb", - externalLink: "https://pdb-redo.eu/db/8elh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "heavy chain HLA-B*15:01", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QTBSBXVTEAMEQO-UHFFFAOYSA-M", "MTHSVFCYNBDYFN-UHFFFAOYSA-N"], - dbauthors: ["Murdolo, L.D.", "Gras, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37468623", - title: - "A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection.", - journal: "Nature 620: 128-136 (2023), 1476-4687", - doi: "https://doi.org/10.1038/s41586-023-06331-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37468623", - pubDate: "2023", - abstract: "", - authors: [ - "Augusto, D.G. (0000-0001-5665-8547)", - "Murdolo, L.D. (0000-0001-5222-9585)", - "Chatzileontiadou, D.S.M. (0000-0003-1132-8952)", - "Sabatino Jr., J.J.", - "Yusufali, T.", - "Peyser, N.D. (0000-0003-4529-8325)", - "Butcher, X.", - "Kizer, K.", - "Guthrie, K.", - "Murray, V.W. (0000-0002-4479-2359)", - "Pae, V.", - "Sarvadhavabhatla, S.", - "Beltran, F.", - "Gill, G.S.", - "Lynch, K.L.", - "Yun, C. (0000-0002-6971-2060)", - "Maguire, C.T. (0000-0001-7890-8375)", - "Peluso, M.J. (0000-0003-0585-6230)", - "Hoh, R.", - "Henrich, T.J.", - "Deeks, S.G. (0000-0001-6371-747X)", - "Davidson, M. (0000-0002-5518-9774)", - "Lu, S.", - "Goldberg, S.A. (0000-0002-8642-1468)", - "Kelly, J.D. (0000-0002-7616-0321)", - "Martin, J.N.", - "Vierra-Green, C.A.", - "Spellman, S.R.", - "Langton, D.J. (0000-0003-1178-3031)", - "Dewar-Oldis, M.J.", - "Smith, C.", - "Barnard, P.J. (0000-0003-1755-7991)", - "Lee, S. (0000-0003-1560-2250)", - "Marcus, G.M. (0000-0001-5197-7696)", - "Olgin, J.E.", - "Pletcher, M.J.", - "Maiers, M.", - "Gras, S. (0000-0001-7416-038X)", - "Hollenbach, J.A. (0000-0001-6572-7962)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8elh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8elh", - }, - }, - { - title: "SARS-CoV2 3C-Like protease complexed with Nemo peptide", - emdb: null, - pdb: { - dbId: "7T2U", - method: "X-RAY DIFFRACTION", - keywords: "SARS CoV2, 3C-Like protease, Nemo peptide., HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7T2U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t2u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t2u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-Like Protease", - details: "", - altNames: "3CL-PRO,3CLP,Main protease,Mpro", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y6K9", - organism: "9606", - name: "NEMO peptide", - details: "", - altNames: - "NF-kappa-B essential modulator,NEMO,FIP-3,IkB kinase-associated protein 1,IKKAP1,Inhibitor of nuclear factor kappa-B kinase subunit gamma,I-kappa-B kinase subunit gamma,IKK-gamma,IKKG,IkB kinase subunit gamma,NF-kappa-B essential modifier", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Mathews, I.I. (0000-0001-6254-3519)", - "Hameedi, M.A.", - "Wakatsuki, S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36075915", - title: - "Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.", - journal: "Nat Commun 13: 5285-5285 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32922-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36075915", - pubDate: "2022", - abstract: "", - authors: [ - "Hameedi, M.A.", - "T Prates, E. (0000-0002-6581-5054)", - "Garvin, M.R.", - "Mathews, I.I. (0000-0001-6254-3519)", - "Amos, B.K. (0000-0003-2152-2927)", - "Demerdash, O.", - "Bechthold, M.", - "Iyer, M.", - "Rahighi, S.", - "Kneller, D.W. (0000-0002-5416-5789)", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Irle, S. (0000-0003-4995-4991)", - "Vuong, V.Q. (0000-0001-8580-8532)", - "Mitchell, J.C. (0000-0002-5031-7343)", - "Labbe, A.", - "Galanie, S.", - "Wakatsuki, S. (0000-0001-5896-7968)", - "Jacobson, D. (0000-0002-9822-8251)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t2u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t2u", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 20A7", - emdb: null, - pdb: { - dbId: "8GB7", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, antibody, spike, receptor binding domain, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8GB7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gb7_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gb7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9544", - name: "20A7 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9544", - name: "20A7 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wilson, I.A. (0000-0002-6469-2419)", "Yuan, M. (0000-0001-9754-4503)"], - details: [ - { - sample: { - name: "", - exprSystem: "Mus musculus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37163615", - title: - "Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.", - journal: "Sci Transl Med 15: eadg7404-eadg7404 (2023), 1946-6242", - doi: "https://doi.org/10.1126/scitranslmed.adg7404", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37163615", - pubDate: "2023", - abstract: "", - authors: [ - "Feng, Y. (0000-0001-8550-2787)", - "Yuan, M. (0000-0001-9754-4503)", - "Powers, J.M. (0000-0002-0485-9109)", - "Hu, M. (0000-0003-4495-7501)", - "Munt, J.E.", - "Arunachalam, P.S. (0000-0003-0090-5689)", - "Leist, S.R. (0000-0002-4989-5381)", - "Bellusci, L. (0000-0001-9945-1706)", - "Kim, J. (0000-0001-5443-8997)", - "Sprouse, K.R. (0000-0003-0007-2226)", - "Adams, L.E. (0000-0001-7780-9973)", - "Sundaramurthy, S. (0009-0004-7066-5662)", - "Zhu, X. (0000-0002-6021-3740)", - "Shirreff, L.M. (0000-0002-8403-451X)", - "Mallory, M.L. (0000-0003-0768-572X)", - "Scobey, T.D.", - "Moreno, A. (0000-0002-3031-7194)", - "O'Hagan, D.T.", - "Kleanthous, H.", - "Villinger, F.J. (0000-0002-7790-2008)", - "Veesler, D. (0000-0002-6019-8675)", - "King, N.P. (0000-0002-2978-4692)", - "Suthar, M.S. (0000-0002-2686-8380)", - "Khurana, S. (0000-0002-0593-7965)", - "Baric, R.S. (0000-0001-6827-8701)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Pulendran, B. 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(0000-0002-6097-4099)", - "Chen, P. (0000-0002-9041-8392)", - "Zhou, B.", - "Wang, R. (0000-0002-8040-7913)", - "Ge, X.", - "Lv, Q.", - "Cheng, L.", - "Zhang, R. (0000-0003-0024-389X)", - "Wong, Y.H.", - "Chen, H.", - "Wang, H.", - "Shan, S. (0000-0002-7184-6818)", - "Liao, X.", - "Shi, X.", - "Liu, L.", - "Chu, J.J.H. (0000-0002-1673-6819)", - "Wang, X. (0000-0003-3136-8070)", - "Zhang, Z. (0000-0002-3544-1389)", - "Zhang, L. 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(0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. 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(0000-0001-5904-1905)", - "Gully, B.S. (0000-0002-8197-0871)", - "Rossjohn, J. (0000-0002-2020-7522)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "24-meric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37036856", - title: - "Inside-out: Antibody-binding reveals potential folding hinge-points within the SARS-CoV-2 replication co-factor nsp9.", - journal: "Plos One 18: e0283194-e0283194 (2023), 1932-6203", - doi: "https://doi.org/10.1371/journal.pone.0283194", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37036856", - pubDate: "2023", - abstract: "", - authors: [ - "Pan, Y.", - "Chandrashekaran, I.R.", - "Tennant, L. (0000-0001-8583-5119)", - "Rossjohn, J.", - "Littler, D.R. 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(0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - "Kiene, A.", - "Galchenkova, M. (0000-0001-8676-0091)", - "Garcia, Y. (0000-0002-9592-2141)", - "Ehr, C. (0000-0003-1428-0042)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8otr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8otr", - }, - }, - { - title: - "Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, M8a-34", - emdb: null, - pdb: { - dbId: "7UZC", - method: "X-RAY DIFFRACTION", - keywords: - "immune system, neutralizing antibody, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7UZC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uzc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uzc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "M8a-34 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "M8a-34 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Fan, C.", "Bjorkman, P.J."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36370711", - title: - "Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes.", - journal: "Immunity 55: 2419-2435.e10 (2022), 1074-7613", - doi: "https://doi.org/10.1016/j.immuni.2022.10.019", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36370711", - pubDate: "2022", - abstract: "", - authors: [ - "Fan, C.", - "Cohen, A.A.", - "Park, M.", - "Hung, A.F.", - "Keeffe, J.R.", - "Gnanapragasam, P.N.P.", - "Lee, Y.E.", - "Gao, H.", - "Kakutani, L.M.", - "Wu, Z.", - "Kleanthous, H.", - "Malecek, K.E.", - "Williams, J.C.", - "Bjorkman, P.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uzc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uzc", - }, - }, - { - title: - "Virtual screening for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors", - emdb: null, - pdb: { - dbId: "8DID", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, MPro, nsp7, COVID-19, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DID", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8did_final.pdb", - externalLink: "https://pdb-redo.eu/db/8did", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "OIJLGOGZDMHSIL-UHFFFAOYSA-N"], - dbauthors: ["Singh, I.", "Shoichet, B.K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37354015", - title: - "Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.", - journal: "Protein Sci. 32: e4712-e4712 (2023), 1469-896X", - doi: "https://doi.org/10.1002/pro.4712", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37354015", - pubDate: "2023", - abstract: "", - authors: [ - "Fink, E.A.", - "Bardine, C.", - "Gahbauer, S.", - "Singh, I.", - "Detomasi, T.", - "White, K.", - "Gu, S.", - "Wan, X.", - "Chen, J.", - "Ary, B.", - "Glenn, I.", - "O'Connell, J.", - "O'Donnell, H.", - "Fajtova, P.", - "Lyu, J.", - "Vigneron, S.", - "Young, N.J.", - "Kondratov, I.S.", - "Alisoltani, A.", - "Simons, L.M.", - "Lorenzo-Redondo, R.", - "Ozer, E.A.", - "Hultquist, J.F.", - "O'Donoghue, A.J.", - "Moroz, Y.", - "Taunton, J.", - "Renslo, A.R.", - "Irwin, J.J.", - "Garcia-Sastre, A.", - "Shoichet, B.K. 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(0000-0002-1627-8467)", - "Edwards, R.A. (0000-0002-6362-5951)", - "Glover, J.N.M. (0000-0003-2733-7052)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of SARS CoV-2 NSP15 Endroribonuclease H250A", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Farraj, R.A. (0000-0002-1627-8467)", - "Edwards, R.A. (0000-0002-6362-5951)", - "Glover, J.N.M. 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(0000-0002-2437-2760)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36610391", - title: - "Structural insights into the activity regulation of full-length non-structural protein 1 from SARS-CoV-2.", - journal: "Structure 31 (2023), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2022.12.006", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36610391", - pubDate: "2023", - abstract: "", - authors: [ - "Wang, Y.", - "Kirkpatrick, J.", - "Lage, S.Z.", - "Carlomagno, T.", - "Wang, Y. (0000-0002-5645-0209)", - "Kirkpatrick, J. (0000-0002-9761-3377)", - "zur Lage, S. (0000-0002-6834-2029)", - "Korn, S.", - "Neissner, K.", - "Schwalbe, H.", - "Schlundt, A.", - "Carlomagno, T. (0000-0002-2437-2760)", - ], - }, - { - pmID: "33770349", - title: - "1H, 13C and 15N backbone chemical-shift assignments of SARS-CoV-2 non-structural protein 1 (leader protein)", - journal: "Biomol NMR Assign 15: 287-295 (2021), 1874-2718", - doi: "https://doi.org/10.1007/s12104-021-10019-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33770349", - pubDate: "2021", - abstract: "", - authors: [ - "Wang, Y.", - "Kirkpatrick, J.", - "Lage, S.Z.", - "Carlomagno, T.", - "Wang, Y. (0000-0002-5645-0209)", - "Kirkpatrick, J. (0000-0002-9761-3377)", - "zur Lage, S. (0000-0002-6834-2029)", - "Korn, S.", - "Neissner, K.", - "Schwalbe, H.", - "Schlundt, A.", - "Carlomagno, T. (0000-0002-2437-2760)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8aou_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8aou", - }, - }, - { - title: - "Crystal structure of SARS CoV-2 Spike Receptor Binding Domain in complex with shark neutralizing VNARs ShAb01 and ShAb02", - emdb: null, - pdb: { - dbId: "7S83", - method: "X-RAY DIFFRACTION", - keywords: - "Shark antibody, IgNAR, VNAR, SARS CoV-2, spike protein, Receptor binding domain, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7S83", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s83_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s83", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "7801", - name: "ShAb02 VNAR", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "7801", - name: "ShAb01 VNAR", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Joyce, M.G.", "Chen, W.-H.", "Hajduczki, A.", "Dooley, H.M."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36737435", - title: - "Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity.", - journal: "Nat Commun 14: 580-580 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-36106-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36737435", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, W.H. (0000-0003-3724-9195)", - "Hajduczki, A.", - "Martinez, E.J. (0000-0002-7755-7056)", - "Bai, H. (0000-0002-3501-3974)", - "Matz, H.", - "Hill, T.M.", - "Lewitus, E.", - "Chang, W.C. (0000-0003-4967-6426)", - "Dawit, L.", - "Peterson, C.E.", - "Rees, P.A.", - "Ajayi, A.B.", - "Golub, E.S.", - "Swafford, I. (0000-0001-8638-2772)", - "Dussupt, V. (0000-0002-8579-6356)", - "David, S.", - "Mayer, S.V.", - "Soman, S.", - "Kuklis, C. (0000-0002-9974-6640)", - "Corbitt, C.", - "King, J. (0000-0003-3348-1632)", - "Choe, M.", - "Sankhala, R.S.", - "Thomas, P.V.", - "Zemil, M. (0000-0002-1700-6658)", - "Wieczorek, L.", - "Hart, T.", - "Duso, D.", - "Kummer, L.", - "Yan, L.", - "Sterling, S.L.", - "Laing, E.D.", - "Broder, C.C. (0000-0001-5382-0510)", - "Williams, J.K.", - "Davidson, E.", - "Doranz, B.J. (0000-0002-8245-3083)", - "Krebs, S.J. (0000-0003-1136-1760)", - "Polonis, V.R.", - "Paquin-Proulx, D. (0000-0003-1407-3414)", - "Rolland, M. (0000-0003-3650-8490)", - "Reiley, W.W.", - "Gromowski, G.D. (0000-0003-4576-4277)", - "Modjarrad, K.", - "Dooley, H. (0000-0002-2570-574X)", - "Joyce, M.G. (0000-0002-6808-7232)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s83_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s83", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 25F9", - emdb: null, - pdb: { - dbId: "8GB5", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, antibody, spike, receptor binding domain, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8GB5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gb5_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gb5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9544", - name: "25F9 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9544", - name: "25F9 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "FSVCELGFZIQNCK-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Wilson, I.A. 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(0000-0001-5443-8997)", - "Sprouse, K.R. (0000-0003-0007-2226)", - "Adams, L.E. (0000-0001-7780-9973)", - "Sundaramurthy, S. (0009-0004-7066-5662)", - "Zhu, X. (0000-0002-6021-3740)", - "Shirreff, L.M. (0000-0002-8403-451X)", - "Mallory, M.L. (0000-0003-0768-572X)", - "Scobey, T.D.", - "Moreno, A. (0000-0002-3031-7194)", - "O'Hagan, D.T.", - "Kleanthous, H.", - "Villinger, F.J. (0000-0002-7790-2008)", - "Veesler, D. (0000-0002-6019-8675)", - "King, N.P. (0000-0002-2978-4692)", - "Suthar, M.S. (0000-0002-2686-8380)", - "Khurana, S. (0000-0002-0593-7965)", - "Baric, R.S. (0000-0001-6827-8701)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Pulendran, B. (0000-0001-6517-4333)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gb5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gb5", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-2B10", - emdb: null, - pdb: { - dbId: "7XSC", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7XSC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xsc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xsc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "P5S-2B10 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P5S-2B10 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wang, X.", "Wang, Z.", "Lin, Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36914890", - title: - "Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.", - journal: "Nat.Immunol. 24: 690-699 (2023), 1529-2916", - doi: "https://doi.org/10.1038/s41590-023-01449-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36914890", - pubDate: "2023", - abstract: "", - authors: [ - "Ju, B.", - "Zhang, Q.", - "Wang, Z.", - "Aw, Z.Q. (0000-0002-6097-4099)", - "Chen, P. (0000-0002-9041-8392)", - "Zhou, B.", - "Wang, R. (0000-0002-8040-7913)", - "Ge, X.", - "Lv, Q.", - "Cheng, L.", - "Zhang, R. (0000-0003-0024-389X)", - "Wong, Y.H.", - "Chen, H.", - "Wang, H.", - "Shan, S. (0000-0002-7184-6818)", - "Liao, X.", - "Shi, X.", - "Liu, L.", - "Chu, J.J.H. (0000-0002-1673-6819)", - "Wang, X. (0000-0003-3136-8070)", - "Zhang, Z. (0000-0002-3544-1389)", - "Zhang, L. (0000-0003-4931-509X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xsc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xsc", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI32", - emdb: null, - pdb: { - dbId: "7S6Y", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S6Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s6y_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s6y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RTEPKJZIQYUGOI-BLTUZGSGSA-N"], - dbauthors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Sankaran, B. (0000-0002-3266-8131)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35839690", - title: - "A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114596-114596 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839690", - pubDate: "2022", - abstract: "", - authors: [ - "Alugubelli, Y.R.", - "Geng, Z.Z.", - "Yang, K.S.", - "Shaabani, N.", - "Khatua, K.", - "Ma, X.R.", - "Vatansever, E.C.", - "Cho, C.C.", - "Ma, Y.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s6y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s6y", - }, - }, - { - title: "Crystal structure of nanobody 1-2C7 with SARS-CoV-2 RBD", - emdb: null, - pdb: { - dbId: "7X2M", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, nanobody, spike, receptor binding domain, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7X2M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x2m_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x2m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "1-2C7", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, L.Q.", "Wang, X.Q.", "Ren, Y.F.", "Li, M.X."], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36575191", - title: - "Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses.", - journal: "Nat Commun 13: 7957-7957 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-35642-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36575191", - pubDate: "2022", - abstract: "", - authors: [ - "Li, M.", - "Ren, Y.", - "Aw, Z.Q. 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(0000-0001-5248-7912)", - "Miller, M.J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e68_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e68", - }, - }, - { - title: - "Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2", - emdb: null, - pdb: { - dbId: "7ZR2", - method: "X-RAY DIFFRACTION", - keywords: "coiled-coil, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZR2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zr2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zr2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Camara-Artigas, A. 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(0000-0002-3215-4472)", - "Liu, L. (0000-0003-0514-281X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Groutas, W.C. (0000-0001-5248-7912)", - "Miller, M.J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)", - journal: "Eur.J.Med.Chem. 254 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115376", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Miller, M.J.", - "Kim, Y.", - "Zabiegala, A.", - "Nguyen, H.N.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Cooper, A.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8e69_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8e69", - }, - }, - { - title: "Crystal structure of nanobody 3-2A2-4 with SARS-CoV-2 RBD", - emdb: null, - pdb: { - dbId: "7X2L", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, nanobody, spike, receptor binding domain, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7X2L", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x2l_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x2l", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "Nanobody 3-2A2-4", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, L.Q.", "Wang, X.Q.", "Ren, Y.F.", "Li, M.X."], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36575191", - title: - "Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses.", - journal: "Nat Commun 13: 7957-7957 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-35642-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36575191", - pubDate: "2022", - abstract: "", - authors: [ - "Li, M.", - "Ren, Y.", - "Aw, Z.Q. (0000-0002-6097-4099)", - "Chen, B.", - "Yang, Z.", - "Lei, Y.", - "Cheng, L.", - "Liang, Q.", - "Hong, J. (0000-0003-1148-0444)", - "Yang, Y. (0000-0001-6824-7446)", - "Chen, J.", - "Wong, Y.H. (0000-0001-6704-9130)", - "Wei, J.", - "Shan, S.", - "Zhang, S. (0000-0003-1703-3848)", - "Ge, J. (0000-0001-9366-1470)", - "Wang, R. (0000-0002-8040-7913)", - "Dong, J.Z.", - "Chen, Y.", - "Shi, X.", - "Zhang, Q.", - "Zhang, Z. (0000-0002-3544-1389)", - "Chu, J.J.H. (0000-0002-1673-6819)", - "Wang, X.", - "Zhang, L. (0000-0003-4931-509X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x2l_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x2l", - }, - }, - { - title: "SARS CoV2 Mpro C145S mutant", - emdb: null, - pdb: { - dbId: "7T2V", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV2 2C-Like Protease, Mpro, 2ClPro, C145S mutation, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7T2V", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t2v_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t2v", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-Like Protease", - details: "", - altNames: "3CL-PRO,3CLP,Main protease,Mpro", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Mathews, I.I. (0000-0001-6254-3519)", - "Wakatsuki, S. (0000-0001-5896-7968)", - "Hameedi, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36075915", - title: - "Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.", - journal: "Nat Commun 13: 5285-5285 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32922-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36075915", - pubDate: "2022", - abstract: "", - authors: [ - "Hameedi, M.A.", - "T Prates, E. (0000-0002-6581-5054)", - "Garvin, M.R.", - "Mathews, I.I. (0000-0001-6254-3519)", - "Amos, B.K. (0000-0003-2152-2927)", - "Demerdash, O.", - "Bechthold, M.", - "Iyer, M.", - "Rahighi, S.", - "Kneller, D.W. (0000-0002-5416-5789)", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Irle, S. (0000-0003-4995-4991)", - "Vuong, V.Q. (0000-0001-8580-8532)", - "Mitchell, J.C. (0000-0002-5031-7343)", - "Labbe, A.", - "Galanie, S.", - "Wakatsuki, S. (0000-0001-5896-7968)", - "Jacobson, D. (0000-0002-9822-8251)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t2v_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t2v", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI30", - emdb: null, - pdb: { - dbId: "7S6X", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S6X", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s6x_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s6x", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PGHPGMLPXLZINT-UHFFFAOYSA-N"], - dbauthors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Sankaran, B. (0000-0002-3266-8131)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35839690", - title: - "A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114596-114596 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839690", - pubDate: "2022", - abstract: "", - authors: [ - "Alugubelli, Y.R.", - "Geng, Z.Z.", - "Yang, K.S.", - "Shaabani, N.", - "Khatua, K.", - "Ma, X.R.", - "Vatansever, E.C.", - "Cho, C.C.", - "Ma, Y.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s6x_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s6x", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab", - emdb: null, - pdb: { - dbId: "7XSB", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7XSB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xsb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xsb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P5S-3B11 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P5S-3B11 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wang, X.", "Wang, Z.", "Gao, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36914890", - title: - "Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.", - journal: "Nat.Immunol. 24: 690-699 (2023), 1529-2916", - doi: "https://doi.org/10.1038/s41590-023-01449-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36914890", - pubDate: "2023", - abstract: "", - authors: [ - "Ju, B.", - "Zhang, Q.", - "Wang, Z.", - "Aw, Z.Q. 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(0000-0003-2719-0302)", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8eyj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8eyj", - }, - }, - { - title: - "crystal structures of diastereomer (S,S,S)-13b (13b-K) in complex with the SARS-CoV-2 Mpro", - emdb: null, - pdb: { - dbId: "8A4T", - method: "X-RAY DIFFRACTION", - keywords: "Zhang, L., ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8A4T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8a4t_final.pdb", - externalLink: "https://pdb-redo.eu/db/8a4t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FRACPXUHUTXLCX-BELIEFIBSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Zhang, L.", - "Ibrahim, M. (0000-0002-1431-9755)", - "Hilgenfeld, R. (0000-0001-8850-2977)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36179320", - title: - "Diastereomeric Resolution Yields Highly Potent Inhibitor of SARS-CoV-2 Main Protease.", - journal: "J.Med.Chem. 65: 13328-13342 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c01131", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36179320", - pubDate: "2022", - abstract: "", - authors: [ - "Cooper, M.S.", - "Zhang, L.", - "Ibrahim, M.", - "Zhang, K.", - "Sun, X.", - "Roske, J.", - "Gohl, M.", - "Bronstrup, M.", - "Cowell, J.K.", - "Sauerhering, L.", - "Becker, S.", - "Vangeel, L.", - "Jochmans, D.", - "Neyts, J.", - "Rox, K.", - "Marsh, G.P.", - "Maple, H.J.", - "Hilgenfeld, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8a4t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8a4t", - }, - }, - { - title: "Crystal Structure of the CoV-Y domain of SARS-CoV-2 Nonstructural Protein 3", - emdb: null, - pdb: { - dbId: "8F2E", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, conronavirus, nonstructural proteins, protein structure, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8F2E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8f2e_final.pdb", - externalLink: "https://pdb-redo.eu/db/8f2e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Li, Y. (0000-0001-6501-9093)", - "Shi, W. (0000-0003-4771-4601)", - "Hao, B. (0000-0003-3029-5340)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36801935", - title: - "Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3.", - journal: "Sci Rep 13: 2890-2890 (2023), 2045-2322", - doi: "https://doi.org/10.1038/s41598-023-30045-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36801935", - pubDate: "2023", - abstract: "", - authors: [ - "Li, Y.", - "Pustovalova, Y.", - "Shi, W.", - "Gorbatyuk, O.", - "Sreeramulu, S.", - "Schwalbe, H.", - "Hoch, J.C.", - "Hao, B.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8f2e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8f2e", - }, - }, - { - title: - "Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp13-nsp14 (C13) cut site sequence", - emdb: null, - pdb: { - dbId: "8DRZ", - method: "X-RAY DIFFRACTION", - keywords: "Viral protease, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DRZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8drz_final.pdb", - externalLink: "https://pdb-redo.eu/db/8drz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "PQYJRMFWJJONBO-UHFFFAOYSA-N", - "JLFNLZLINWHATN-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Lee, J. (0000-0003-3229-2397)", - "Kenward, C. (0000-0002-3771-0044)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Vuckovic, M. (0000-0002-0452-8270)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36057636", - title: - "X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.", - journal: "Nat Commun 13: 5196-5196 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32854-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36057636", - pubDate: "2022", - abstract: "", - authors: [ - "Lee, J.", - "Kenward, C.", - "Worrall, L.J.", - "Vuckovic, M.", - "Gentile, F. (0000-0001-8299-1976)", - "Ton, A.T. (0000-0001-7418-6563)", - "Ng, M.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Paetzel, M. (0000-0002-7408-5487)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8drz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8drz", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease in complex with inhibitor TKB-248", - emdb: null, - pdb: { - dbId: "8DPR", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 main protease, 3C-like proteinase, VIRAL PROTEIN, SARS-CoV-2, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DPR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dpr_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dpr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "GDKLDALGJZVEKT-MCUUEWDYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Bulut, H. (0000-0003-0262-6296)", - "Hayashi, H.", - "Tsuji, K.", - "Kuwata, N.", - "Das, D.", - "Tamamura, H.", - "Mitsuya, H. (0000-0001-9274-3853)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "A small molecule compound inhibits the main protease of SARS-CoV-2 and blocks virus replication.", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Bulut, H. (0000-0003-0262-6296)", - "Hayashi, H.", - "Tsuji, K.", - "Higashi-Kuwata, N. (0000-0002-9404-3532)", - "Das, D. (0000-0001-9943-5888)", - "Tamamura, H.", - "Mitsuya, H. (0000-0001-9274-3853)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dpr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dpr", - }, - }, - { - title: "SARS-CoV-2 nsp10-16 methyltransferase in complex with MTA and glycine", - emdb: null, - pdb: { - dbId: "8OT0", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, methyltransferase, complex, inhibitor", - refModels: [ - { - emdbId: null, - pdbId: "8OT0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ot0_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ot0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "WUUGFSXJNOTRMR-IOSLPCCCSA-N", - "DHMQDGOQFOQNFH-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Sprenger, J. (0000-0001-7977-3484)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kremling, V. (0000-0002-4877-2902)", - "Oberthuer, D. (0000-0002-0894-9590)", - "Falke, S. (0000-0003-3409-1791)", - "Yefanov, O. (0000-0001-8676-0091)", - "Galchenkova, M. (0000-0003-0978-5695)", - "Middendorf, P. (0000-0002-5243-8384)", - "Fernandez Garcia, Y. (0000-0002-9592-2141)", - "Ehrt, C. (0000-0003-1428-0042)", - "Kiene, A. (0000-0001-7480-8027)", - "Klopprogge, B. (0000-0002-0718-1786)", - "Chapman, H. (0000-0002-4655-1743)", - "Sprenger, J. (0000-0001-7977-3484)", - "Kiene, A.", - "Galchenkova, M. (0000-0001-8676-0091)", - "Garcia, Y. (0000-0002-9592-2141)", - "Ehr, C. (0000-0003-1428-0042)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ot0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ot0", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with peptide from human tRNA methyltransferase TRMT1", - emdb: null, - pdb: { - dbId: "8D35", - method: "X-RAY DIFFRACTION", - keywords: - "protease, host-virus protein interaction, RNA modifying enzyme, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8D35", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8d35_final.pdb", - externalLink: "https://pdb-redo.eu/db/8d35", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9NXH9", - organism: null, - name: "tRNA (guanine(26)-N(2))-dimethyltransferase", - details: "", - altNames: - "tRNA 2,2-dimethylguanosine-26 methyltransferase,tRNA(guanine-26,N(2)-N(2)) methyltransferase,tRNA(m(2,2)G26)dimethyltransferase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "D'Oliviera, A. (0000-0002-5944-9609)", - "Mugridge, J.S. (0000-0002-1553-3008)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36865253", - title: - "Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease.", - journal: "Biorxiv (2023), 2692-8205", - doi: "https://doi.org/10.1101/2023.02.20.529306", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36865253", - pubDate: "2023", - abstract: "", - authors: [ - "Da Oliviera, A.", - "Dai, X.", - "Mottaghinia, S.", - "Geissler, E.P.", - "Etienne, L.", - "Zhang, Y.", - "Mugridge, J.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8d35_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8d35", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 Receptor Binding Domain bound to A6 repebody", - emdb: null, - pdb: { - dbId: "7YCO", - method: "X-RAY DIFFRACTION", - keywords: - "Severe acute respiratory syndrome coronavirus 2, Complex, PROTEIN BINDING", - refModels: [ - { - emdbId: null, - pdbId: "7YCO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7yco_final.pdb", - externalLink: "https://pdb-redo.eu/db/7yco", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "97265", - name: "Repebody (A6)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Kim, U.J. (0000-0002-9062-5842)", "Cho, H.S. (0000-0003-4067-4715)"], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 Receptor Binding Domain bound to A6 repebody", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kim, U.J. (0000-0002-9062-5842)", - "Cho, H.S. (0000-0003-4067-4715)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7yco_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7yco", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 main protease in its apo-form", - emdb: null, - pdb: { - dbId: "7UU9", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7UU9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uu9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uu9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36629751", - title: - "A Novel Y-Shaped, S-O-N-O-S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease.", - journal: "Acs Chem.Biol. 18: 449-455 (2023), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.2c00695", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36629751", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, K.S.", - "Blankenship, L.R.", - "Kuo, S.A.", - "Sheng, Y.J.", - "Li, P.", - "Fierke, C.A.", - "Russell, D.H.", - "Yan, X.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uu9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uu9", - }, - }, - { - title: - "Virtual screening for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors", - emdb: null, - pdb: { - dbId: "8DIG", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, MPro, nsp7, COVID-19, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DIG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dig_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dig", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "ZKUHTBIQDMFRSK-UHFFFAOYSA-N"], - dbauthors: ["Singh, I.", "Shoichet, B.K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37354015", - title: - "Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.", - journal: "Protein Sci. 32: e4712-e4712 (2023), 1469-896X", - doi: "https://doi.org/10.1002/pro.4712", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37354015", - pubDate: "2023", - abstract: "", - authors: [ - "Fink, E.A.", - "Bardine, C.", - "Gahbauer, S.", - "Singh, I.", - "Detomasi, T.", - "White, K.", - "Gu, S.", - "Wan, X.", - "Chen, J.", - "Ary, B.", - "Glenn, I.", - "O'Connell, J.", - "O'Donnell, H.", - "Fajtova, P.", - "Lyu, J.", - "Vigneron, S.", - "Young, N.J.", - "Kondratov, I.S.", - "Alisoltani, A.", - "Simons, L.M.", - "Lorenzo-Redondo, R.", - "Ozer, E.A.", - "Hultquist, J.F.", - "O'Donoghue, A.J.", - "Moroz, Y.", - "Taunton, J.", - "Renslo, A.R.", - "Irwin, J.J.", - "Garcia-Sastre, A.", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Craik, C.S.", - "Detomasi, T.C.", - "Moroz, Y.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dig_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dig", - }, - }, - { - title: - "Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S761-775", - emdb: null, - pdb: { - dbId: "8CMI", - method: "X-RAY DIFFRACTION", - keywords: - "HLA-II, HLA-DR, HLA-DR1, human leukocyte antigen, major histocompatibility complex, major histocompatibility complex class 2, SARS-CoV-2, coronavirus, COVID-19, Spike, omicron, BA.1, immune escape, viral variants, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CMI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cmi_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cmi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01903", - organism: "9606", - name: "HLA class II histocompatibility antigen, DR alpha chain", - details: "", - altNames: "MHC class II antigen DRA", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "MacLachlan, B.J. (0000-0002-2685-2733)", - "Mason, G.H. (0000-0002-7844-7190)", - "Sourfield, D.O. (0000-0002-0836-7718)", - "Godkin, A.J. (0000-0002-1910-7567)", - "Rizkallah, P.J. (0000-0002-9290-0369)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37471227", - title: - "Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.", - journal: "Cell Rep 42: 112827-112827 (2023), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2023.112827", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37471227", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, Y.", - "Mason, G.H.", - "Scourfield, D.O.", - "Greenshields-Watson, A.", - "Haigh, T.A.", - "Sewell, A.K.", - "Long, H.M.", - "Gallimore, A.M.", - "Rizkallah, P.", - "MacLachlan, B.J.", - "Godkin, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cmi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cmi", - }, - }, - { - title: - "Co-structure of SARS-CoV-2 (COVID-19 with covalent pyrazoline based inhibitors)", - emdb: null, - pdb: { - dbId: "8SK4", - method: "X-RAY DIFFRACTION", - keywords: "inhibitor, sars2, HYDROLASE, Viral Protein-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8SK4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8sk4_final.pdb", - externalLink: "https://pdb-redo.eu/db/8sk4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "RAXXELZNTBOGNW-UHFFFAOYSA-O", "DGVUQOIRXYABFV-QGZVFWFLSA-N"], - dbauthors: ["Ornelas, E.", "Knapp, M.S."], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "37069799", - title: - "Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors.", - journal: "Chembiochem: e202300116-e202300116 (2023), 1439-7633", - doi: "https://doi.org/10.1002/cbic.202300116", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37069799", - pubDate: "2023", - abstract: "", - authors: [ - "Moon, P.", - "Zammit, C.M.", - "Shao, Q.", - "Dovala, D.", - "Boike, L.", - "Henning, N.J.", - "Knapp, M.", - "Spradlin, J.N.", - "Ward, C.C.", - "Wolleb, H.", - "Fuller, D.", - "Blake, G.", - "Murphy, J.P.", - "Wang, F.", - "Lu, Y.", - "Moquin, S.A.", - "Tandeske, L.", - "Hesse, M.J.", - "McKenna, J.M.", - "Tallarico, J.A.", - "Schirle, M.", - "Toste, F.D. (0000-0001-8018-2198)", - "Nomura, D.K. (0000-0003-1614-8360)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8sk4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8sk4", - }, - }, - { - title: - "Virtual screening for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors", - emdb: null, - pdb: { - dbId: "8DIC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, MPro, nsp7, COVID-19, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DIC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dic_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dic", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "OOQAVDHJTTURSY-UHFFFAOYSA-N"], - dbauthors: ["Singh, I.", "Shoichet, B.K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37354015", - title: - "Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.", - journal: "Protein Sci. 32: e4712-e4712 (2023), 1469-896X", - doi: "https://doi.org/10.1002/pro.4712", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37354015", - pubDate: "2023", - abstract: "", - authors: [ - "Fink, E.A.", - "Bardine, C.", - "Gahbauer, S.", - "Singh, I.", - "Detomasi, T.", - "White, K.", - "Gu, S.", - "Wan, X.", - "Chen, J.", - "Ary, B.", - "Glenn, I.", - "O'Connell, J.", - "O'Donnell, H.", - "Fajtova, P.", - "Lyu, J.", - "Vigneron, S.", - "Young, N.J.", - "Kondratov, I.S.", - "Alisoltani, A.", - "Simons, L.M.", - "Lorenzo-Redondo, R.", - "Ozer, E.A.", - "Hultquist, J.F.", - "O'Donoghue, A.J.", - "Moroz, Y.", - "Taunton, J.", - "Renslo, A.R.", - "Irwin, J.J.", - "Garcia-Sastre, A.", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Craik, C.S.", - "Detomasi, T.C.", - "Moroz, Y.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dic_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dic", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 Spike RBD in complex with FP-12A Fab", - emdb: null, - pdb: { - dbId: "7YCK", - method: "X-RAY DIFFRACTION", - keywords: - "antibody, SARS-CoV-2, Spike, RBD, class 4, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7YCK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7yck_final.pdb", - externalLink: "https://pdb-redo.eu/db/7yck", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "FP-12A Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "FP-12A Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Chen, X.", "Nguyen, V.H.T."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36658148", - title: - "Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.", - journal: "Nat Commun 14: 311-311 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-35949-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36658148", - pubDate: "2023", - abstract: "", - authors: [ - "Huang, K.A. (0000-0001-6891-6945)", - "Chen, X. (0000-0002-4492-0883)", - "Mohapatra, A. (0000-0003-3468-6912)", - "Nguyen, H.T.V. (0000-0001-7577-3452)", - "Schimanski, L.", - "Tan, T.K. (0000-0001-8746-8308)", - "Rijal, P.", - "Vester, S.K. (0000-0002-4210-118X)", - "Hills, R.A.", - "Howarth, M. (0000-0001-8870-7147)", - "Keeffe, J.R. (0000-0002-5317-6398)", - "Cohen, A.A.", - "Kakutani, L.M.", - "Wu, Y.M.", - "Shahed-Al-Mahmud, M.", - "Chou, Y.C.", - "Bjorkman, P.J. (0000-0002-2277-3990)", - "Townsend, A.R. (0000-0002-3702-0107)", - "Ma, C. (0000-0002-4741-2307)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7yck_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7yck", - }, - }, - { - title: - "Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SGC8158", - emdb: null, - pdb: { - dbId: "8FRK", - method: "X-RAY DIFFRACTION", - keywords: "N7-guanine methyl transferase, SARS-CoV-2, nsp14, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8FRK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8frk_final.pdb", - externalLink: "https://pdb-redo.eu/db/8frk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P41212", - organism: "2697049", - name: - "Transcription factor ETV6,Guanine-N7 methyltransferase nsp14 chimera", - details: - "Fusion protein containing TELSAM (uniprot P41212) and SARS-CoV-2 nsp14 N7-Methyl Transferase domain (P0DTD1)", - altNames: - "ETS translocation variant 6,ETS-related protein Tel1,Tel,Non-structural protein 14,nsp14,Proofreading exoribonuclease nsp14,ExoN", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "LFQSCWFLJHTTHZ-UHFFFAOYSA-N", - "UDFJXRJYAZANFF-VBHAUSMQSA-N", - "NPYPAHLBTDXSSS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kottur, J. (0000-0002-8075-3883)", - "Aggarwal, A.K. (0000-0003-4389-0173)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37523415", - title: - "Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals.", - journal: "Plos Pathog. 19: e1011546-e1011546 (2023), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1011546", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37523415", - pubDate: "2023", - abstract: "", - authors: [ - "Kottur, J.", - "White, K.M.", - "Rodriguez, M.L.", - "Rechkoblit, O.", - "Quintana-Feliciano, R.", - "Nayar, A.", - "Garcia-Sastre, A.", - "Aggarwal, A.K. (0000-0003-4389-0173)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8frk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8frk", - }, - }, - { - title: - "Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates", - emdb: null, - pdb: { - dbId: "8DKK", - method: "X-RAY DIFFRACTION", - keywords: - "viral protein, HYDROLASE-HYDROLASE INHIBITOR complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DKK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dkk_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dkk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lu, J. (0000-0002-4090-5176)", - "Khan, M.B. (0000-0002-4164-9573)", - "Young, H.S. (0000-0002-5990-8422)", - "Lemieux, M.J. (0000-0003-4745-9153)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Mpro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals", - journal: "Acs Cent.Sci. 9: 696-708 (2023), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.3c00054", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, S.A.", - "Arutyunova, E.", - "Lu, J.", - "Khan, M.B.", - "Rut, W.", - "Zmudzinski, M.", - "Shahbaz, S.", - "Iyyathurai, J.", - "Moussa, E.W.", - "Turner, Z.", - "Bai, B.", - "Lamer, T.", - "Nieman, J.A.", - "Vederas, J.C.", - "Julien, O.", - "Drag, M.", - "Elahi, S.", - "Young, H.S.", - "Lemieux, M.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dkk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dkk", - }, - }, - { - title: - "Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, HSW-2", - emdb: null, - pdb: { - dbId: "7UZD", - method: "X-RAY DIFFRACTION", - keywords: - "immune system, neutralizing antibody, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7UZD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uzd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uzd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "HSW-2 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "HSW-2 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Fan, C.", "Bjorkman, P.J."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36370711", - title: - "Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes.", - journal: "Immunity 55: 2419-2435.e10 (2022), 1074-7613", - doi: "https://doi.org/10.1016/j.immuni.2022.10.019", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36370711", - pubDate: "2022", - abstract: "", - authors: [ - "Fan, C.", - "Cohen, A.A.", - "Park, M.", - "Hung, A.F.", - "Keeffe, J.R.", - "Gnanapragasam, P.N.P.", - "Lee, Y.E.", - "Gao, H.", - "Kakutani, L.M.", - "Wu, Z.", - "Kleanthous, H.", - "Malecek, K.E.", - "Williams, J.C.", - "Bjorkman, P.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uzd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uzd", - }, - }, - { - title: - "PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework -- Crystal structure of SARS-CoV-2 main protease in complex with Z1365651030 (Mpro-IBM0078)", - emdb: null, - pdb: { - dbId: "5SMN", - method: "X-RAY DIFFRACTION", - keywords: - "Diamond I04-1, single sequence-guideddeep generative framework, PanDDA, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5SMN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5smn_final.pdb", - externalLink: "https://pdb-redo.eu/db/5smn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "VADYKWPOUVEKIU-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Lukacik, P.", - "Strain-Damerell, C.M.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5smn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5smn", - }, - }, - { - title: - "Structure of N-terminal SARS-CoV-2 nonstructural protein 1 (nsp1) at atomic resolution", - emdb: null, - pdb: { - dbId: "8A55", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, nonstructural protein 1 (nsp1), N-terminal domain, atomic resolution, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8A55", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8a55_final.pdb", - externalLink: "https://pdb-redo.eu/db/8a55", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Host translation inhibitor nsp1", - details: "", - altNames: "Leader protein,Non-structural protein 1,nsp1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Ma, S. (0000-0002-9560-5082)", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Kozielski, F. (0000-0001-6096-9102)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36293303", - title: - "Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening.", - journal: "Int J Mol Sci 23 (2022), 1422-0067", - doi: "https://doi.org/10.1021/ci200227u", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36293303", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S. (0000-0002-2070-7770)", - "Lou, J.", - "Pinotsis, N. (0000-0002-5096-257X)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Haider, S. (0000-0003-2650-2925)", - "Kozielski, F. (0000-0001-6096-9102)", - "Ma, S.", - "Mykhaylyk, V. (0000-0003-0106-2724)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8a55_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8a55", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the non-covalent inhibitor GA-17S", - emdb: null, - pdb: { - dbId: "8ACD", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Main Protease, Non-covalent Inhibitor, Drug Design, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8ACD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8acd_final.pdb", - externalLink: "https://pdb-redo.eu/db/8acd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PBLOKSLGZKWIQI-KRWDZBQOSA-N"], - dbauthors: [ - "Liu, X.", - "Gao, S.", - "Strater, N. (0000-0002-2001-0500)", - "Mueller, C.", - "Sylvester, K.", - "Claff, T.", - "Weisse, R.H.", - "Tollefson, A.E.", - "Zhan, P.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36107752", - title: - "Discovery and Crystallographic Studies of Trisubstituted Piperazine Derivatives as Non-Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity and Low Toxicity.", - journal: "J.Med.Chem. 65: 13343-13364 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c01146", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36107752", - pubDate: "2022", - abstract: "", - authors: [ - "Gao, S.", - "Sylvester, K.", - "Song, L.", - "Claff, T.", - "Jing, L.", - "Woodson, M.", - "Weisse, R.H.", - "Cheng, Y.", - "Schakel, L.", - "Petry, M.", - "Gutschow, M.", - "Schiedel, A.C.", - "Strater, N.", - "Kang, D.", - "Xu, S.", - "Toth, K.", - "Tavis, J.", - "Tollefson, A.E.", - "Muller, C.E.", - "Liu, X.", - "Zhan, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8acd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8acd", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with antibody CC12.1 Fab and nanobody Nb-C4-225", - emdb: null, - pdb: { - dbId: "8ELO", - method: "X-RAY DIFFRACTION", - keywords: - "synthetic, nanobody, SARS-CoV-2, coronavirus, neutralization, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8ELO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8elo_final.pdb", - externalLink: "https://pdb-redo.eu/db/8elo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "32630", - name: "Nanobody Nb-C4-225", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.1 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.1 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Liu, H. 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(0009-0000-4564-8132)", - "Liu, J. (0000-0002-6038-593X)", - "Stanfield, R.L. (0000-0001-9521-9184)", - "Zhu, X. (0000-0002-6021-3740)", - "Turner, H.L.", - "Sok, D.", - "Huang, P.S. (0000-0002-7948-2895)", - "Burton, D.R. (0000-0001-6711-9864)", - "Ward, A.B. (0000-0001-7153-3769)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Jardine, J.G. 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(0000-0002-5531-6972)", - "Wang, Z.", - "Zhuang, X.", - "Zhang, S.", - "Chen, Z.", - "Zou, Y.", - "Sheng, J.", - "Li, T.", - "Tai, W.", - "Yu, J.", - "Wang, Y.", - "Zhang, Z.", - "Chen, Y. (0000-0002-5185-4781)", - "Tong, L. (0000-0002-2717-919X)", - "Yu, X. (0000-0002-7724-8317)", - "Wu, L.", - "Chen, D.", - "Zhang, R. (0000-0001-5037-1035)", - "Jin, N.", - "Shen, W. (0000-0001-8388-729X)", - "Zhao, J. (0000-0003-2515-5589)", - "Tian, M. (0000-0003-0360-3635)", - "Wang, X. (0000-0003-3136-8070)", - "Cheng, G. (0000-0001-7447-5488)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x2h_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x2h", - }, - }, - { - title: - "Crystal structure of F2F-2020209-00X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.", - emdb: null, - pdb: { - dbId: "7Q5E", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7Q5E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7q5e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7q5e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "AJCTZJFZKXWMHB-OJJQZRKESA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36332546", - title: - "Easy access to alpha-ketoamides as SARS-CoV-2 and MERS M pro inhibitors via the PADAM oxidation route.", - journal: "Eur.J.Med.Chem. 244: 114853-114853 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114853", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36332546", - pubDate: "2022", - abstract: "", - authors: [ - "Pelliccia, S.", - "Cerchia, C.", - "Esposito, F.", - "Cannalire, R.", - "Corona, A.", - "Costanzi, E.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Brindisi, M.", - "Storici, P.", - "Tramontano, E.", - "Summa, V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7q5e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7q5e", - }, - }, - { - title: "SARS-CoV-2 RBD in complex with a Fab fragment of a neutralising antibody mRBD2", - emdb: null, - pdb: { - dbId: "8BE1", - method: "X-RAY DIFFRACTION", - keywords: "FAB, antibody, SARS-COV-2, RBD, neutralising, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8BE1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8be1_final.pdb", - externalLink: "https://pdb-redo.eu/db/8be1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "10090", - name: "Antibody heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "Antibody light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Lulla, A.", - "Brear, P.", - "Fischer, K.", - "Hollfelder, F.", - "Hyvonen, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Microfluidics-enabled fluorescence-activated cell sorting of single pathogen-specific antibody secreting cells for the rapid discovery of monoclonal antibodies", - journal: "Biorxiv (2023), 2692-8205", - doi: "https://doi.org/10.1101/2023.01.10.523494", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Fischer, K.", - "Lulla, A.", - "So, T.Y.", - "Pereyra-Gerber, P.", - "Raybould, M.I.J.", - "Kohler, T.N.", - "Kaminski, T.S.", - "Yam-Puc, J.C.", - "Hughes, R.", - "Leiss-Maier, F.", - "Brear, P.", - "Matheson, N.J.", - "Deane, C.M.", - "Hyvonen, M.", - "Thaventhiran, J.E.D.", - "Hollfelder, F.", - 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(0000-0001-6078-4095)", - "Afonine, P.V.", - "Grosse-Kunstleve, R.W.", - "Echols, N.", - "Headd, J.J.", - "Moriarty, N.W.", - "Mustyakimov, M.", - "Terwilliger, T.C.", - "Urzhumtsev, A.", - "Zwart, P.H.", - "Adams, P.D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z2k_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z2k", - }, - }, - { - title: - "crystal structures of diastereomer (R,S,S)-13b (13b-H) in complex with the SARS-CoV-2 Mpro.", - emdb: null, - pdb: { - dbId: "8A4Q", - method: "X-RAY DIFFRACTION", - keywords: "SARSCoV2, COVID19, Mpro, 3CLpro, inhibitor, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8A4Q", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8a4q_final.pdb", - externalLink: "https://pdb-redo.eu/db/8a4q", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "HIQXVKIISKTUPK-FTZGMBJCSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, L.", - "Ibrahim, M. (0000-0002-1431-9755)", - "Hilgenfeld, R. (0000-0001-8850-2977)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36179320", - title: - "Diastereomeric Resolution Yields Highly Potent Inhibitor of SARS-CoV-2 Main Protease.", - journal: "J.Med.Chem. 65: 13328-13342 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c01131", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36179320", - pubDate: "2022", - abstract: "", - authors: [ - "Cooper, M.S.", - "Zhang, L.", - "Ibrahim, M.", - "Zhang, K.", - "Sun, X.", - "Roske, J.", - "Gohl, M.", - "Bronstrup, M.", - "Cowell, J.K.", - "Sauerhering, L.", - "Becker, S.", - "Vangeel, L.", - "Jochmans, D.", - "Neyts, J.", - "Rox, K.", - "Marsh, G.P.", - "Maple, H.J.", - "Hilgenfeld, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8a4q_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8a4q", - }, - }, - { - title: - "Improved Feline Drugs as SARS-CoV-2 Mpro Inhibitors: Structure-Activity Studies & Micellar Solubilization for Enhanced Bioavailability", - emdb: null, - pdb: { - dbId: "7LCR", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, 3CLpro, coronavirus, main protease, kinetics, SARS, VIRAL PROTEIN, Hydrolase-Hydrolase Inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LCR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lcr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lcr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KSFOLLAEZGAOFV-SZMVWBNQSA-N"], - dbauthors: [ - "Khan, M.B. (0000-0002-4164-9573)", - "Lemieux, M.J. (0000-0003-4745-9153)", - "Arutyunova, E.", - "Young, H.S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli O103:H2", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34118724", - title: - "Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies.", - journal: "Eur.J.Med.Chem. 222: 113584-113584 (2021), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2021.113584", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34118724", - pubDate: "2021", - abstract: "", - authors: [ - "Vuong, W.", - "Fischer, C.", - "Khan, M.B.", - "van Belkum, M.J.", - "Lamer, T.", - "Willoughby, K.D.", - "Lu, J.", - "Arutyunova, E.", - "Joyce, M.A.", - "Saffran, H.A.", - "Shields, J.A.", - "Young, H.S.", - "Nieman, J.A.", - "Tyrrell, D.L.", - "Lemieux, M.J.", - "Vederas, J.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lcr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lcr", - }, - }, - { - title: "an engineered 5-helix bundle derived from SARS-CoV-2 S2 in complex with HR2P", - emdb: null, - pdb: { - dbId: "7Y9N", - method: "X-RAY DIFFRACTION", - keywords: "5HB, VIRUS PROTEIN/INHIBITOR, VIRUS PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7Y9N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7y9n_final.pdb", - externalLink: "https://pdb-redo.eu/db/7y9n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2',5HB-H2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "SARS-coV-2 S2 subunit", - details: "", - altNames: "Spike protein S2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Lin, X.", "Lu, G.W.", "Guo, L.Y.", "Lin, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35757908", - title: - "An engineered 5-helix bundle derived from SARS-CoV-2 S2 pre-binds sarbecoviral spike at both serological- and endosomal-pH to inhibit virus entry.", - journal: "Emerg Microbes Infect 11: 1920-1935 (2022), 2222-1751", - doi: "https://doi.org/10.1080/22221751.2022.2095308", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35757908", - pubDate: "2022", - abstract: "", - authors: [ - "Lin, X.", - "Guo, L.", - "Lin, S.", - "Chen, Z.", - "Yang, F.", - "Yang, J.", - "Wang, L.", - "Wen, A.", - "Duan, Y.", - "Zhang, X.", - "Dai, Y.", - "Yin, K.", - "Yuan, X.", - "Yu, C.", - "He, B.", - "Cao, Y.", - "Dong, H.", - "Li, J.", - "Zhao, Q.", - "Lu, G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7y9n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7y9n", - }, - }, - { - title: "3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7Y8J", - method: "X-RAY DIFFRACTION", - keywords: - "human antibody, broad, coronavirus, ANTIMICROBIAL PROTEIN, ANTIMICROBIAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7Y8J", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7y8j_final.pdb", - externalLink: "https://pdb-redo.eu/db/7y8j", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "heavy chain of 3D1", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "light chain of 3D1", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Lei, Y. (0000-0003-1775-5533)"], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Cross-reactive epitopes between HIV and Coronavirus revealed by 3D1", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Lei, Y. (0000-0003-1775-5533)"], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7y8j_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7y8j", - }, - }, - { - title: - "Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates", - emdb: null, - pdb: { - dbId: "8DKJ", - method: "X-RAY DIFFRACTION", - keywords: - "viral protein, HYDROLASE-HYDROLASE INHIBITOR complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DKJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dkj_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dkj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lu, J. (0000-0002-4090-5176)", - "Khan, M.B. (0000-0002-4164-9573)", - "Young, H.S. (0000-0002-5990-8422)", - "Lemieux, M.J. (0000-0003-4745-9153)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Mpro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals", - journal: "Acs Cent.Sci. 9: 696-708 (2023), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.3c00054", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, S.A.", - "Arutyunova, E.", - "Lu, J.", - "Khan, M.B.", - "Rut, W.", - "Zmudzinski, M.", - "Shahbaz, S.", - "Iyyathurai, J.", - "Moussa, E.W.", - "Turner, Z.", - "Bai, B.", - "Lamer, T.", - "Nieman, J.A.", - "Vederas, J.C.", - "Julien, O.", - "Drag, M.", - "Elahi, S.", - "Young, H.S.", - "Lemieux, M.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dkj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dkj", - }, - }, - { - title: - "Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SGC0946", - emdb: null, - pdb: { - dbId: "8FRJ", - method: "X-RAY DIFFRACTION", - keywords: "N7-guanine methyl transferase, SARS-CoV-2, nsp14, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8FRJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8frj_final.pdb", - externalLink: "https://pdb-redo.eu/db/8frj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P41212", - organism: "2697049", - name: - "Transcription factor ETV6,Guanine-N7 methyltransferase nsp14 chimera", - details: - "Fusion protein containing TELSAM (uniprot P41212) and SARS-CoV-2 nsp14 N7-Methyl Transferase domain (P0DTD1)", - altNames: - "ETS translocation variant 6,ETS-related protein Tel1,Tel,Non-structural protein 14,nsp14,Proofreading exoribonuclease nsp14,ExoN", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "IQCKJUKAQJINMK-HUBRGWSESA-N"], - dbauthors: [ - "Kottur, J. (0000-0002-8075-3883)", - "Aggarwal, A.K. (0000-0003-4389-0173)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37523415", - title: - "Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals.", - journal: "Plos Pathog. 19: e1011546-e1011546 (2023), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1011546", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37523415", - pubDate: "2023", - abstract: "", - authors: [ - "Kottur, J.", - "White, K.M.", - "Rodriguez, M.L.", - "Rechkoblit, O.", - "Quintana-Feliciano, R.", - "Nayar, A.", - "Garcia-Sastre, A.", - "Aggarwal, A.K. (0000-0003-4389-0173)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8frj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8frj", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab", - emdb: null, - pdb: { - dbId: "7WNB", - method: "X-RAY DIFFRACTION", - keywords: - "spike, coronavirus, viral protein, Fab, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7WNB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wnb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wnb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Yamamoto, A. (0000-0002-2928-2828)", - "Higashiura, A. (0000-0001-8448-9349)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37041231", - title: - "Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.", - journal: "Commun Biol 6: 395-395 (2023), 2399-3642", - doi: "https://doi.org/10.1038/s42003-023-04782-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37041231", - pubDate: "2023", - abstract: "", - authors: [ - "Shitaoka, K. (0000-0002-2070-1520)", - "Higashiura, A.", - "Kawano, Y.", - "Yamamoto, A.", - "Mizoguchi, Y.", - "Hashiguchi, T. (0000-0001-7578-7571)", - "Nishimichi, N.", - "Huang, S.", - "Ito, A. (0000-0002-7552-0073)", - "Ohki, S.", - "Kanda, M.", - "Taniguchi, T.", - "Yoshizato, R.", - "Azuma, H.", - "Kitajima, Y.", - "Yokosaki, Y.", - "Okada, S. (0000-0002-4622-5657)", - "Sakaguchi, T. (0000-0002-3754-1252)", - "Yasuda, T. (0000-0001-9997-6852)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wnb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wnb", - }, - }, - { - title: - "Virtual screening for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors", - emdb: null, - pdb: { - dbId: "8DIB", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, MPro, nsp7, COVID-19, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DIB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dib_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dib", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "CNGABJMZUSIMFZ-UHFFFAOYSA-N"], - dbauthors: ["Singh, I.", "Shoichet, B.K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37354015", - title: - "Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.", - journal: "Protein Sci. 32: e4712-e4712 (2023), 1469-896X", - doi: "https://doi.org/10.1002/pro.4712", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37354015", - pubDate: "2023", - abstract: "", - authors: [ - "Fink, E.A.", - "Bardine, C.", - "Gahbauer, S.", - "Singh, I.", - "Detomasi, T.", - "White, K.", - "Gu, S.", - "Wan, X.", - "Chen, J.", - "Ary, B.", - "Glenn, I.", - "O'Connell, J.", - "O'Donnell, H.", - "Fajtova, P.", - "Lyu, J.", - "Vigneron, S.", - "Young, N.J.", - "Kondratov, I.S.", - "Alisoltani, A.", - "Simons, L.M.", - "Lorenzo-Redondo, R.", - "Ozer, E.A.", - "Hultquist, J.F.", - "O'Donoghue, A.J.", - "Moroz, Y.", - "Taunton, J.", - "Renslo, A.R.", - "Irwin, J.J.", - "Garcia-Sastre, A.", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Craik, C.S.", - "Detomasi, T.C.", - "Moroz, Y.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dib_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dib", - }, - }, - { - title: - "Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates", - emdb: null, - pdb: { - dbId: "8DKH", - method: "X-RAY DIFFRACTION", - keywords: - "viral protein, HYDROLASE-HYDROLASE INHIBITOR complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DKH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dkh_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dkh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lu, J. (0000-0002-4090-5176)", - "Khan, M.B. (0000-0002-4164-9573)", - "Young, H.S. (0000-0002-5990-8422)", - "Lemieux, M.J. (0000-0003-4745-9153)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Mpro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals", - journal: "Acs Cent.Sci. 9: 696-708 (2023), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.3c00054", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Chen, S.A.", - "Arutyunova, E.", - "Lu, J.", - "Khan, M.B.", - "Rut, W.", - "Zmudzinski, M.", - "Shahbaz, S.", - "Iyyathurai, J.", - "Moussa, E.W.", - "Turner, Z.", - "Bai, B.", - "Lamer, T.", - "Nieman, J.A.", - "Vederas, J.C.", - "Julien, O.", - "Drag, M.", - "Elahi, S.", - "Young, H.S.", - "Lemieux, M.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dkh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dkh", - }, - }, - { - title: "SARS-CoV-2 3CLPro Peptidomimetic Inhibitor TPM5", - emdb: null, - pdb: { - dbId: "7WO2", - method: "X-RAY DIFFRACTION", - keywords: "SARA-CoV-2 main protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WO2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wo2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wo2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "BLZXYDNCPITFHC-JPLJXNOCSA-N"], - dbauthors: ["Wang, Y.", "Ye, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35216507", - title: - "Discovery of SARS-CoV-2 3CL Pro Peptidomimetic Inhibitors through the Catalytic Dyad Histidine-Specific Protein-Ligand Interactions.", - journal: "Int J Mol Sci 23 (2022), 1422-0067", - doi: "https://doi.org/10.3390/ijms23042392", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35216507", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, Y.", - "Xu, B. (0000-0002-0137-3381)", - "Ma, S.", - "Wang, H.", - "Shang, L.", - "Zhu, C. (0000-0003-0260-6287)", - "Ye, S. (0000-0001-9300-6257)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wo2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wo2", - }, - }, - { - title: - "A SARS-CoV2 major protease non-covalent ligand structure determined to 2.0 A resolution", - emdb: null, - pdb: { - dbId: "7PFM", - method: "X-RAY DIFFRACTION", - keywords: "cysteine protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7PFM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7pfm_final.pdb", - externalLink: "https://pdb-redo.eu/db/7pfm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AJXIAISTEXNTHM-OAQYLSRUSA-N"], - dbauthors: [ - "Moche, M. (0000-0002-4834-7076)", - "Moodie, L. (0000-0002-9500-4535)", - "Strandback, E. (0000-0003-3990-0084)", - "Nyman, T. (0000-0003-0141-8989)", - "Sandstrom, A. (0000-0001-5720-2904)", - "Akaberi, D. (0000-0002-9595-9796)", - "Lennerstrand, J. (0000-0002-1093-0530)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The SARS-CoV2 major protease (Mpro) in complex with a non-covalent inhibitory ligand at 2 A resolution", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Moche, M. (0000-0002-4834-7076)", - "Moodie, L. (0000-0002-9500-4535)", - "Strandback, E. (0000-0003-3990-0084)", - "Nyman, T. (0000-0003-0141-8989)", - "Akaberi, D. (0000-0002-9595-9796)", - "Lennerstrand, J. (0000-0002-1093-0530)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7pfm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7pfm", - }, - }, - { - title: - "Crystal structure of antibody Ab246 in complex with SARS-CoV-2 receptor binding domain", - emdb: null, - pdb: { - dbId: "7U8E", - method: "X-RAY DIFFRACTION", - keywords: - "Neutralizing antibody, SARS-CoV-2, Ab246, receptor binding domain, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7U8E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u8e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u8e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Antibody Ab246 Fab heavy chain", - details: "fragment antigen-binding (Fab) heavy chain", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Antibody Ab246 Fab light chain", - details: "fragment antigen-binding (Fab) light chain", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Sankhala, R.S. (0000-0001-8639-5290)", - "Joyce, M.G. (0000-0002-6808-7232)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain.", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Sankhala, R.S. (0000-0001-8639-5290)", - "Dussupt, V.", - "Modjarrad, K.", - "Joyce, M.G. (0000-0002-6808-7232)", - "Jensen, J. (0000-0002-8818-7513)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7u8e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7u8e", - }, - }, - { - title: - "PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework -- Crystal structure of SARS-CoV-2 main protease in complex with Z1633315555 (Mpro-IBM0058)", - emdb: null, - pdb: { - dbId: "5SMM", - method: "X-RAY DIFFRACTION", - keywords: - "Diamond I04-1, single sequence-guideddeep generative framework, PanDDA, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5SMM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5smm_final.pdb", - externalLink: "https://pdb-redo.eu/db/5smm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "UQVBMSYLQWGFOX-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Lukacik, P.", - "Strain-Damerell, C.M.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5smm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5smm", - }, - }, - { - title: - "Crystal structure of the recombinant protein HR121 from the S2 protein of SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7WXZ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, S2, recombinant protein, HR121, fusion intermediate, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WXZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wxz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wxz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Lu, Y.", "Zheng, Y.T.", "Ouyang, S.", "Pang, W.", "Zhao, Y.B."], - details: [ - { - sample: { - name: "", - exprSystem: "Severe acute respiratory syndrome coronavirus 2", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36357786", - title: - "A variant-proof SARS-CoV-2 vaccine targeting HR1 domain in S2 subunit of spike protein.", - journal: "Cell Res. 32: 1068-1085 (2022), 1001-0602", - doi: "https://doi.org/10.1038/s41422-022-00746-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36357786", - pubDate: "2022", - abstract: "", - authors: [ - "Pang, W.", - "Lu, Y.", - "Zhao, Y.B.", - "Shen, F.", - "Fan, C.F.", - "Wang, Q.", - "He, W.Q.", - "He, X.Y.", - "Li, Z.K.", - "Chen, T.T.", - "Yang, C.X.", - "Li, Y.Z.", - "Xiao, S.X.", - "Zhao, Z.J.", - "Huang, X.S.", - "Luo, R.H.", - "Yang, L.M.", - "Zhang, M.", - "Dong, X.Q.", - "Li, M.H.", - "Feng, X.L.", - "Zhou, Q.C.", - "Qu, W.", - "Jiang, S.", - "Ouyang, S.", - "Zheng, Y.T.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wxz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wxz", - }, - }, - { - title: - "Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism", - emdb: null, - pdb: { - dbId: "8CX9", - method: "X-RAY DIFFRACTION", - keywords: - "inhibitor complex, allosteric inhibition, VIRAL PROTEIN, VIRAL PROTEIN-SIGNALING PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "8CX9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cx9_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cx9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62987", - organism: "9606", - name: "Ubiquitin variant UbV.CV2.1", - details: "", - altNames: "CEP52,Ubiquitin A-52 residue ribosomal protein fusion product 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "CPELXLSAUQHCOX-UHFFFAOYSA-M", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Patel, A.", - "Singer, A.U.", - "Slater, C.L.", - "Russel, R.", - "Mark, B.L.", - "Sidhu, S.S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36548304", - title: - "Ubiquitin variants potently inhibit SARS-CoV-2 PLpro and viral replication via a novel site distal to the protease active site.", - journal: "Plos Pathog. 18: e1011065-e1011065 (2022), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1011065", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36548304", - pubDate: "2022", - abstract: "", - authors: [ - "van Vliet, V.J.E. (0000-0003-0401-3055)", - "Huynh, N.", - "Pala, J.", - "Patel, A.", - "Singer, A.", - "Slater, C.", - "Chung, J.", - "van Huizen, M.", - "Teyra, J.", - "Miersch, S.", - "Luu, G.K.", - "Ye, W.", - "Sharma, N.", - "Ganaie, S.S.", - "Russell, R.", - "Chen, C.", - "Maynard, M.", - "Amarasinghe, G.K.", - "Mark, B.L.", - "Kikkert, M.", - "Sidhu, S.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cx9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cx9", - }, - }, - { - title: - "Epitope-directed anti-SARS CoV 2 scFv engineered against the key spike protein region.", - emdb: null, - pdb: { - dbId: "7YUE", - method: "X-RAY DIFFRACTION", - keywords: "Antibody, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7YUE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7yue_final.pdb", - externalLink: "https://pdb-redo.eu/db/7yue", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Single chain variable Fragment", - details: - "Gly109-Gly132 are glycine-serine linker(disordered in the structure);Ala243-His253 is a purification tag", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2", - details: - "Lysine at N-terminal is used for biochemical assays; two serines were added at N-terminal to increase the peptide solubility in PBS", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Kumar, U. (0000-0001-6080-3313)", - "Jaiswal, D. (0000-0002-9565-1302)", - "Gaur, V. (0000-0002-7292-2720)", - "Salunke, D.M. (0000-0001-9003-7373)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36691733", - title: - "Epitope-directed anti-SARS-CoV-2 scFv engineered against the key spike protein region could block membrane fusion.", - journal: "Protein Sci. 32: e4575-e4575 (2023), 1469-896X", - doi: "https://doi.org/10.1002/pro.4575", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36691733", - pubDate: "2023", - abstract: "", - authors: [ - "Jaiswal, D.", - "Kumar, U.", - "Gaur, V.", - "Salunke, D.M. (0000-0002-7800-965X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7yue_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7yue", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab", - emdb: null, - pdb: { - dbId: "8I5I", - method: "X-RAY DIFFRACTION", - keywords: - "spike, coronavirus, viral protein, Fab, VIRUS, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8I5I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8i5i_final.pdb", - externalLink: "https://pdb-redo.eu/db/8i5i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Yamamoto, A. (0000-0002-2928-2828)", - "Higashiura, A. (0000-0001-8448-9349)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37041231", - title: - "Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.", - journal: "Commun Biol 6: 395-395 (2023), 2399-3642", - doi: "https://doi.org/10.1038/s42003-023-04782-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37041231", - pubDate: "2023", - abstract: "", - authors: [ - "Shitaoka, K. (0000-0002-2070-1520)", - "Higashiura, A.", - "Kawano, Y.", - "Yamamoto, A.", - "Mizoguchi, Y.", - "Hashiguchi, T. (0000-0001-7578-7571)", - "Nishimichi, N.", - "Huang, S.", - "Ito, A. (0000-0002-7552-0073)", - "Ohki, S.", - "Kanda, M.", - "Taniguchi, T.", - "Yoshizato, R.", - "Azuma, H.", - "Kitajima, Y.", - "Yokosaki, Y.", - "Okada, S. (0000-0002-4622-5657)", - "Sakaguchi, T. (0000-0002-3754-1252)", - "Yasuda, T. (0000-0001-9997-6852)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8i5i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8i5i", - }, - }, - { - title: "Crystal structure of nanobody Nb70 with antibody 1F11 fab and SARS-CoV-2 RBD", - emdb: null, - pdb: { - dbId: "7X2K", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, nanobody, spike, receptor binding domain, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7X2K", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x2k_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x2k", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "1F11-H", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "1F11-L", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "Nb70", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Zhang, L.Q.", "Wang, X.Q.", "Ren, Y.F.", "Li, M.X."], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36575191", - title: - "Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses.", - journal: "Nat Commun 13: 7957-7957 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-35642-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36575191", - pubDate: "2022", - abstract: "", - authors: [ - "Li, M.", - "Ren, Y.", - "Aw, Z.Q. (0000-0002-6097-4099)", - "Chen, B.", - "Yang, Z.", - "Lei, Y.", - "Cheng, L.", - "Liang, Q.", - "Hong, J. (0000-0003-1148-0444)", - "Yang, Y. (0000-0001-6824-7446)", - "Chen, J.", - "Wong, Y.H. (0000-0001-6704-9130)", - "Wei, J.", - "Shan, S.", - "Zhang, S. (0000-0003-1703-3848)", - "Ge, J. (0000-0001-9366-1470)", - "Wang, R. (0000-0002-8040-7913)", - "Dong, J.Z.", - "Chen, Y.", - "Shi, X.", - "Zhang, Q.", - "Zhang, Z. (0000-0002-3544-1389)", - "Chu, J.J.H. (0000-0002-1673-6819)", - "Wang, X.", - "Zhang, L. (0000-0003-4931-509X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x2k_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x2k", - }, - }, - { - title: "SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex", - emdb: null, - pdb: { - dbId: "7XIK", - method: "X-RAY DIFFRACTION", - keywords: "COVID-19, antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7XIK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xik_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xik", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "B38 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "B38 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wang, Y.", - "Wu, Z.", - "Shi, R.", - "Han, X. (0000-0003-4751-1740)", - "Yan, J. (0000-0001-7140-5548)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Shi, R.", - "Wang, Y.", - "Wu, Z.", - "Han, X. (0000-0003-4751-1740)", - "Yan, J. (0000-0001-7140-5548)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xik_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xik", - }, - }, - { - title: - "Crystal structure of F2F-2020216-01X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.", - emdb: null, - pdb: { - dbId: "7Q5F", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7Q5F", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7q5f_final.pdb", - externalLink: "https://pdb-redo.eu/db/7q5f", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "GYPKOWHKPVSQIO-RZOLNQLPSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "NHNBFGGVMKEFGY-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36332546", - title: - "Easy access to alpha-ketoamides as SARS-CoV-2 and MERS M pro inhibitors via the PADAM oxidation route.", - journal: "Eur.J.Med.Chem. 244: 114853-114853 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114853", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36332546", - pubDate: "2022", - abstract: "", - authors: [ - "Pelliccia, S.", - "Cerchia, C.", - "Esposito, F.", - "Cannalire, R.", - "Corona, A.", - "Costanzi, E.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Brindisi, M.", - "Storici, P.", - "Tramontano, E.", - "Summa, V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7q5f_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7q5f", - }, - }, - { - title: - "Crystal structure of neutralizing VHH P17 in complex with SARS-CoV-2 Alpha variant spike receptor-binding domain", - emdb: null, - pdb: { - dbId: "8GZ5", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, spike RBD, nanobody, VHH, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8GZ5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gz5_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gz5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "Nanobody P17", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Yamaguchi, K. (0000-0002-5940-6924)", - "Anzai, I. (0000-0001-9307-943X)", - "Maeda, R. (0000-0002-1514-1071)", - "Moriguchi, M.", - "Watanabe, T.", - "Imura, A. (0000-0002-8673-8983)", - "Takaori-Kondo, A. (0000-0001-7678-4284)", - "Inoue, T. (0000-0001-5337-5066)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36413757", - title: - "Structural insights into the rational design of a nanobody that binds with high affinity to the SARS-CoV-2 spike variant.", - journal: "J.Biochem. 173: 115-127 (2023), 0021-924X", - doi: "https://doi.org/10.1093/jb/mvac096", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36413757", - pubDate: "2023", - abstract: "", - authors: [ - "Yamaguchi, K.", - "Anzai, I.", - "Maeda, R.", - "Moriguchi, M.", - "Watanabe, T.", - "Imura, A.", - "Takaori-Kondo, A.", - "Inoue, T.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gz5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gz5", - }, - }, - { - title: "Crystal structure of auxiliary protein in complex with human nuclear protein", - emdb: null, - pdb: { - dbId: "7F60", - method: "X-RAY DIFFRACTION", - keywords: "immune system, auxiliary protein, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7F60", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f60_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f60", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P78406", - organism: "9606", - name: "mRNA export factor", - details: "", - altNames: "Rae1 protein homolog,mRNA-associated protein mrnp 41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P52948", - organism: "9606", - name: "Nuclear pore complex protein Nup98-Nup96", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC6", - organism: "2697049", - name: "ORF6 protein", - details: "", - altNames: - "ORF6,Accessory protein 6,Non-structural protein 6,ns6,Protein X3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Gao, X.", "Cui, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Insect cell expression vector pTIE1", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport", - journal: "Nat Commun 13 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-32489-5", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Gao, X.", - "Tian, H.", - "Zhu, K.", - "Li, Q.", - "Hao, W.", - "Wang, L.", - "Qin, B.", - "Deng, H.", - "Cui, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7f60_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7f60", - }, - }, - { - title: "SARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody", - emdb: null, - pdb: { - dbId: "8BH5", - method: "X-RAY DIFFRACTION", - keywords: - "Viral Protein/Immune system, SARS-CoV-2, Omicron, BA.2.12.1, RBD, Beta-27, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8BH5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8bh5_final.pdb", - externalLink: "https://pdb-redo.eu/db/8bh5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Beta-27 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-27 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody C1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "NBIIXXVUZAFLBC-UHFFFAOYSA-K"], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I.", "Huo, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36319620", - title: - "Humoral responses against SARS-CoV-2 Omicron BA.2.11, BA.2.12.1 and BA.2.13 from vaccine and BA.1 serum.", - journal: "Cell Discov 8: 119-119 (2022), 2056-5968", - doi: "https://doi.org/10.1038/s41421-022-00482-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36319620", - pubDate: "2022", - abstract: "", - authors: [ - "Huo, J. (0000-0002-7899-1815)", - "Dijokaite-Guraliuc, A.", - "Nutalai, R.", - "Das, R.", - "Zhou, D.", - "Mentzer, A.J. (0000-0002-4502-2209)", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8bh5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8bh5", - }, - }, - { - title: "SARS-CoV-2-prototyped-RBD and CB6-092-Fab complex", - emdb: null, - pdb: { - dbId: "7XEI", - method: "X-RAY DIFFRACTION", - keywords: - "complex, antibody, receptor, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7XEI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xei_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xei", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CB6-092-Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CB6-092-Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wang, Y.", "Feng, Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2-prototyped-RBD and CB6-092-Fab complex", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Wang, Y.", "Feng, Y."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xei_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xei", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab", - emdb: null, - pdb: { - dbId: "8I5H", - method: "X-RAY DIFFRACTION", - keywords: - "spike, coronavirus, viral protein, Fab, VIRAL PROTEIN-IMMUNE SYSTEM complex, VIRUS", - refModels: [ - { - emdbId: null, - pdbId: "8I5H", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8i5h_final.pdb", - externalLink: "https://pdb-redo.eu/db/8i5h", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Yamamoto, A. (0000-0002-2928-2828)", - "Higashiura, A. (0000-0001-8448-9349)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37041231", - title: - "Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.", - journal: "Commun Biol 6: 395-395 (2023), 2399-3642", - doi: "https://doi.org/10.1038/s42003-023-04782-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37041231", - pubDate: "2023", - abstract: "", - authors: [ - "Shitaoka, K. (0000-0002-2070-1520)", - "Higashiura, A.", - "Kawano, Y.", - "Yamamoto, A.", - "Mizoguchi, Y.", - "Hashiguchi, T. (0000-0001-7578-7571)", - "Nishimichi, N.", - "Huang, S.", - "Ito, A. (0000-0002-7552-0073)", - "Ohki, S.", - "Kanda, M.", - "Taniguchi, T.", - "Yoshizato, R.", - "Azuma, H.", - "Kitajima, Y.", - "Yokosaki, Y.", - "Okada, S. (0000-0002-4622-5657)", - "Sakaguchi, T. (0000-0002-3754-1252)", - "Yasuda, T. (0000-0001-9997-6852)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8i5h_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8i5h", - }, - }, - { - title: - "PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework -- Crystal structure of SARS-CoV-2 main protease in complex with Z68337194 (Mpro-IBM0045)", - emdb: null, - pdb: { - dbId: "5SML", - method: "X-RAY DIFFRACTION", - keywords: - "Diamond I04-1, single sequence-guideddeep generative framework, PanDDA, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5SML", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sml_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sml", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "UMTNBAIWJVAAGI-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Lukacik, P.", - "Strain-Damerell, C.M.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sml_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sml", - }, - }, - { - title: "The SARS-CoV2 major protease (Mpro) apo structure to 1.8 A resolution", - emdb: null, - pdb: { - dbId: "7PFL", - method: "X-RAY DIFFRACTION", - keywords: "cysteine protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7PFL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7pfl_final.pdb", - externalLink: "https://pdb-redo.eu/db/7pfl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: [ - "Moche, M. (0000-0002-4834-7076)", - "Moodie, L. (0000-0002-9500-4535)", - "Strandback, E. (0000-0003-3990-0084)", - "Nyman, T. (0000-0003-0141-8989)", - "Akaberi, D. (0000-0002-9595-9796)", - "Lennerstrand, J. (0000-0002-1093-0530)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The SARS-CoV2 major protease (Mpro) in complex with a non-covalent inhibitory ligand at 2 A resolution", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Moche, M. (0000-0002-4834-7076)", - "Moodie, L. (0000-0002-9500-4535)", - "Strandback, E. (0000-0003-3990-0084)", - "Nyman, T. (0000-0003-0141-8989)", - "Akaberi, D. (0000-0002-9595-9796)", - "Lennerstrand, J. (0000-0002-1093-0530)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7pfl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7pfl", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 main protease in complex with Z-DEVD-FMK", - emdb: null, - pdb: { - dbId: "7WQ8", - method: "X-RAY DIFFRACTION", - keywords: "main protease, 3C-like protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WQ8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wq8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wq8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Z-DEVD-FMK", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Chen, Y.", "Wang, Y.C.", "Yang, C.S.", "Hou, M.H.", "Tsai, C.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 main protease in complex with Z-DEVD-FMK", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Wang, Y.C.", - "Yang, C.S.", - "Hou, M.H.", - "Tsai, C.L.", - "Chen, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wq8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wq8", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 main protease in complex with Z-IETD-FMK", - emdb: null, - pdb: { - dbId: "7WQ9", - method: "X-RAY DIFFRACTION", - keywords: "main protease, 3C-like protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WQ9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wq9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wq9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Z-IETD-FMK", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Chen, Y.", "Wang, Y.C.", "Yang, C.S.", "Hou, M.H.", "Tsai, C.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 main protease in complex with Z-IETD-FMK", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Wang, Y.C.", - "Yang, C.S.", - "Hou, M.H.", - "Tsai, C.L.", - "Chen, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wq9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wq9", - }, - }, - { - title: "wild-type SARS-CoV-2 main protease in complex with MG-132", - emdb: null, - pdb: { - dbId: "7WQK", - method: "X-RAY DIFFRACTION", - keywords: "main protease, 3C-like protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WQK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wqk_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wqk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JLVVSXFLKOJNIY-UHFFFAOYSA-N", "WUJQMWDTZKIKQZ-VABKMULXSA-N"], - dbauthors: ["Chen, Y.", "Wang, Y.C.", "Yang, C.S.", "Hou, M.H.", "Tsai, C.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "wild-type SARS-CoV-2 main protease in complex with MG-132", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Wang, Y.C.", - "Yang, C.S.", - "Hou, M.H.", - "Tsai, C.L.", - "Chen, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wqk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wqk", - }, - }, - { - title: "SARS-CoV-2 main protease mutant (P168A) in complex with MG-132", - emdb: null, - pdb: { - dbId: "7WQB", - method: "X-RAY DIFFRACTION", - keywords: "main protease, 3C-like protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WQB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wqb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wqb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WUJQMWDTZKIKQZ-VABKMULXSA-N", "JLVVSXFLKOJNIY-UHFFFAOYSA-N"], - dbauthors: ["Chen, Y.", "Wang, Y.C.", "Yang, C.S.", "Hou, M.H.", "Tsai, C.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 main protease mutant (P168A) in complex with MG-132", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Wang, Y.C.", - "Yang, C.S.", - "Hou, M.H.", - "Tsai, C.L.", - "Chen, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wqb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wqb", - }, - }, - { - title: - "Crystal structure of chimeric omicron RBD (strain XBB.1.5) complexed with human ACE2", - emdb: null, - pdb: { - dbId: "8SPI", - method: "X-RAY DIFFRACTION", - keywords: "SARS2, CELL INVASION, HYDROLASE-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "8SPI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8spi_final.pdb", - externalLink: "https://pdb-redo.eu/db/8spi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, W.", - "Shi, K. (0000-0003-4175-3714)", - "Aihara, H. (0000-0001-7508-6230)", - "Li, F. (0000-0002-1958-366X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37578233", - title: - "Structural evolution of SARS-CoV-2 omicron in human receptor recognition.", - journal: "J.Virol. 97: e0082223-e0082223 (2023), 1098-5514", - doi: "https://doi.org/10.1128/jvi.00822-23", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37578233", - pubDate: "2023", - abstract: "", - authors: [ - "Zhang, W.", - "Shi, K.", - "Geng, Q.", - "Herbst, M.", - "Wang, M.", - "Huang, L.", - "Bu, F.", - "Liu, B.", - "Aihara, H.", - "Li, F. (0000-0002-1958-366X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8spi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8spi", - }, - }, - { - title: - "Crystal structure of chimeric omicron RBD (strain XBB.1) complexed with human ACE2", - emdb: null, - pdb: { - dbId: "8SPH", - method: "X-RAY DIFFRACTION", - keywords: "SARS2, CELL INVASION, HYDROLASE-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "8SPH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8sph_final.pdb", - externalLink: "https://pdb-redo.eu/db/8sph", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: [ - "Li, F.", - "Zhang, W.", - "Shi, K. (0000-0003-4175-3714)", - "Aihara, H. (0000-0001-7508-6230)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37578233", - title: - "Structural evolution of SARS-CoV-2 omicron in human receptor recognition.", - journal: "J.Virol. 97: e0082223-e0082223 (2023), 1098-5514", - doi: "https://doi.org/10.1128/jvi.00822-23", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37578233", - pubDate: "2023", - abstract: "", - authors: [ - "Zhang, W.", - "Shi, K.", - "Geng, Q.", - "Herbst, M.", - "Wang, M.", - "Huang, L.", - "Bu, F.", - "Liu, B.", - "Aihara, H.", - "Li, F. (0000-0002-1958-366X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8sph_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8sph", - }, - }, - { - title: "Co-crystal structure of SARS-CoV-2 Mpro with Pomotrelvir", - emdb: null, - pdb: { - dbId: "8TBE", - method: "X-RAY DIFFRACTION", - keywords: "main protease, viral protein, 3cl protease", - refModels: [ - { - emdbId: null, - pdbId: "8TBE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8tbe_final.pdb", - externalLink: "https://pdb-redo.eu/db/8tbe", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "IOEBZYOQTDUOBG-BQFCYCMXSA-N"], - dbauthors: [ - "Olland, A. (0000-0003-0039-2334)", - "Fontano, E.", - "White, A. (0000-0002-4393-1062)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Evaluation of In Vitro Antiviral Activity of SARS-CoV-2 Mpro Inhibitor Pomotrelvir (PBI-0451) and Cross-Resistance to Nirmatrelvir Resistance Substitutions", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Tong, X.", - "Keung, W.", - "Arnold, L.D.", - "Stevens, L.J.", - "Lopatin, U.", - "Denison, M.", - "Kwong, A.D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8tbe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8tbe", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10541R", - emdb: null, - pdb: { - dbId: "8FIV", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 Mpro, Main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8FIV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8fiv_final.pdb", - externalLink: "https://pdb-redo.eu/db/8fiv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "WSBQTFUCGVUNEH-PZGXJGMVSA-N"], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37482021", - title: - "Exploring diverse reactive warheads for the design of SARS-CoV-2 main protease inhibitors.", - 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}, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "HCNIOVAEECJZKZ-PZGXJGMVSA-N", "HCNIOVAEECJZKZ-ZTOMLWHTSA-N"], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37482021", - title: - "Exploring diverse reactive warheads for the design of SARS-CoV-2 main protease inhibitors.", - journal: "Eur.J.Med.Chem. 259: 115667-115667 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115667", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37482021", - pubDate: "2023", - abstract: "", - authors: [ - "Tan, B.", - "Sacco, M.", - "Tan, H.", - "Li, K.", - "Joyce, R.", - "Zhang, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8fiw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8fiw", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 main protease in complex with 32j", - emdb: null, - pdb: { - dbId: "8I30", - method: "X-RAY DIFFRACTION", - keywords: - "Severe acute respiratory syndrome coronavirus 2, main protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8I30", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8i30_final.pdb", - externalLink: "https://pdb-redo.eu/db/8i30", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - 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(0000-0001-8951-1074)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gf2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gf2", - }, - }, - { - title: "SARS-CoV-2 Mpro 1-302/C145A in complex with peptide 8-1", - emdb: null, - pdb: { - dbId: "8GW4", - method: "X-RAY DIFFRACTION", - keywords: "Mpro, inhibitor, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8GW4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gw4_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gw4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "peptide 8-1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Huang, H.", "Liu, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2 Mpro in complex with peptide8m", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Liu, M.", "Huang, H."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gw4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gw4", - }, - }, - { - title: "SARS-CoV-2 Mpro 1-302 c145a in complex with peptide 4", - emdb: null, - pdb: { - dbId: "8GWS", - method: "X-RAY DIFFRACTION", - keywords: "Mpro, substrate, hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "8GWS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gws_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gws", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "VAL-LYS-LEU-GLN-ALA-ILE-PHE-ARG", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Huang, H.", "Liu, M.", "Fu, Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2 Mpro 1-302 c145a in complex with peptide 4", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Liu, M.", "Huang, H."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gws_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gws", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2173.", - emdb: null, - pdb: { - dbId: "7N4J", - method: "X-RAY DIFFRACTION", - keywords: - "Neutralizing antibody, SARS-CoV-2, WRAIR-2173, receptor binding domain, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7N4J", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n4j_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n4j", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2173 antibody Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2173 antibody Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Sankhala, R.S. (0000-0001-8639-5290)", - "Joyce, M.G. (0000-0002-6808-7232)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34716452", - title: - "Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations.", - journal: "Nat.Immunol. 22: 1503-1514 (2021), 1529-2916", - doi: "https://doi.org/10.1038/s41590-021-01068-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34716452", - pubDate: "2021", - abstract: "", - authors: [ - "Dussupt, V. (0000-0002-8579-6356)", - "Sankhala, R.S.", - "Mendez-Rivera, L.", - "Townsley, S.M.", - "Schmidt, F.", - "Wieczorek, L.", - "Lal, K.G.", - "Donofrio, G.C.", - "Tran, U.", - "Jackson, N.D. (0000-0002-9654-6926)", - "Zaky, W.I.", - "Zemil, M. (0000-0002-1700-6658)", - "Tritsch, S.R.", - "Chen, W.H.", - "Martinez, E.J.", - "Ahmed, A. (0000-0003-3093-4982)", - "Choe, M.", - "Chang, W.C. 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"Lempp, F.A.", - "Tortorici, M.A.", - "Pinto, D.", - "Walls, A.C.", - "Beltramello, M.", - "Chen, A.", - "Liu, Z.", - "Zatta, F.", - "Zepeda, S.", - "di Iulio, J.", - "Bowen, J.E.", - "Montiel-Ruiz, M.", - "Zhou, J.", - "Rosen, L.E.", - "Bianchi, S.", - "Guarino, B.", - "Fregni, C.S.", - "Abdelnabi, R.", - "Foo, S.C.", - "Rothlauf, P.W.", - "Bloyet, L.M.", - "Benigni, F.", - "Cameroni, E.", - "Neyts, J.", - "Riva, A.", - "Snell, G.", - "Telenti, A.", - "Whelan, S.P.J.", - "Virgin, H.W.", - "Corti, D.", - "Pizzuto, M.S.", - "Veesler, D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ly3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ly3", - }, - }, - { - title: - "AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2, RESIDUES 217-222, CRYSTAL FORM 1", - emdb: null, - pdb: { - dbId: "7LTU", - method: "X-RAY DIFFRACTION", - keywords: "amyloid fibril, PROTEIN FIBRIL", - refModels: [ - { - emdbId: null, - pdbId: "7LTU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ltu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ltu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: null, - name: - "AALALL SEGMENT FROM THE NUCLEOPROTEIN OF SARS-COV-2,RESIDUES 217-222", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DTQVDTLACAAQTR-UHFFFAOYSA-N"], - dbauthors: ["Zee, C.-T.", "Sawaya, M.R.", "Rodriguez, J.A.", "Eisenberg, D.S."], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "33688654", - title: - "Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.05.434000", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33688654", - pubDate: "2021", - abstract: "", - authors: [ - "Tayeb-Fligelman, E.", - "Cheng, X.", - "Tai, C.", - "Bowler, J.T.", - "Griner, S.", - "Sawaya, M.R.", - "Seidler, P.M.", - "Jiang, Y.X.", - "Lu, J.", - "Rosenberg, G.M.", - "Salwinski, L.", - "Abskharon, R.", - "Zee, C.T.", - "Hou, K.", - "Li, Y.", - "Boyer, D.R.", - "Murray, K.A.", - "Falcon, G.", - "Anderson, D.H.", - "Cascio, D.", - "Saelices, L.", - "Damoiseaux, R.", - "Guo, F.", - "Eisenberg, D.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ltu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ltu", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1247413608", - emdb: null, - pdb: { - dbId: "5SM7", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SM7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sm7_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sm7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "UPEFDWJLNXWMOW-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sm7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sm7", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-44 and Beta-54 Fabs", - emdb: null, - pdb: { - dbId: "7PS6", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-COV-2 B.1.1.7 (Alpha) VARIANT, B.1.351 (Beta) VARIANT, P.1 (Gamma) VARIANT, B.1.617.2 (Delta) VARIANT, ANTIBODY, RECEPTOR-BINDING-DOMAIN, SPIKE, NEUTRALISATION, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7PS6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ps6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ps6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Beta-54 Fab heavy chain", - details: "", - 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{ - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34921776", - title: - "The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.", - journal: "Cell Host Microbe 30 (2022), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2021.11.013", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34921776", - pubDate: "2022", - abstract: "", - authors: [ - "Liu, C.", - "Zhou, D.", - "Nutalai, R.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Dejnirattisai, W.", - "Supasa, P.", - "Mentzer, A.J.", - "Wang, B.", - "Case, J.B.", - "Zhao, Y.", - "Skelly, D.T.", - "Chen, R.E.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Malik, T.", - "Temperton, N.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Clare, D.K.", - "Howe, A.", - "Goulder, P.J.R.", - "Fry, E.E.", - "Diamond, M.S.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Afonine, P.V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ps6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ps6", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z223688272", - emdb: null, - pdb: { - dbId: "5SL3", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SL3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sl3_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sl3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "VCOQVAJFXPHUAM-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sl3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sl3", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000078036511 - (R) and (S) isomers", - emdb: null, - pdb: { - dbId: "5SOI", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5soi_final.pdb", - externalLink: "https://pdb-redo.eu/db/5soi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ADFCTPSWZLLXQI-SNVBAGLBSA-N", "ADFCTPSWZLLXQI-JTQLQIEISA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5soi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5soi", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant Spike glycoprotein in complex with ACE2", - emdb: null, - pdb: { - dbId: "7NXC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, HYDROLASE, VIRAL PROTEIN-HYDROLASE complex", - refModels: [ - { - emdbId: null, - pdbId: "7NXC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nxc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nxc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Processed angiotensin-converting enzyme 2", - details: "", - altNames: "", - isAntibody: false, - 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"Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - { - pmID: "", - title: "Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.12.435194", - pmidLink: "", - pubDate: "2021", - abstract: "", - 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"Gilbert, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nxc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nxc", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2073741691", - emdb: null, - pdb: { - dbId: "5SLR", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slr_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "KVTKFHLTYQIGCM-KNVOCYPGSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slr", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW247", - emdb: null, - pdb: { - dbId: "6XBH", - method: "X-RAY DIFFRACTION", - keywords: - "COVID, COVID19, COVID-19, SARS, SARS COV2, COV, NCOV 19, CORONAVIRUS, MAIN PROTEASE, 3CL, MPRO, PRO, VIRAL PROTEIN, GC376, calpain inhibitor II, leupeptin, calpain, aldehyde, GC-376, 3cl-like, a-ketoamide, UAW41, UAW246, UAW247, UAW248, 246, 247, 248, alpheketoamide, alpha, ketoamide, PEPTIDOMIMETIC, PROTEASE, CYSTEINE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "6XBH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xbh_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xbh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "inhibitor UAW247", - 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"Xiang, Y.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xbh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xbh", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2856434890", - emdb: null, - pdb: { - dbId: "5SMA", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SMA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sma_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sma", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "SXNAOFHNRSEHNL-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sma_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sma", - }, - }, - { - title: "Crystal structure of CoV-2 Nsp3 Macrodomain", - emdb: null, - pdb: { - dbId: "7KG3", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, SARS-CoV-2, macrodomain", - refModels: [ - { - emdbId: null, - pdbId: "7KG3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kg3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kg3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OFOBLEOULBTSOW-UHFFFAOYSA-L", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: [ - "Arvai, A. (0000-0002-5376-3728)", - "Brosey, C.A. (0000-0002-0990-0262)", - "Link, T.", - "Jones, D.E. (0000-0003-1581-3453)", - "Ahmed, Z. (0000-0003-3400-6577)", - "Tainer, J.A. (0000-0003-1659-2429)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33636189", - title: - "Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors.", - journal: "Prog.Biophys.Mol.Biol. 163: 171-186 (2021), 0079-6107", - doi: "https://doi.org/10.1016/j.pbiomolbio.2021.02.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33636189", - pubDate: "2021", - abstract: "", - authors: [ - "Brosey, C.A.", - "Houl, J.H.", - "Katsonis, P.", - "Balapiti-Modarage, L.P.F.", - "Bommagani, S.", - "Arvai, A.", - "Moiani, D.", - "Bacolla, A.", - "Link, T.", - "Warden, L.S.", - "Lichtarge, O.", - "Jones, D.E.", - "Ahmed, Z.", - "Tainer, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kg3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kg3", - }, - }, - { - title: "Complex Structure of antibody BD-503 and RBD-S477N of COVID-19", - emdb: null, - pdb: { - dbId: "7EJZ", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, Neutralization Antibody, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7EJZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ejz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ejz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy Chain of BD-503", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light Chain of BD-503", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Xu, H.", "Wang, B.", "Zhao, T.N.", "Su, X.D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34480123", - title: - "Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants.", - journal: "Cell Res. 31: 1126-1129 (2021), 1001-0602", - doi: "https://doi.org/10.1038/s41422-021-00554-1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34480123", - pubDate: "2021", - abstract: "", - authors: [ - "Xu, H. (0000-0001-9283-080X)", - "Wang, B. (0000-0002-3380-4473)", - "Zhao, T.N.", - "Liang, Z.T.", - "Peng, T.B.", - "Song, X.H.", - "Wu, J.J.", - "Wang, Y.C. (0000-0001-9769-5141)", - "Su, X.D. (0000-0001-6948-2317)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ejz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ejz", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibody AZD8895", - emdb: null, - pdb: { - dbId: "7L7D", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, spike protein, receptor binding domain, human monoclonal antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7L7D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l7d_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l7d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "heavy chain of human monoclonal antibody Fab AZD8895", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "light chain of human monoclonal antibody Fab AZD8895", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Crowe, J.E.", "Dong, J. 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(0000-0001-5553-1616)", - "Logue, J. (0000-0002-7410-9741)", - "Weston, S.", - "McGrath, M.E. (0000-0002-7451-4958)", - "Frieman, M.B. (0000-0003-0107-0775)", - "Brady, T.", - "Tuffy, K.M.", - "Bright, H.", - "Loo, Y.M.", - "McTamney, P.M.", - "Esser, M.T.", - "Carnahan, R.H. (0000-0001-5230-1532)", - "Diamond, M.S. (0000-0002-8791-3165)", - "Bloom, J.D. (0000-0003-1267-3408)", - "Crowe Jr., J.E. 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], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "OLTOJZGRSVNYRB-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sle_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sle", - }, - }, - { - title: - "1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with a deuterated GC376 alpha-ketoamide analog (compound 5)", - emdb: null, - pdb: { - dbId: "7K0F", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, deuterated hydrolase inhibitor", - refModels: [ - { - emdbId: null, - pdbId: "7K0F", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k0f_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k0f", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MPMTWRHFCLPCDF-OJJQZRKESA-N", "UWHCKJMYHZGTIT-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34210738", - title: - "Postinfection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection.", - journal: "Proc.Natl.Acad.Sci.USA 118 (2021), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2101555118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34210738", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Zheng, J.", - "Perera, K.D.", - "Wong, L.R.", - "Meyerholz, D.K.", - "Nguyen, H.N.", - "Kashipathy, M.M.", - "Battaile, K.P.", - "Lovell, S.", - "Kim, Y.", - "Perlman, S.", - "Groutas, W.C.", - "Chang, K.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k0f_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k0f", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z239136710", - emdb: null, - pdb: { - dbId: "5SA4", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SA4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sa4_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sa4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LUFRABHJXNJTNZ-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sa4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sa4", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease treated with ebselen derivative of MR6-31-2", - emdb: null, - pdb: { - dbId: "7BAL", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, COVID19, ebselen, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7BAL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bal_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bal", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Main Protease", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BUGBHKTXTAQXES-UHFFFAOYSA-N"], - dbauthors: [ - "Amporndanai, K. (0000-0001-8527-9394)", - "O'Neill, P.M. (0000-0003-4338-0317)", - "Hasnain, S.S. (0000-0002-2854-4718)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34031399", - title: - "Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives.", - journal: "Nat Commun 12: 3061-3061 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23313-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34031399", - pubDate: "2021", - abstract: "", - authors: [ - "Amporndanai, K.", - "Meng, X. (0000-0002-7774-2075)", - "Shang, W.", - "Jin, Z. (0000-0001-6448-820X)", - "Rogers, M.", - "Zhao, Y.", - "Rao, Z. (0000-0001-9866-2384)", - "Liu, Z.J. (0000-0001-7279-2893)", - "Yang, H. (0000-0002-1875-3268)", - "Zhang, L. (0000-0002-2593-2571)", - "O'Neill, P.M. (0000-0003-4338-0317)", - "Samar Hasnain, S. (0000-0002-2854-4718)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bal_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bal", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z31504642", - emdb: null, - pdb: { - dbId: "5SAB", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SAB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sab_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sab", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "LEQAQBFYCMENLP-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sab_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sab", - }, - }, - { - title: - "PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain", - emdb: null, - pdb: { - dbId: "5S73", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S73", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s73_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s73", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Schuller, M.", - "Rangel, V.L.", - "Douangamath, A.", - "Aimon, A.", - "Powell, A.J.", - "Dias, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Gorrie-Stone, T.J.", - "Thompson, W.", - "Krojer, T.", - "Rack, J.G.M.", - "Zhu, K.", - "Ahel, I.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s73_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s73", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with SF051", - emdb: null, - pdb: { - dbId: "5S4I", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S4I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s4i_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s4i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YRTFBBSKIRZNAW-LURJTMIESA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-3532-3868)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tj0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tj0", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 47D1", - emdb: null, - pdb: { - dbId: "7MF1", - method: "X-RAY DIFFRACTION", - keywords: "COVID-19, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7MF1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mf1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mf1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "47D1 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "47D1 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Wilson, I.A. 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"Qi, F.", - "Wang, G.", - "Du, X.", - "Bao, L.", - "Deng, W.", - "Zhu, H.", - "Liu, J.", - "Nie, J.", - "Zheng, Y.", - "Liang, H.", - "Liu, R.", - "Gong, S.", - "Xu, H.", - "Yisimayi, A.", - "Lv, Q.", - "Wang, B.", - "He, R.", - "Han, Y.", - "Zhao, W.", - "Bai, Y.", - "Qu, Y.", - "Gao, X.", - "Ji, C.", - "Wang, Q.", - "Gao, N.", - "Huang, W.", - "Wang, Y.", - "Xie, X.S.", - "Su, X.D.", - "Xiao, J.", - "Qin, C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7chc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7chc", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with POB0073", - emdb: null, - pdb: { - dbId: "5RF0", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RF0", - source: "PDB-REDO", - 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(0000-0003-4966-7175)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Lee, J.", - "Paetzel, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33208735", - title: - "Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.", - journal: "Nat Commun 11: 5877-5877 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-19662-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33208735", - pubDate: "2020", - abstract: "", - authors: [ - "Lee, J.", - "Worrall, L.J.", - "Vuckovic, M.", - "Rosell, F.I.", - "Gentile, F.", - "Ton, A.T. (0000-0001-7418-6563)", - "Caveney, N.A. (0000-0003-4828-3479)", - "Ban, F.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7joy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7joy", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease (3CL Mpro) in complex with NBH-2", - emdb: null, - pdb: { - dbId: "7TFR", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 main protease, homodimer, cysteine protease, covalent inhibitor, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TFR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tfr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tfr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RXHKWDZUWDFTBO-QXMOZHRRSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35477935", - title: - "Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease", - journal: "Nat Commun 13 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-29915-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35477935", - pubDate: "2022", - abstract: "", - authors: [ - "Kneller, D.W.", - "Li, H.", - "Phillips, G.", - "Weiss, K.L.", - "Zhang, Q.", - "Arnould, M.A.", - "Jonsson, C.B.", - "Surendranathan, S.", - "Parvathareddy, J.", - "Blakeley, M.P.", - "Coates, L.", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A.", - "Kneller, D.", - "Phillips, G. 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(0000-0003-4459-9142)", - "Adams, P.D.", - "Mustyakimov, M.", - "Afonine, P.V.", - "Langan, P.", - ], - }, - { - pmID: "35169792", - title: - "Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease: room-temperature X-ray and neutron crystallography, binding thermodynamics, and antiviral activity.", - journal: "Res Sq (2022), 2693-5015", - doi: "https://doi.org/10.21203/rs.3.rs-1318037/v1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35169792", - pubDate: "2022", - abstract: "", - authors: [ - "Kneller, D.W.", - "Li, H.", - "Phillips, G.", - "Weiss, K.L.", - "Zhang, Q.", - "Arnould, M.A.", - "Jonsson, C.B.", - "Surendranathan, S.", - "Parvathareddy, J.", - "Blakeley, M.P.", - "Coates, L.", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A.", - "Kneller, D.", - "Phillips, G. (0000-0001-5858-3825)", - "Weiss, K. (0000-0002-6486-8007)", - "Arnould, M. (0000-0003-0172-8311)", - "Jonsson, C.", - "Blakeley, M. (0000-0002-6412-4358)", - "Coates, L. 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(0000-0003-4459-9142)", - "Adams, P.D.", - "Mustyakimov, M.", - "Afonine, P.V.", - "Langan, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tfr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tfr", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z4444622180 (Mpro-x2562)", - emdb: null, - pdb: { - dbId: "5RGU", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RGU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rgu_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rgu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SGVQMOZIVBYLOT-OAHLLOKOSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgu", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 Papain-like protease C111S", - emdb: null, - pdb: { - dbId: "7D47", - method: "X-RAY DIFFRACTION", - keywords: "Protease, PLpro, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7D47", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7d47_final.pdb", - externalLink: "https://pdb-redo.eu/db/7d47", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "BHPQYMZQTOCNFJ-UHFFFAOYSA-N"], - dbauthors: [ - "Wu, K.-P. 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(0000-0002-1525-6004)", - "Chen, S.-K.", - "Lu, Y.-C.", - "Huang, Y.-C.J.", - "Lee, M.-H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7d47_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7d47", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102704", - emdb: null, - pdb: { - dbId: "5RFF", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rff_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rff", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "VTRBWFKJTCGLDP-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0001-8287-0269)", - "Knecht, W. 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(0000-0002-3869-615X)", - "Qi, J.X. (0000-0002-9358-4732)", - "Shi, R. (0000-0001-8469-8730)", - "Yan, J.H. (0000-0003-0502-3829)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "A neutralizing MAb targeting receptor-binding-domain of SARS-CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Shi, R. (0000-0001-8469-8730)", - "Qi, J.X. (0000-0002-9358-4732)", - "Gao, G.F. (0000-0002-3869-615X)", - "Yan, J.H. (0000-0003-0502-3829)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7d6i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7d6i", - }, - }, - { - title: "Ensemble refinement structure of SARS-CoV-2 main protease (Mpro) at 100 K", - emdb: null, - pdb: { - dbId: "7MHL", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Coronavirus, main protease, 3CLpro, Mpro, hydrolase, ensemble refinement, temperature series, temperature, multitemperature", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36071812", - title: - "The tem-per-ature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).", - journal: "Iucrj 9: 682-694 (2022), 2052-2525", - doi: "https://doi.org/10.1107/S2052252522007497", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36071812", - pubDate: "2022", - abstract: "", - authors: [ - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. 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(0000-0002-9184-7586)", - "Ebrahim, A.", - "Riley, B.T.", - "Andi, B.", - "Fuchs, M.R.", - "McSweeney, S.", - "Keedy, D.A.", - ], - }, - { - pmID: "", - title: - "The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)", - journal: "Iucrj 9 (2022), 2052-2525", - doi: "https://doi.org/10.1107/S2052252522007497", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - "Ebrahim, A.", - "Riley, B.T.", - "Andi, B.", - "Fuchs, M.R.", - "McSweeney, S.", - "Keedy, D.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mhl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mhl", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Mpro at 2.25 A resolution-13", - emdb: null, - pdb: { - dbId: "7VK6", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, SFX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VK6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vk6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vk6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "DeMirci, H. (0000-0002-9135-5397)", - "Yuksel, B. (0000-0003-4396-7142)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography", - journal: "Crystals 11 (2021), 2073-4352", - doi: "https://doi.org/10.3390/cryst11121579", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Guven, O.", - "Gul, M.", - "Ayan, E.", - "Johnson, J.A.", - "Cakilkaya, B.", - "Usta, G.", - "Ertem, F.B.", - "Tokay, N.", - "Yuksel, B.", - "Gocenler, O.", - "Buyukdag, C.", - "Botha, S.", - "Ketawala, G.", - "Su, Z.", - "Hayes, B.", - "Poitevin, F.", - "Batyuk, A.", - "Yoon, C.H.", - "Kupitz, C.", - "Durdagi, S.", - "Sierra, R.G.", - "DeMirci, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vk6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vk6", - }, - }, - { - title: - "Structural Plasticity of the SARS-CoV-2 3CL Mpro Active Site Cavity Revealed by Room Temperature X-ray Crystallography", - emdb: null, - pdb: { - dbId: "6WQF", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 Main Protease, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6WQF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wqf_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wqf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32581217", - title: - "Structural plasticity of SARS-CoV-2 3CL Mproactive site cavity revealed by room temperature X-ray crystallography.", - journal: "Nat Commun 11: 3202-3202 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-16954-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32581217", - pubDate: "2020", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Phillips, G. (0000-0001-5858-3825)", - "O'Neill, H.M. (0000-0003-2966-5527)", - "Jedrzejczak, R.", - "Stols, L.", - "Langan, P.", - "Joachimiak, A.", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wqf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wqf", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000002560357", - emdb: null, - pdb: { - dbId: "5RSP", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsp_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CVHZOJJKTDOEJC-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsp", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor Narlaprevir", - emdb: null, - pdb: { - dbId: "7JYC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Main Protease, 3CLpro/Mpro, Narlaprevir, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JYC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jyc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jyc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "BZXRATSZUNDEEV-FZFXNXQRSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Shi, W.", - "McSweeney, S. (0000-0002-3758-3161)", - "Fuchs, M.R.", - "Kreitler, D.F.", - "Soares, A.S.", - "Jakoncic, J.", - "Keereetaweep, J.", - "Shanklin, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35842458", - title: - "Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.", - journal: "Sci Rep 12: 12197-12197 (2022), 2045-2322", - doi: "https://doi.org/10.1038/s41598-022-15930-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35842458", - pubDate: "2022", - abstract: "", - authors: [ - "Andi, B.", - "Kumaran, D.", - "Kreitler, D.F.", - "Soares, A.S.", - "Keereetaweep, J.", - "Jakoncic, J.", - "Lazo, E.O.", - "Shi, W.", - "Fuchs, M.R.", - "Sweet, R.M.", - "Shanklin, J.", - "Adams, P.D.", - "Schmidt, J.G.", - "Head, M.S.", - "McSweeney, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jyc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jyc", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Maleate.", - emdb: null, - pdb: { - dbId: "7AHA", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, MPro, COVID-19, PEPTIDE BINDING PROTEIN, virus protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7AHA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aha_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aha", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "KDYFGRWQOYBRFD-UHFFFAOYSA-N", - ], - dbauthors: [ - "Oberthuer, D. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7aha_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7aha", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000263392672", - emdb: null, - pdb: { - dbId: "5RSG", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsg_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GRUOKIVOQBHPDL-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsg", - }, - }, - { - title: "The crystal structure of RBD-Nanobody complex, DL4 (SA4)", - emdb: null, - pdb: { - dbId: "7F5G", - method: "X-RAY DIFFRACTION", - keywords: - "Nanobody, RBD, neutralizing antibody, receptor-binding domain, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7F5G", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f5g_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f5g", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "Nanobody DL4", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "QTBSBXVTEAMEQO-UHFFFAOYSA-M"], - dbauthors: ["Li, T.", "Tan, J.", "Zhou, Y.", "Li, D.", "Lai, Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35460753", - title: - "Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2.", - journal: "Int.J.Biol.Macromol. 209: 1379-1388 (2022), 0141-8130", - doi: "https://doi.org/10.1016/j.ijbiomac.2022.04.096", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35460753", - pubDate: "2022", - abstract: "", - authors: [ - "Li, T.", - "Zhou, B.", - "Li, Y.", - "Huang, S.", - "Luo, Z.", - "Zhou, Y.", - "Lai, Y.", - "Gautam, A.", - "Bourgeau, S.", - "Wang, S.", - "Bao, J.", - "Tan, J.", - "Lavillette, D.", - "Li, D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7f5g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7f5g", - }, - }, - { - title: - "Structure of SARS-CoV-2 Papain-like Protease bound to N-(3-methoxy-4-hydroxy-acetophenone)thiosemicarbazone", - emdb: null, - pdb: { - dbId: "7QCM", - method: "X-RAY DIFFRACTION", - keywords: - "Cystein-Protease, Inhibitor, SARS-CoV-2, Thiosemicarbazone, Deubiquitination, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7QCM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qcm_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qcm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LSGUOKMONPPTRD-WUXMJOGZSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Reinke, P.", - "Hinrichs, W.", - "Han, H.", - "Srinivasan, V.", - "Lorenzen, K.", - "Betzel, C.", - "Meents, A.", - "Falke, S.", - "Gunther, S.", - "Lieske, J.", - "Ewert, W.", - "Niebling, S.", - "Miglioli, F.", - "Carcelli, M.", - "Guenther, C.", - "Garcia-Alai, M.", - "Rogolino, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35480391", - title: - "Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease.", - journal: "Front Chem 10: 832431-832431 (2022), 2296-2646", - doi: "https://doi.org/10.3389/fchem.2022.832431", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35480391", - pubDate: "2022", - abstract: "", - authors: [ - "Ewert, W.", - "Gunther, S.", - "Miglioli, F.", - "Falke, S.", - "Reinke, P.Y.A.", - "Niebling, S.", - "Gunther, C.", - "Han, H.", - "Srinivasan, V.", - "Brognaro, H.", - "Lieske, J.", - "Lorenzen, K.", - "Garcia-Alai, M.M.", - "Betzel, C.", - "Carcelli, M.", - "Hinrichs, W.", - "Rogolino, D.", - "Meents, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qcm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qcm", - }, - }, - { - title: - "Complex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD)", - emdb: null, - pdb: { - dbId: "7MSQ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 receptor binding domain AB-3467, ANTIVIRAL PROTEIN, VIRAL PROTEIN-ANTIVIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7MSQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7msq_final.pdb", - externalLink: "https://pdb-redo.eu/db/7msq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "AB-3467 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "AB-3467 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "ZMZDMBWJUHKJPS-UHFFFAOYSA-M", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: ["Langley, D.B.", "Christ, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34788600", - title: - "Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability.", - journal: "Immunity 54: 2908-2921.e6 (2021), 1074-7613", - doi: "https://doi.org/10.1016/j.immuni.2021.10.019", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34788600", - pubDate: "2021", - abstract: "", - authors: [ - "Burnett, D.L.", - "Jackson, K.J.L.", - "Langley, D.B.", - "Aggrawal, A.", - "Stella, A.O.", - "Johansen, M.D.", - "Balachandran, H.", - "Lenthall, H.", - "Rouet, R.", - "Walker, G.", - "Saunders, B.M.", - "Singh, M.", - "Li, H.", - "Henry, J.Y.", - "Jackson, J.", - "Stewart, A.G.", - "Witthauer, F.", - "Spence, M.A.", - "Hansbro, N.G.", - "Jackson, C.", - "Schofield, P.", - "Milthorpe, C.", - "Martinello, M.", - "Schulz, S.R.", - "Roth, E.", - "Kelleher, A.", - "Emery, S.", - "Britton, W.J.", - "Rawlinson, W.D.", - "Karl, R.", - "Schafer, S.", - "Winkler, T.H.", - "Brink, R.", - "Bull, R.A.", - "Hansbro, P.M.", - "Jack, H.M.", - "Turville, S.", - "Christ, D.", - "Goodnow, C.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7msq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7msq", - }, - }, - { - title: - "SARS-CoV-2 main protease in a covalent complex with SDZ 224015 derivative, compound 5", - emdb: null, - pdb: { - dbId: "7AEG", - method: "X-RAY DIFFRACTION", - keywords: "covid-19, inhibitor, protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AEG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aeg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aeg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: - "N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Stuart, D.I.", - "Brewitz, L.", - "Malla, T.R.", - "Tumber, A.", - "Lukacik, P.", - "Strain-Damerell, C.", - "Walsh, M.A.", - "Schofield, C.J.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Redhead, M.A.", - "Collette, A.", - "Robinson, C.", - "Collins, P.", - "Radoux, C.", - "Navratilova, I.", - "Nugen, T.", - "Hull, H.", - "Hallet, D.", - "Hopkins, A.L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34168183", - title: - "Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19.", - journal: "Sci Rep 11: 13208-13208 (2021), 2045-2322", - doi: "https://doi.org/10.1038/s41598-021-92416-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34168183", - pubDate: "2021", - abstract: "", - authors: [ - "Redhead, M.A.", - "Owen, C.D.", - "Brewitz, L.", - "Collette, A.H.", - "Lukacik, P.", - "Strain-Damerell, C.", - "Robinson, S.W.", - "Collins, P.M.", - "Schafer, P.", - "Swindells, M.", - "Radoux, C.J.", - "Hopkins, I.N.", - "Fearon, D.", - "Douangamath, A.", - "von Delft, F.", - "Malla, T.R.", - "Vangeel, L.", - "Vercruysse, T.", - "Thibaut, J.", - "Leyssen, P.", - "Nguyen, T.T.", - "Hull, M.", - "Tumber, A.", - "Hallett, D.J.", - "Schofield, C.J.", - "Stuart, D.I.", - "Hopkins, A.L.", - "Walsh, M.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7aeg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7aeg", - }, - }, - { - title: "The crystal structure of SARS-CoV-2 Main Protease in complex with masitinib", - emdb: null, - pdb: { - dbId: "7JU7", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, 3CL, main protease, masitinib, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7JU7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ju7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ju7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "WJEOLQLKVOPQFV-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Joachimiak, A. (0000-0003-2535-6209)", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Tan, K. 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(0000-0002-0962-9468)", "Malla, T. (0000-0002-1387-0801)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS CoV-2 MAIN PROTEASE 3CLpro, ROOM TEMPERATURE, DAMAGE FREE XFEL MONOCLINIC STRUCTURE", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Schmidt, M. (0000-0002-0962-9468)", - "Malla, T. (0000-0002-1387-0801)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jvz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jvz", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000026180281", - emdb: null, - pdb: { - dbId: "5RSF", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsf_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NMJOZGVQPPGGFV-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsf", - }, - }, - { - title: - "Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 4-(2-hydroxyethyl)phenol", - emdb: null, - pdb: { - dbId: "7OFS", - method: "X-RAY DIFFRACTION", - keywords: - "Papain-like protease SARS-CoV-2 Hydrolase Zinc binding protein, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7OFS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ofs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ofs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "YCCILVSKPBXVIP-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Wang, M.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Turk, D.", - "Hinrichs, W.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "Brognaro, H.", - "Brings, L.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Ginn, H.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Ullah, N.", - "Andaleeb, H.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Saouane, S.", - "Hakanpaeae, J.", - "Wolf, M.", - "Lieske, J.", - "Ewert, W.", - "Srinivasan, V. (0000-0002-8895-5885)", - "Sprenger, J.", - "Perk, A.", - "Wahab, A.", - "Choudary, I.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35953531", - title: - "Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.", - journal: "Commun Biol 5: 805-805 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03737-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35953531", - pubDate: "2022", - abstract: "", - authors: [ - "Srinivasan, V. (0000-0002-8895-5885)", - "Brognaro, H.", - "Prabhu, P.R.", - "de Souza, E.E.", - "Gunther, S. (0000-0002-7329-6653)", - "Reinke, P.Y.A.", - "Lane, T.J. (0000-0003-2627-4432)", - "Ginn, H.", - "Han, H.", - "Ewert, W. (0000-0001-8626-4864)", - "Sprenger, J.", - "Koua, F.H.M. 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(0000-0002-3879-5019)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ofs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ofs", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000158490", - emdb: null, - pdb: { - dbId: "5RSQ", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsq_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PENHKTNQUJMHIR-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1595-431X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography", - journal: "Crystals 11 (2021), 2073-4352", - doi: "https://doi.org/10.3390/cryst11121579", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Guven, O.", - "Gul, M.", - "Ayan, E.", - "Johnson, J.A.", - "Cakilkaya, B.", - "Usta, G.", - "Ertem, F.B.", - "Tokay, N.", - "Yuksel, B.", - "Gocenler, O.", - "Buyukdag, C.", - "Botha, S.", - "Ketawala, G.", - "Su, Z.", - "Hayes, B.", - "Poitevin, F.", - "Batyuk, A.", - "Yoon, C.H.", - "Kupitz, C.", - "Durdagi, S.", - "Sierra, R.G.", - "DeMirci, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vk7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vk7", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-39", - emdb: null, - pdb: { - dbId: "7JMP", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, RBD, Antibody, SARS, Spike, IMMUNE SYSTEM, Viral Protein-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7JMP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jmp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jmp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA2-39 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA2-39 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Liu, H. (0000-0002-2412-7853)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. 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(0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36071812", - title: - "The tem-per-ature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).", - journal: "Iucrj 9: 682-694 (2022), 2052-2525", - doi: "https://doi.org/10.1107/S2052252522007497", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36071812", - pubDate: "2022", - abstract: "", - authors: [ - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - "Ebrahim, A.", - "Riley, B.T.", - "Andi, B.", - "Fuchs, M.R.", - "McSweeney, S.", - "Keedy, D.A.", - ], - }, - { - pmID: "33972941", - title: - "The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).", - journal: "Biorxiv (2021), 2692-8205", - doi: "https://doi.org/10.1101/2021.05.03.437411", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33972941", - pubDate: "2021", - abstract: "", - authors: [ - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - "Ebrahim, A.", - "Riley, B.T.", - "Andi, B.", - "Fuchs, M.R.", - "McSweeney, S.", - "Keedy, D.A.", - ], - }, - { - pmID: "", - title: - "The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)", - journal: "Iucrj 9 (2022), 2052-2525", - doi: "https://doi.org/10.1107/S2052252522007497", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - "Ebrahim, A.", - "Riley, B.T.", - "Andi, B.", - "Fuchs, M.R.", - "McSweeney, S.", - "Keedy, D.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mhm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mhm", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 papain-like protease (PLPro) C112S mutant", - emdb: null, - pdb: { - dbId: "7D6H", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Deubiquitinase, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7D6H", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7d6h_final.pdb", - externalLink: "https://pdb-redo.eu/db/7d6h", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "NBIIXXVUZAFLBC-UHFFFAOYSA-K"], - dbauthors: [ - "Liu, J. (0000-0001-7090-2112)", - "Wang, Y. (0000-0001-8300-0847)", - "Pan, L. (0000-0002-9229-6288)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33979649", - title: - "Development of potent and selective inhibitors targeting the papain-like protease of SARS-CoV-2.", - journal: "Cell Chem Biol 28 (2021), 2451-9456", - doi: "https://doi.org/10.1016/j.chembiol.2021.04.020", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33979649", - pubDate: "2021", - abstract: "", - authors: [ - "Shan, H.", - "Liu, J.", - "Shen, J.", - "Dai, J.", - "Xu, G.", - "Lu, K.", - "Han, C.", - "Wang, Y.", - "Xu, X.", - "Tong, Y.", - "Xiang, H.", - "Ai, Z.", - "Zhuang, G.", - "Hu, J.", - "Zhang, Z.", - "Li, Y.", - "Pan, L.", - "Tan, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7d6h_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7d6h", - }, - }, - { - title: - "Non-structural protein 10 (nsp10) from SARS CoV-2 in complex with fragment VT00239", - emdb: null, - pdb: { - dbId: "7ORV", - method: "X-RAY DIFFRACTION", - keywords: "Fragment, complex, small molecule, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ORV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7orv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7orv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "QEDNABCLVCJRLV-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Wang, Q.", - "Lou, J.", - "Kozielski, F.", - "Shi, X.", - "Krojer, T.", - "Talibov, V.O.", - "Sele, C.", - "Dong, D.", - "Nyblom, M.", - "Rogstam, A.", - "Knecht, W.", - "Fisher, S.Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35128408", - title: - "Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16.", - journal: "Rsc Chem Biol 3: 44-55 (2022), 2633-0679", - doi: "https://doi.org/10.1039/d1cb00135c", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35128408", - pubDate: "2022", - abstract: "", - authors: [ - "Kozielski, F.", - "Sele, C.", - "Talibov, V.O.", - "Lou, J.", - "Dong, D.", - "Wang, Q.", - "Shi, X.", - "Nyblom, M.", - "Rogstam, A.", - "Krojer, T.", - "Fisher, Z. (0000-0001-8287-0269)", - "Knecht, W. (0000-0001-9530-7598)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7orv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7orv", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102372", - emdb: null, - pdb: { - dbId: "5RFG", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfg_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "KBIYZUQDVPCCPL-LBPRGKRZSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0002-8995-2635)", - "Hai, R.", - "Song, J. (0000-0002-4958-1032)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33999154", - title: - "Two conserved oligomer interfaces of NSP7 and NSP8 underpin the dynamic assembly of SARS-CoV-2 RdRP.", - journal: "Nucleic Acids Res. 49: 5956-5966 (2021), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkab370", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33999154", - pubDate: "2021", - abstract: "", - authors: [ - "Biswal, M.", - "Diggs, S.", - "Xu, D.", - "Khudaverdyan, N.", - "Lu, J.", - "Fang, J.", - "Blaha, G.", - "Hai, R.", - "Song, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jlt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jlt", - }, - }, - { - title: "The crystal structure of COVID-19 main protease in the apo state", - emdb: null, - pdb: { - dbId: "7C2Q", - method: "X-RAY DIFFRACTION", - keywords: "COVID-2019, main protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7C2Q", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c2q_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c2q", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhang, J.", - "Zhou, H.", - "Hu, X.H.", - "Zhou, X.L.", - "Zhong, F.L.", - "Lin, C.", - "Wang, Q.S.", - "Li, j.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32880863", - title: "Structure of SARS-CoV-2 main protease in the apo state.", - 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refModels: [ - { - emdbId: null, - pdbId: "5RGT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rgt_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rgt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "BFKJCDNTNNMOGO-GOSISDBHSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - 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refModels: [ - { - emdbId: null, - pdbId: "7TEH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7teh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7teh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NJQHWGAQENWSGZ-KOUJMVCDSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35477935", - title: - "Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease", - journal: "Nat Commun 13 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-29915-z", - 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}, - refdoc: [ - { - pmID: "34242578", - title: - "Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.", - journal: "Cell 184: 4220-4236.e13 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.06.020", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34242578", - pubDate: "2021", - abstract: "", - authors: [ - "Liu, C.", - "Ginn, H.M.", - "Dejnirattisai, W.", - "Supasa, P.", - "Wang, B.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Zhou, D.", - "Mentzer, A.J.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Costa Clemens, S.A.", - "Gomes Naveca, F.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Temperton, N.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Malik, T.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Baillie, V.", - "Serafin, N.", - "Ditse, Z.", - "Da Silva, K.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Madhi, S.", - "Nunes, M.C.", - "Goulder, P.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ora_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ora", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102327", - emdb: null, - pdb: { - dbId: "5REK", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5REK", - source: "PDB-REDO", - 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(0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rf1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rf1", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 RBD in complex with BD-236 Fab", - emdb: null, - pdb: { - dbId: "7CHB", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-Cov-2, RBD, mAb, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7CHB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7chb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7chb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "BD-236 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-236 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Xiao, J. 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(0000-0001-7020-2044)"], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32970990", - title: - "Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.", - journal: "Cell 183: 1013-1023.e13 (2020), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2020.09.035", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32970990", - pubDate: "2020", - abstract: "", - authors: [ - "Du, S.", - "Cao, Y.", - "Zhu, Q.", - "Yu, P.", - "Qi, F.", - "Wang, G.", - "Du, X.", - "Bao, L.", - "Deng, W.", - "Zhu, H.", - "Liu, J.", - "Nie, J.", - "Zheng, Y.", - "Liang, H.", - "Liu, R.", - "Gong, S.", - "Xu, H.", - "Yisimayi, A.", - "Lv, Q.", - "Wang, B.", - "He, R.", - "Han, Y.", - "Zhao, W.", - "Bai, Y.", - "Qu, Y.", - "Gao, X.", - "Ji, C.", - "Wang, Q.", - "Gao, N.", - "Huang, W.", - "Wang, Y.", - "Xie, X.S.", - "Su, X.D.", - "Xiao, J.", - "Qin, C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7chb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7chb", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 S RBD in complex with BD-604 Fab", - emdb: null, - pdb: { - dbId: "7CH4", - method: "X-RAY DIFFRACTION", - keywords: "Complex, PROTEIN BINDING-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7CH4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ch4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ch4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "BD-604 Fab H", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-604 Fab L", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Du, S. (0000-0003-0936-0785)", "Xiao, J.Y. (0000-0001-8224-1374)"], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32970990", - title: - "Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.", - journal: "Cell 183: 1013-1023.e13 (2020), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2020.09.035", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32970990", - pubDate: "2020", - abstract: "", - authors: [ - "Du, S.", - "Cao, Y.", - "Zhu, Q.", - "Yu, P.", - "Qi, F.", - "Wang, G.", - "Du, X.", - "Bao, L.", - "Deng, W.", - "Zhu, H.", - "Liu, J.", - "Nie, J.", - "Zheng, Y.", - "Liang, H.", - "Liu, R.", - "Gong, S.", - "Xu, H.", - "Yisimayi, A.", - "Lv, Q.", - "Wang, B.", - "He, R.", - "Han, Y.", - "Zhao, W.", - "Bai, Y.", - "Qu, Y.", - "Gao, X.", - "Ji, C.", - "Wang, Q.", - "Gao, N.", - "Huang, W.", - "Wang, Y.", - "Xie, X.S.", - "Su, X.D.", - "Xiao, J.", - "Qin, C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ch4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ch4", - }, - }, - { - title: - "Crystal structure of SARS CoV2 main protease in complex with DN_EG_002 (modelled using PanDDA event map)", - emdb: null, - pdb: { - dbId: "7NTV", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NTV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ntv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ntv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "XGQYGJKFUOSIIU-UHFFFAOYSA-N"], - dbauthors: [ - "Oerlemans, R. (0000-0001-7114-3736)", - "Eris, D.", - "Wang, M. (0000-0002-5340-3036)", - "Sharpe, M.", - "Domling, A. (0000-0002-9923-8873)", - "Groves, M.R. (0000-0001-9859-5177)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34097796", - title: - "Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.", - journal: - "Angew.Chem.Int.Ed.Engl. 60: 18231-18239 (2021), 1521-3773", - doi: "https://doi.org/10.1002/anie.202105584", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34097796", - pubDate: "2021", - abstract: "", - authors: [ - "Sutanto, F.", - "Shaabani, S. (0000-0001-5546-7140)", - "Oerlemans, R.", - "Eris, D.", - "Patil, P.", - "Hadian, M.", - "Wang, M.", - "Sharpe, M.E.", - "Groves, M.R.", - "Domling, A. 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(0000-0003-2687-0699)", - "Walsh, M.A. (0000-0001-5683-1151)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4h_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4h", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with BBL029427", - emdb: null, - pdb: { - dbId: "5S72", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5S72", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s72_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s72", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "YZKMURMKJCXVIE-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. 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(2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sa5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sa5", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212)", - emdb: null, - pdb: { - dbId: "7L8J", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, SARS2, COVID19, PROTEASE, PROTEASE INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, RUPINTRIVIR, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7L8J", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l8j_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l8j", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LMIUALQNZXJHOG-IFILWLFVSA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Henes, M. (0000-0001-8667-541X)", - "Lee, J.M.", - "Timm, J. (0000-0001-9750-3293)", - "Nalivaika, E.A.", - "Yilmaz, N.K. (0000-0002-5036-676X)", - "Thompson, P.R. (0000-0002-1621-3372)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34506130", - title: - "Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode.", - journal: "Biochemistry 60: 2925-2931 (2021), 0006-2960", - doi: "https://doi.org/10.1021/acs.biochem.1c00414", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34506130", - pubDate: "2021", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Henes, M.", - "Lee, J.M.", - "Timm, J. (0000-0001-9750-3293)", - "Nalivaika, E.A.", - "Thompson, P.R. (0000-0002-1621-3372)", - "Kurt Yilmaz, N. 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dbauthors: ["Greasley, S.E.", "Ferre, R.A.", "Liu, W.", "Stewart, A.E."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34726479", - title: - "An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19.", - journal: "Science 374: 1586-1593 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abl4784", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34726479", - pubDate: "2021", - abstract: "", - authors: [ - "Owen, D.R.", - "Allerton, C.M.N.", - "Anderson, A.S.", - "Aschenbrenner, L.", - "Avery, M.", - "Berritt, S.", - "Boras, B.", - "Cardin, R.D.", - "Carlo, A.", - "Coffman, K.J.", - "Dantonio, A.", - "Di, L.", - "Eng, H.", - "Ferre, R.", - "Gajiwala, K.S.", - "Gibson, S.A.", - "Greasley, S.E.", - "Hurst, B.L.", - "Kadar, E.P.", - "Kalgutkar, A.S.", - "Lee, J.C.", - "Lee, J.", - "Liu, W.", - "Mason, S.W.", - "Noell, S.", - 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(0000-0002-0070-955X)", - "Abraham, J. (0000-0002-7937-3920)", - "Clark, L. (0000-0002-6093-7597)", - "Clark, S. (0000-0001-9944-0919)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33200128", - title: - "Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.11.13.381533", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33200128", - pubDate: "2020", - abstract: "", - authors: [ - "Clark, S.A.", - "Clark, L.E.", - "Pan, J. (0000-0002-0070-955X)", - "Coscia, A.", - "McKay, L.G.A.", - "Shankar, S.", - "Johnson, R.I.", - "Griffiths, A.", - "Abraham, J. 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(0000-0002-9358-4732)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ekh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ekh", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-40 Fab", - emdb: null, - pdb: { - dbId: "7PS7", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-COV-2 B.1.1.7 (Alpha) VARIANT, B.1.351 (Beta) VARIANT, P.1 (Gamma) VARIANT, B.1.617.2 (Delta) VARIANT, ANTIBODY, RECEPTOR-BINDING-DOMAIN, SPIKE, NEUTRALISATION, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7PS7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ps7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ps7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-40 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-40 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34921776", - title: - "The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.", - journal: "Cell Host Microbe 30 (2022), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2021.11.013", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34921776", - pubDate: "2022", - abstract: "", - authors: [ - "Liu, C.", - "Zhou, D.", - "Nutalai, R.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Dejnirattisai, W.", - "Supasa, P.", - "Mentzer, A.J.", - "Wang, B.", - "Case, J.B.", - "Zhao, Y.", - "Skelly, D.T.", - "Chen, R.E.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Malik, T.", - "Temperton, N.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Clare, D.K.", - "Howe, A.", - "Goulder, P.J.R.", - "Fry, E.E.", - "Diamond, M.S.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Afonine, P.V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ps7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ps7", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW248", - emdb: null, - pdb: { - dbId: "6XBI", - method: "X-RAY DIFFRACTION", - keywords: - "COVID, COVID19, COVID-19, SARS, SARS COV2, COV, NCOV 19, CORONAVIRUS, MAIN PROTEASE, 3CL, MPRO, PRO, VIRAL PROTEIN, GC376, calpain inhibitor II, leupeptin, calpain, aldehyde, GC-376, 3cl-like, a-ketoamide, UAW41, UAW246, UAW247, UAW248, 246, 247, 248, alpheketoamide, alpha, ketoamide, PEPTIDOMIMETIC, PROTEASE, CYSTEINE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "6XBI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xbi_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xbi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "inhibitor UAW248", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - ], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M.", "Ma, C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33158912", - title: - "Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L.", - journal: "Sci Adv 6 (2020), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abe0751", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33158912", - pubDate: "2020", - abstract: "", - authors: [ - "Sacco, M.D.", - "Ma, C.", - "Lagarias, P.", - "Gao, A.", - "Townsend, J.A.", - "Meng, X.", - "Dube, P.", - "Zhang, X.", - "Hu, Y.", - "Kitamura, N.", - "Hurst, B.", - "Tarbet, B.", - "Marty, M.T.", - "Kolocouris, A.", - "Xiang, Y.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xbi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xbi", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1373445602", - emdb: null, - pdb: { - dbId: "5SLS", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sls_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sls", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "LOFSFVFRUNIULW-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sls_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sls", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant Spike glycoprotein in complex with COVOX-222 and EY6A Fabs", - emdb: null, - pdb: { - dbId: "7NXB", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7NXB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nxb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nxb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33852911", - title: "Antibody evasion by the P.1 strain of SARS-CoV-2.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.03.055", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33852911", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - { - pmID: "", - title: "Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.12.435194", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nxb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nxb", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z100643660", - emdb: null, - pdb: { - dbId: "5SL2", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SL2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sl2_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sl2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "OHXYWSIWHXTWCT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sl2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sl2", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1899842917", - emdb: null, - pdb: { - dbId: "5SM6", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SM6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sm6_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sm6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "QMZRSGJUZDOFDN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sm6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sm6", - }, - }, - { - title: - "Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein", - emdb: null, - pdb: { - dbId: "7EJL", - method: "X-RAY DIFFRACTION", - keywords: "HLA-A*2402, MHC CLASS I, IMMUNE SYSTEM, coronavirus", - refModels: [ - { - emdbId: null, - pdbId: "7EJL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ejl_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ejl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "9-mer peptide from the HCoV spike protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Shirouzu, M.", "Murayama, K.", "Kato-Murayama, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34857854", - title: - "Identification of TCR repertoires in functionally competent cytotoxic T cells cross-reactive to SARS-CoV-2.", - journal: "Commun Biol 4: 1365-1365 (2021), 2399-3642", - doi: "https://doi.org/10.1038/s42003-021-02885-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34857854", - pubDate: "2021", - abstract: "", - authors: [ - "Shimizu, K.", - "Iyoda, T.", - "Sanpei, A.", - "Nakazato, H.", - "Okada, M.", - "Ueda, S.", - "Kato-Murayama, M.", - "Murayama, K.", - "Shirouzu, M.", - "Harada, N.", - "Hidaka, M.", - "Fujii, S.I. (0000-0003-3586-3976)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ejl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ejl", - }, - }, - { - title: "NMR solution structure of SUD-C domain of SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7P2O", - method: "SOLUTION NMR", - keywords: "SARS-CoV-2, SUD, SUD-C, nsP3, RNA binding, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Gallo, A. (0000-0001-9778-4822)", - "Tsika, A.C. (0000-0002-3723-0606)", - "Fourkiotis, N.K. (0000-0002-5197-4142)", - "Spyroulias, G.A. (0000-0003-1799-3312)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "NMR solution structure of SUD-C domain of SARS-CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Gallo, A. (0000-0001-9778-4822)", - "Tsika, A.C. (0000-0002-3723-0606)", - "Fourkiotis, N.K. (0000-0002-5197-4142)", - "Spyroulias, G.A. (0000-0003-1799-3312)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7p2o_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7p2o", - }, - }, - { - title: - "Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2", - emdb: null, - pdb: { - dbId: "6VW1", - method: "X-RAY DIFFRACTION", - keywords: "coronavirus, CELL INVASION", - refModels: [ - { - emdbId: null, - pdbId: "6VW1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6vw1_final.pdb", - externalLink: "https://pdb-redo.eu/db/6vw1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P59594", - organism: "694009", - name: "SARS-CoV-2 chimeric RBD", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: [ - "Shi, K. (0000-0003-4175-3714)", - "Ye, G.", - "Aihara, H. (0000-0001-7508-6230)", - "Li, F. (0000-0002-1958-366X)", - "Shang, J.", - "Wan, Y.S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32225175", - title: "Structural basis of receptor recognition by SARS-CoV-2.", - journal: "Nature 581: 221-224 (2020), 1476-4687", - doi: "https://doi.org/10.1038/s41586-020-2179-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32225175", - pubDate: "2020", - abstract: "", - authors: [ - "Shang, J.", - "Ye, G.", - "Shi, K.", - "Wan, Y.", - "Luo, C.", - "Aihara, H.", - "Geng, Q.", - "Auerbach, A.", - "Li, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6vw1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6vw1", - }, - }, - { - title: - "Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2, crystal form II", - emdb: null, - pdb: { - dbId: "6ZCO", - method: "X-RAY DIFFRACTION", - keywords: "Nucleoprotein, SARS Coronavirus 2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6ZCO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6zco_final.pdb", - externalLink: "https://pdb-redo.eu/db/6zco", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zinzula, L.", - "Basquin, J.", - "Nagy, I.", - "Bracher, A. (0000-0001-8530-7594)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33039147", - title: - "High-resolution structure and biophysical characterization of the nucleocapsid phosphoprotein dimerization domain from the Covid-19 severe acute respiratory syndrome coronavirus 2.", - journal: "Biochem.Biophys.Res.Commun. 538: 54-62 (2021), 1090-2104", - doi: "https://doi.org/10.1016/j.bbrc.2020.09.131", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33039147", - pubDate: "2021", - abstract: "", - authors: [ - "Zinzula, L.", - "Basquin, J.", - "Bohn, S.", - "Beck, F.", - "Klumpe, S.", - "Pfeifer, G.", - "Nagy, I.", - "Bracher, A.", - "Hartl, F.U.", - "Baumeister, W.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zco_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zco", - }, - }, - { - title: - "Crystal structure of human neutralizing mAb CV3-25 binding to SARS-CoV-2 S MPER peptide 1140-1165", - emdb: null, - pdb: { - dbId: "7NAB", - method: "X-RAY DIFFRACTION", - keywords: - "human neutralizing mAb, MPER-targeting, SARS-CoV-2, spike, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7NAB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nab_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nab", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "CV3-25 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV3-25 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2", - details: - "Lysine at N-terminal is used for biochemical assays; two serines were added at N-terminal to increase the peptide solubility in PBS", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N", "KRKNYBCHXYNGOX-UHFFFAOYSA-N"], - dbauthors: [ - "Chen, Y. (0000-0001-5380-2339)", - "Tolbert, W.D. (0000-0001-7549-9596)", - "Pazgier, M. (0000-0003-0594-5057)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34971573", - title: - "Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern.", - journal: "Cell Rep 38: 110210-110210 (2022), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2021.110210", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34971573", - pubDate: "2022", - abstract: "", - authors: [ - "Li, W.", - "Chen, Y.", - "Prevost, J.", - "Ullah, I.", - "Lu, M.", - "Gong, S.Y.", - "Tauzin, A.", - "Gasser, R.", - "Vezina, D.", - "Anand, S.P.", - "Goyette, G.", - "Chaterjee, D.", - "Ding, S.", - "Tolbert, W.D.", - "Grunst, M.W.", - "Bo, Y.", - "Zhang, S.", - "Richard, J.", - "Zhou, F.", - "Huang, R.K.", - "Esser, L.", - "Zeher, A.", - "Cote, M.", - "Kumar, P.", - "Sodroski, J.", - "Xia, D.", - "Uchil, P.D.", - "Pazgier, M.", - "Finzi, A.", - "Mothes, W.", - "Zhou, P.", - "Yuan, M.", - "Song, G.", - "Beutler, N.", - "Shaabani, N.", - "Huang, D.", - "He, W.T.", - "Zhu, X.", - "Callaghan, S.", - "Yong, P.", - "Anzanello, F.", - "Peng, L.", - "Ricketts, J.", - "Parren, M.", - "Garcia, E.", - "Rawlings, S.A.", - "Smith, D.M.", - "Nemazee, D.", - "Teijaro, J.R.", - "Rogers, T.F.", - "Wilson, I.A.", - "Burton, D.R.", - "Andrabi, R.", - ], - }, - { - pmID: "", - title: - "A protective broadly cross-reactive human antibody defines a conserved site of vulnerability on beta-coronavirus spikes.", - journal: "bioRxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.30.437769", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Li, W.", - "Chen, Y.", - "Prevost, J.", - "Ullah, I.", - "Lu, M.", - "Gong, S.Y.", - "Tauzin, A.", - "Gasser, R.", - "Vezina, D.", - "Anand, S.P.", - "Goyette, G.", - "Chaterjee, D.", - "Ding, S.", - "Tolbert, W.D.", - "Grunst, M.W.", - "Bo, Y.", - "Zhang, S.", - "Richard, J.", - "Zhou, F.", - "Huang, R.K.", - "Esser, L.", - "Zeher, A.", - "Cote, M.", - "Kumar, P.", - "Sodroski, J.", - "Xia, D.", - "Uchil, P.D.", - "Pazgier, M.", - "Finzi, A.", - "Mothes, W.", - "Zhou, P.", - "Yuan, M.", - "Song, G.", - "Beutler, N.", - "Shaabani, N.", - "Huang, D.", - "He, W.T.", - "Zhu, X.", - "Callaghan, S.", - "Yong, P.", - "Anzanello, F.", - "Peng, L.", - "Ricketts, J.", - "Parren, M.", - "Garcia, E.", - "Rawlings, S.A.", - "Smith, D.M.", - "Nemazee, D.", - "Teijaro, J.R.", - "Rogers, T.F.", - "Wilson, I.A.", - "Burton, D.R.", - "Andrabi, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nab_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nab", - }, - }, - { - title: - "Crystal structure of SU3327 (halicin) covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.", - emdb: null, - pdb: { - dbId: "7NBY", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN, halicin, SU3327", - refModels: [ - { - emdbId: null, - pdbId: "7NBY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nby_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nby", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Main Protease", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VVVCJCRUFSIVHI-UHFFFAOYSA-N", - "NHNBFGGVMKEFGY-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P.", "Giabbai, B."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SU3327 (halicin) covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Costanzi, E.", - "Demitri, N.", - "Giabbai, B.", - "Storici, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nby_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nby", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 NendoU in complex with Z2472938267", - emdb: null, - pdb: { - dbId: "7N7R", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7N7R", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n7r_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n7r", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OYRHWZOYGOUXNC-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n7r_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n7r", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2057.", - emdb: null, - pdb: { - dbId: "7N4I", - method: "X-RAY DIFFRACTION", - keywords: - "Neutralizing antibody, SARS-CoV-2, WRAIR-2057, receptor binding domain, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7N4I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n4i_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n4i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2057 Antibody Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2057 Antibody Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Sankhala, R.S. (0000-0001-8639-5290)", - "Joyce, M.G. (0000-0002-6808-7232)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34716452", - title: - "Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations.", - journal: "Nat.Immunol. 22: 1503-1514 (2021), 1529-2916", - doi: "https://doi.org/10.1038/s41590-021-01068-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34716452", - pubDate: "2021", - abstract: "", - authors: [ - "Dussupt, V. (0000-0002-8579-6356)", - "Sankhala, R.S.", - "Mendez-Rivera, L.", - "Townsley, S.M.", - "Schmidt, F.", - "Wieczorek, L.", - "Lal, K.G.", - "Donofrio, G.C.", - "Tran, U.", - "Jackson, N.D. (0000-0002-9654-6926)", - "Zaky, W.I.", - "Zemil, M. (0000-0002-1700-6658)", - "Tritsch, S.R.", - "Chen, W.H.", - "Martinez, E.J.", - "Ahmed, A. (0000-0003-3093-4982)", - "Choe, M.", - "Chang, W.C. (0000-0003-4967-6426)", - "Hajduczki, A.", - "Jian, N.", - "Peterson, C.E.", - "Rees, P.A.", - "Rutkowska, M.", - "Slike, B.M. (0000-0003-4132-4637)", - "Selverian, C.N. (0000-0002-1047-4336)", - "Swafford, I. (0000-0001-8638-2772)", - "Teng, I.T.", - "Thomas, P.V.", - "Zhou, T. (0000-0002-3935-4637)", - "Smith, C.J.", - "Currier, J.R. (0000-0002-5696-0268)", - "Kwong, P.D. (0000-0003-3560-232X)", - "Rolland, M. (0000-0003-3650-8490)", - "Davidson, E.", - "Doranz, B.J. (0000-0002-8245-3083)", - "Mores, C.N. (0000-0001-6678-9049)", - "Hatziioannou, T.", - "Reiley, W.W.", - "Bieniasz, P.D. (0000-0002-2368-3719)", - "Paquin-Proulx, D. (0000-0003-1407-3414)", - "Gromowski, G.D.", - "Polonis, V.R.", - "Michael, N.L. (0000-0001-5882-5548)", - "Modjarrad, K.", - "Joyce, M.G. (0000-0002-6808-7232)", - "Krebs, S.J. (0000-0003-1136-1760)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n4i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n4i", - }, - }, - { - title: "SARS-CoV-2 Main protease C145S mutant", - emdb: null, - pdb: { - dbId: "7N5Z", - method: "X-RAY DIFFRACTION", - keywords: "3CL, protease, SARS, SARS-CoV-2, covid, main protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7N5Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n5z_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n5z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Noske, G.D.", - "Oliva, G.", - "Godoy, A.S.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Lima, G.M.A.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34174328", - title: - "A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.", - journal: "J.Mol.Biol. 433: 167118-167118 (2021), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2021.167118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34174328", - pubDate: "2021", - abstract: "", - authors: [ - "Noske, G.D.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Lima, G.M.A.", - "Rosa, H.V.D.", - "Pereira, H.D.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "Freire, M.C.L.C.", - "Fearon, D.", - "Douangamath, A.", - "von Delft, F.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n5z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n5z", - }, - }, - { - title: - "Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary complex with EY6A Fab and a nanobody.", - emdb: null, - pdb: { - dbId: "6ZCZ", - method: "X-RAY DIFFRACTION", - keywords: - "EY6a, RBD, Spike glycoprotein, SARS-CoV-2, human neutralizing antibody, VIRAL PROTEIN, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "6ZCZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6zcz_final.pdb", - externalLink: "https://pdb-redo.eu/db/6zcz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - ], - dbauthors: ["Zhao, Y.", "Zhou, D.", "Ren, J.", "Stuart, D.I.", "Fry, E.E."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32737466", - title: - "Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient.", - journal: "Nat.Struct.Mol.Biol. 27: 950-958 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0480-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32737466", - pubDate: "2020", - abstract: "", - authors: [ - "Zhou, D.", - "Duyvesteyn, H.M.E.", - "Chen, C.P.", - "Huang, C.G.", - "Chen, T.H.", - "Shih, S.R.", - "Lin, Y.C.", - "Cheng, C.Y.", - "Cheng, S.H.", - "Huang, Y.C.", - "Lin, T.Y.", - "Ma, C. (0000-0002-4741-2307)", - "Huo, J.", - "Carrique, L.", - "Malinauskas, T. (0000-0002-4847-5529)", - "Ruza, R.R.", - "Shah, P.N.M.", - "Tan, T.K. (0000-0001-8746-8308)", - "Rijal, P.", - "Donat, R.F.", - "Godwin, K.", - "Buttigieg, K.R.", - "Tree, J.A.", - "Radecke, J.", - "Paterson, N.G. (0000-0003-4292-6971)", - "Supasa, P.", - "Mongkolsapaya, J.", - "Screaton, G.R. (0000-0002-3549-4309)", - "Carroll, M.W.", - "Gilbert-Jaramillo, J. (0000-0003-1268-2304)", - "Knight, M.L. (0000-0002-8780-1630)", - "James, W. (0000-0002-2506-1198)", - "Owens, R.J. (0000-0002-3705-2993)", - "Naismith, J.H. (0000-0001-6744-5061)", - "Townsend, A.R.", - "Fry, E.E. (0000-0001-9754-5303)", - "Zhao, Y. (0000-0001-8916-8552)", - "Ren, J. (0000-0003-4015-1404)", - "Stuart, D.I. (0000-0002-3426-4210)", - "Huang, K.A. (0000-0001-6891-6945)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zcz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zcz", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 310 K)", - emdb: null, - pdb: { - dbId: "7KR1", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7KR1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kr1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kr1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. 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(0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kr1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kr1", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z57260516", - emdb: null, - pdb: { - dbId: "5SL0", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SL0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sl0_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sl0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "XZMRSYKEMFCZKR-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sl0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sl0", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000642067873 - (R) isomer", - emdb: null, - pdb: { - dbId: "5SOJ", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5soj_final.pdb", - externalLink: "https://pdb-redo.eu/db/5soj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LEHSMGCFXRLFLE-SNVBAGLBSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5soj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5soj", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2856434829", - emdb: null, - pdb: { - dbId: "5SLQ", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slq_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "ZCPNSVBDWJVJSY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slq", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-47 Fab", - 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"Williams, M.A.", - "Hall, D.R.", - "Clare, D.K.", - "Howe, A.", - "Goulder, P.J.R.", - "Fry, E.E.", - "Diamond, M.S.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Afonine, P.V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ps5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ps5", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and two Magnesium (Mg) ions.", - emdb: null, - pdb: { - dbId: "7L6T", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, VIRAL PROTEIN, SAH, Cap-1, VIRAL PROTEIN-RNA complex", - refModels: [ - { - emdbId: null, - pdbId: "7L6T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l6t_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l6t", - 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(0000-0001-5460-3462)", - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Brunzelle, J.S. (0000-0001-9197-0018)", - "Daczkowski, C.M.", - "Hoover, P.", - "Mesecar, A.D. (0000-0002-1241-2577)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l6t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l6t", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2856434944", - emdb: null, - pdb: { - dbId: "5SM4", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SM4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sm4_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sm4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "MDBPFVSVLGYVCQ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sm4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sm4", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 Receptor Binding Domain in complex with the monoclonal antibody m31A7", - emdb: null, - pdb: { - dbId: "7WUE", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Spike, receptor binding domain, m31A7, monoclonal antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7WUE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wue_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wue", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "m31A7 Fab HEAVY CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "m31A7 Fab LIGHT CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Mohapatra, A. (0000-0003-3468-6912)"], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35230146", - title: - "Vaccination with SARS-CoV-2 spike protein lacking glycan shields elicits enhanced protective responses in animal models.", - journal: "Sci Transl Med 14: eabm0899-eabm0899 (2022), 1946-6242", - doi: "https://doi.org/10.1126/scitranslmed.abm0899", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35230146", - pubDate: "2022", - abstract: "", - authors: [ - "Huang, H.Y. (0000-0002-6824-6993)", - "Liao, H.Y. (0000-0002-7105-612X)", - "Chen, X. (0000-0002-4492-0883)", - "Wang, S.W. (0000-0002-1240-6126)", - "Cheng, C.W. (0000-0003-3491-8920)", - "Shahed-Al-Mahmud, M. (0000-0002-4285-7016)", - "Liu, Y.M.", - "Mohapatra, A. (0000-0003-3468-6912)", - "Chen, T.H.", - "Lo, J.M. (0000-0002-3002-9491)", - "Wu, Y.M. (0000-0001-9745-6298)", - "Ma, H.H. (0000-0003-0073-6985)", - "Chang, Y.H. (0000-0002-8643-9959)", - "Tsai, H.Y. (0000-0002-7666-5688)", - "Chou, Y.C. (0000-0002-0783-1339)", - "Hsueh, Y.P. (0000-0002-0866-6275)", - "Tsai, C.Y.", - "Huang, P.Y.", - "Chang, S.Y. (0000-0002-6009-6724)", - "Chao, T.L. (0000-0002-9815-6702)", - "Kao, H.C. (0000-0001-7996-3448)", - "Tsai, Y.M. (0000-0002-2529-8988)", - "Chen, Y.H.", - "Wu, C.Y. (0000-0003-2843-2633)", - "Jan, J.T. (0000-0002-9721-0017)", - "Cheng, T.R. (0000-0003-4297-018X)", - "Lin, K.I. (0000-0003-4477-0798)", - "Ma, C. (0000-0002-4741-2307)", - "Wong, C.H. (0000-0002-9961-7865)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wue_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wue", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z198195770", - emdb: null, - pdb: { - dbId: "5SLF", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slf_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "GVNXANNAMKHSRF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slf", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs", - emdb: null, - pdb: { - dbId: "7NX6", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7NX6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nx6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nx6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33852911", - title: "Antibody evasion by the P.1 strain of SARS-CoV-2.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.03.055", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33852911", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - { - pmID: "", - title: "Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.12.435194", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nx6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nx6", - }, - }, - { - title: - "1.90 A resolution structure of SARS-CoV-2 3CL protease in complex with deuterated GC376", - emdb: null, - pdb: { - dbId: "7K0E", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, deuterated hydrolase inhibitor, Hydrolase-Hydrolase Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7K0E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k0e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k0e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N", "UWHCKJMYHZGTIT-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34210738", - title: - "Postinfection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection.", - journal: "Proc.Natl.Acad.Sci.USA 118 (2021), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2101555118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34210738", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Zheng, J.", - "Perera, K.D.", - "Wong, L.R.", - "Meyerholz, D.K.", - "Nguyen, H.N.", - "Kashipathy, M.M.", - "Battaile, K.P.", - "Lovell, S.", - "Kim, Y.", - "Perlman, S.", - "Groutas, W.C.", - "Chang, K.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k0e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k0e", - }, - }, - { - title: "Crystal structure from SARS-CoV-2 NendoU NSP15", - emdb: null, - pdb: { - dbId: "7KF4", - method: "X-RAY DIFFRACTION", - keywords: - "NSP15, NendoU, covid-19, covid, sars, sars-cov-2, endoribonuclease, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7KF4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kf4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kf4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Oliveira, K.I.Z.", - "Pereira, H.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. 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(0000-0001-9283-080X)", - "Wang, B. (0000-0002-3380-4473)", - "Zhao, T.N.", - "Liang, Z.T.", - "Peng, T.B.", - "Song, X.H.", - "Wu, J.J.", - "Wang, Y.C. (0000-0001-9769-5141)", - "Su, X.D. 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(0000-0002-7963-6241)", - "Fragai, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34278402", - title: - "SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design.", - journal: "Chem.Commun.(Camb.) 57: 7910-7913 (2021), 1364-548X", - doi: "https://doi.org/10.1039/d1cc02956h", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34278402", - pubDate: "2021", - abstract: "", - authors: [ - "Grifagni, D. (0000-0001-5402-6781)", - "Calderone, V. (0000-0002-7963-6241)", - "Giuntini, S.", - "Cantini, F. (0000-0003-0526-6732)", - "Fragai, M. (0000-0002-8440-1690)", - "Banci, L. (0000-0003-0562-5774)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nwx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nwx", - }, - }, - { - title: "Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor YH-53", - emdb: null, - pdb: { - dbId: "7E18", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 3CL protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7E18", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e18_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e18", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JBLLRCOZJMVOAE-HSQYWUDLSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Senda, M. (0000-0003-3863-4503)", - "Konno, S.", - "Hayashi, Y.", - "Senda, T. (0000-0002-5153-928X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34313428", - title: - "3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.", - journal: "J.Med.Chem. 65: 2926-2939 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34313428", - pubDate: "2022", - abstract: "", - authors: [ - "Konno, S.", - "Kobayashi, K.", - "Senda, M.", - "Funai, Y.", - "Seki, Y.", - "Tamai, I.", - "Schakel, L.", - "Sakata, K.", - "Pillaiyar, T.", - "Taguchi, A.", - "Taniguchi, A.", - "Gutschow, M.", - "Muller, C.E.", - "Takeuchi, K.", - "Hirohama, M.", - "Kawaguchi, A.", - "Kojima, M.", - "Senda, T.", - "Shirasaka, Y.", - "Kamitani, W.", - "Hayashi, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e18_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e18", - }, - }, - { - title: "Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor", - emdb: null, - pdb: { - dbId: "7RFW", - method: "X-RAY DIFFRACTION", - keywords: - "Protease SARS-CoV-2 Covalent complex inhibitor, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RFW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rfw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rfw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Greasley, S.E.", "Ferre, R.A.", "Liu, W.", "Stewart, A.E."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34726479", - title: - "An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19.", - journal: "Science 374: 1586-1593 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abl4784", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34726479", - pubDate: "2021", - abstract: "", - authors: [ - "Owen, D.R.", - "Allerton, C.M.N.", - "Anderson, A.S.", - "Aschenbrenner, L.", - "Avery, M.", - "Berritt, S.", - "Boras, B.", - "Cardin, R.D.", - "Carlo, A.", - "Coffman, K.J.", - "Dantonio, A.", - "Di, L.", - "Eng, H.", - "Ferre, R.", - "Gajiwala, K.S.", - "Gibson, S.A.", - "Greasley, S.E.", - "Hurst, B.L.", - "Kadar, E.P.", - "Kalgutkar, A.S.", - "Lee, J.C.", - "Lee, J.", - "Liu, W.", - "Mason, S.W.", - "Noell, S.", - "Novak, J.J.", - "Obach, R.S.", - "Ogilvie, K.", - "Patel, N.C.", - "Pettersson, M.", - "Rai, D.K.", - "Reese, M.R.", - "Sammons, M.F.", - "Sathish, J.G.", - "Singh, R.S.P.", - "Steppan, C.M.", - "Stewart, A.E.", - "Tuttle, J.B.", - "Updyke, L.", - "Verhoest, P.R.", - "Wei, L.", - "Yang, Q.", - "Zhu, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rfw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rfw", - }, - }, - { - title: - "Structure of SARS CoV-2 main protease shows simultaneous processing of its N- and C-terminii", - emdb: null, - pdb: { - dbId: "7LMC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS, protease, coronavirus-2, COVID-19, auto-processing, maturation, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7LMC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lmc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lmc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 4 peptide", - details: "", - altNames: "nsp4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Ferre, R.A.", "Liu, W.", "Gajiwala, K.S.", "Ryan, K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS coronavirus-2 main protease dimer auto-processes N-terminus in cis and C-terminus in trans", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Ferre, R.A.", - "Liu, W.", - "Ryan, K.", - "Grodsky, N.", - "Gajiwala, K.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lmc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lmc", - 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"Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. 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(0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sa7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sa7", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 Main Protease", - emdb: null, - pdb: { - dbId: "7NTT", - method: "X-RAY DIFFRACTION", - keywords: "3CLpro, main protease, SARS-CoV-2, 2019-nCov, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NTT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ntt_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ntt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N", "BDAGIHXWWSANSR-UHFFFAOYSA-N"], - dbauthors: [ - "Hanoulle, X. (0000-0002-3755-2680)", - "Dupre, E. (0000-0001-5281-0337)", - "Villeret, V. (0000-0003-4504-056X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Crystal structure of the SARS-CoV-2 Main Protease", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Dupre, E. (0000-0001-5281-0337)", - "Villeret, V. (0000-0003-4504-056X)", - "Hanoulle, X. (0000-0002-3755-2680)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ntt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ntt", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 nsp10/nsp16 in complex with the SS148 inhibitor", - emdb: null, - pdb: { - dbId: "7R1T", - method: "X-RAY DIFFRACTION", - keywords: "methyltransferase, nsp10, nsp16, inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7R1T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7r1t_final.pdb", - externalLink: "https://pdb-redo.eu/db/7r1t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "XLTWYAYAFLGUEQ-OPYVMVOTSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Li, F.", - "Klima, M. (0000-0002-9083-509X)", - "Boura, E. (0000-0002-9652-4065)", - "Yazdi, A.K.", - "Vedadi, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36040262", - title: - "Crystal structure of SARS-CoV-2 nsp10-nsp16 in complex with small molecule inhibitors, SS148 and WZ16.", - journal: "Protein Sci. 31: e4395-e4395 (2022), 1469-896X", - doi: "https://doi.org/10.1002/pro.4395", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36040262", - pubDate: "2022", - abstract: "", - authors: [ - "Klima, M.", - "Khalili Yazdi, A.", - "Li, F.", - "Chau, I.", - "Hajian, T.", - "Bolotokova, A.", - "Kaniskan, H.U.", - "Han, Y.", - "Wang, K.", - "Li, D.", - "Luo, M.", - "Jin, J.", - "Boura, E. (0000-0002-9652-4065)", - "Vedadi, M. (0000-0002-0574-0169)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7r1t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7r1t", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-181428", - emdb: null, - pdb: { - dbId: "5S70", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5S70", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s70_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s70", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "JGCNHPQMPGHGHT-ZCFIWIBFSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. 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(0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s70_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s70", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with SF054", - emdb: null, - pdb: { - dbId: "5S4J", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S4J", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s4j_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s4j", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RRBQGBYFXZPPAH-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - { - pmID: "34045440", - title: - "Exploring protein hotspots by optimized fragment pharmacophores.", - journal: "Nat Commun 12: 3201-3201 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23443-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34045440", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. 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(0000-0003-2687-0699)", - "Walsh, M.A. (0000-0001-5683-1151)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4j_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4j", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284", - emdb: null, - pdb: { - dbId: "5SAA", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SAA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5saa_final.pdb", - externalLink: "https://pdb-redo.eu/db/5saa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "IUKADXXFBFQTOO-VIFPVBQESA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5saa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5saa", - }, - }, - { - title: "Crystal Structure of VP12E7 Fab in complex with SARS-CoV-2 S fusion peptide", - emdb: null, - pdb: { - dbId: "7SL5", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 spike, COVID-19, fusion peptide, Fab, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID", - refModels: [ - { - emdbId: null, - pdbId: "7SL5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sl5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sl5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain VP12E7 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain VP12E7 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "PRO-SER-LYS-ARG-SER-PHE-ILE-GLU-ASP-LEU-LEU-PHE-ASN", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Seattle Structural Genomics Center for Infectious Disease (SSGCID)", - "Veesler, D.", - "Tortorici, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35857703", - title: - "ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.", - journal: "Science 377: 735-742 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abq2679", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35857703", - pubDate: "2022", - abstract: "", - authors: [ - "Low, J.S.", - "Jerak, J.", - "Tortorici, M.A.", - "McCallum, M.", - "Pinto, D.", - "Cassotta, A.", - "Foglierini, M.", - "Mele, F.", - "Abdelnabi, R.", - "Weynand, B.", - "Noack, J.", - "Montiel-Ruiz, M.", - "Bianchi, S.", - "Benigni, F.", - "Sprugasci, N.", - "Joshi, A.", - "Bowen, J.E.", - "Stewart, C.", - "Rexhepaj, M.", - "Walls, A.C.", - "Jarrossay, D.", - "Morone, D.", - "Paparoditis, P.", - "Garzoni, C.", - "Ferrari, P.", - "Ceschi, A.", - "Neyts, J.", - "Purcell, L.A.", - "Snell, G.", - "Corti, D.", - "Lanzavecchia, A.", - "Veesler, D.", - "Sallusto, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sl5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sl5", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z4444621965 (Mpro-x2764)", - emdb: null, - pdb: { - dbId: "5RH8", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RH8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rh8_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rh8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "PZOXHLAZHKNFDQ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rh8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rh8", - }, - }, - { - title: "THSC20.HVTR04 Fab bound to SARS-CoV-2 Receptor Binding Domain", - emdb: null, - pdb: { - dbId: "7Z0Y", - method: "X-RAY DIFFRACTION", - keywords: - "Neutralizing antibody, SARS-CoV-2, Spike, RBD, ANTIVIRAL PROTEIN, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7Z0Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7z0y_final.pdb", - externalLink: "https://pdb-redo.eu/db/7z0y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "THSC20.HVTR04 Fab heavy chain", - details: - "Residue 1 has been modelled as a cyclized Pyroglutamic acid. The last 7 amino acids GLEVLFQ are a protease sequence used to cleave off purification tags, but may be listed as 'expression tag'.", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "THSC20.HVTR04 Fab light chain", - details: "Position 1 has been modelled as a cyclized Pyroglutamic acid.", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: ["Wibmer, C.K. (0000-0003-2329-2280)"], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35482816", - title: - "A combination of potently neutralizing monoclonal antibodies isolated from an Indian convalescent donor protects against the SARS-CoV-2 Delta variant.", - journal: "Plos Pathog. 18: e1010465-e1010465 (2022), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1010465", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35482816", - pubDate: "2022", - abstract: "", - authors: [ - "Hingankar, N.", - "Deshpande, S.", - "Das, P.", - "Rizvi, Z.A.", - "Wibmer, C.K.", - "Mashilo, P.", - "Ansari, M.Y.", - "Burns, A.", - "Barman, S.", - "Zhao, F.", - "Mukherjee, S.", - "Torres, J.L.", - "Chattopadhyay, S.", - "Mehdi, F.", - "Sutar, J.", - "Rathore, D.K.", - "Pargai, K.", - "Singh, J.", - "Sonar, S.", - "Jakhar, K.", - "Dandotiya, J.", - "Bhattacharyya, S.", - "Mani, S.", - "Samal, S.", - "Singh, S.", - "Kshetrapal, P.", - "Thiruvengadam, R.", - "Batra, G.", - "Medigeshi, G.", - "Ward, A.B.", - "Bhatnagar, S.", - "Awasthi, A.", - "Sok, D.", - "Bhattacharya, J. (0000-0002-1531-3822)", - "Bhattacharya, J.", - ], - }, - { - pmID: "", - title: - "A combination of potently neutralizing monoclonal antibodies isolated from an Indian convalescent donor protects against the SARS-CoV-2 delta variant", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.12.25.474152", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Hingankar, N.", - "Deshpande, S.", - "Das, P.", - "Rizvi, Z.A.", - "Wibmer, C.K.", - "Mashilo, P.", - "Ansari, M.Y.", - "Burns, A.", - "Barman, S.", - "Zhao, F.", - "Mukherjee, S.", - "Torres, J.L.", - "Chattopadhyay, S.", - "Mehdi, F.", - "Sutar, J.", - "Rathore, D.K.", - "Pargai, K.", - "Singh, J.", - "Sonar, S.", - "Jakhar, K.", - "Dandotiya, J.", - "Bhattacharyya, S.", - "Mani, S.", - "Samal, S.", - "Singh, S.", - "Kshetrapal, P.", - "Thiruvengadam, R.", - "Batra, G.", - "Medigeshi, G.", - "Ward, A.B.", - "Bhatnagar, S.", - "Awasthi, A.", - "Sok, D.", - "Bhattacharya, J. (0000-0002-1531-3822)", - "Bhattacharya, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z0y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z0y", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z4444622066 (Mpro-x2563)", - emdb: null, - pdb: { - dbId: "5RGV", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RGV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rgv_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rgv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XBRJTBLYIAYTOZ-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgv", - }, - }, - { - title: "Structure of the SARS-CoV-2 NSP3 Macro X domain in complex with cyclic AMP", - emdb: null, - pdb: { - dbId: "7JME", - method: "X-RAY DIFFRACTION", - keywords: - "macro domain, cAMP, cyclic AMP, viral protein, sars-cov-2, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JME", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jme_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jme", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IVOMOUWHDPKRLL-KQYNXXCUSA-N"], - dbauthors: [ - "Vuksanovic, N. (0000-0003-2883-6312)", - "Melkonian, T.R. (0000-0001-7566-1346)", - "Silvaggi, N.R. (0000-0003-0576-0714)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32981460", - title: - "Discovery of Drug-Like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3.", - journal: "Slas Discov 25: 1162-1170 (2020), 2472-5560", - doi: "https://doi.org/10.1177/2472555220960428", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32981460", - pubDate: "2020", - abstract: "", - authors: [ - "Virdi, R.S.", - "Bavisotto, R.V.", - "Hopper, N.C.", - "Vuksanovic, N.", - "Melkonian, T.R.", - "Silvaggi, N.R.", - "Frick, D.N. (0000-0002-2434-7223)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jme_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jme", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1741970824", - emdb: null, - pdb: { - dbId: "5RF3", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RF3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rf3_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rf3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "FVLAYJRLBLHIPV-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rf3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rf3", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434856", - emdb: null, - pdb: { - dbId: "5REI", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5REI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rei_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rei", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "NWMZWMSJQLEJTG-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsd", - }, - }, - { - title: - "Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with 7-methyl-GpppA and S-adenosyl-L-homocysteine.", - emdb: null, - pdb: { - dbId: "6WQ3", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, 7-methyl-GpppA, S-adenosyl-L-homocysteine, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WQ3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wq3_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wq3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "QQOHNVHGNZYSBP-XPWFQUROSA-O", - "SBASPRRECYVBRF-KQYNXXCUSA-O", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Brunzelle, J.S.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32994211", - title: - "High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design.", - journal: "Sci.Signal. 13 (2020), 1937-9145", - doi: "https://doi.org/10.1126/scisignal.abe1202", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32994211", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Minasov, G. (0000-0001-5460-3462)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Kiryukhina, O. (0000-0001-5962-8423)", - "Brunzelle, J. (0000-0001-9197-0018)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.L.", - "Kiryukhina, O.", - "Wiersum, G.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Endres, M.", - "Jaroszewski, L.", - "Godzik, A.", - "Joachimiak, A.", - "Satchell, K.J.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wq3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wq3", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 RBD and horse ACE2", - emdb: null, - pdb: { - dbId: "7FC5", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, spike, receptor binding domain, horse, ACE2, VIRAL PROTEIN, VIRAL PROTEIN-PROTEIN BINDING complex", - refModels: [ - { - emdbId: null, - pdbId: "7FC5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fc5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fc5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TEF4", - organism: "9986", - name: "Angiotensin-converting enzyme", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Ge, J.W.", "Wang, X.Q.", "Lan, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35917815", - title: - "Structural insights into the binding of SARS-CoV-2, SARS-CoV, and hCoV-NL63 spike receptor-binding domain to horse ACE2.", - journal: "Structure 30: 1432-1442.e4 (2022), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2022.07.005", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35917815", - pubDate: "2022", - abstract: "", - authors: [ - "Lan, J.", - "Chen, P.", - "Liu, W.", - "Ren, W.", - "Zhang, L.", - "Ding, Q.", - "Zhang, Q.", - "Wang, X.", - "Ge, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fc5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fc5", - }, - }, - { - title: "Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope pep4", - emdb: null, - pdb: { - dbId: "7F4W", - method: "X-RAY DIFFRACTION", - keywords: "MHC, HLA, SARS-CoV-2, epitope, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7F4W", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f4w_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f4w", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "SARS-CoV-2 T-cell Epitope pep4", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Jin, T.", "Deng, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34506741", - title: - "Profiling CD8 + T cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.", - journal: "Cell Rep 36: 109708-109708 (2021), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2021.109708", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34506741", - pubDate: "2021", - abstract: "", - authors: [ - "Zhang, H.", - "Deng, S.", - "Ren, L.", - "Zheng, P.", - "Hu, X.", - "Jin, T.", - "Tan, X.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7f4w_deposited_chain_front_image-200x200.png", - 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{ - emdbId: null, - pdbId: "7ADW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7adw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7adw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "VLKIRFAISMBUCB-UHFFFAOYSA-N", - "RAXXELZNTBOGNW-UHFFFAOYSA-O", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7adw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7adw", - }, - }, - { - title: "The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant", - emdb: null, - pdb: { - dbId: "6WRH", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6WRH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wrh_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wrh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Tesar, C.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Welk, L.", - "Babnigg, G.", - "Michalska, K.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33531496", - title: - "Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.", - journal: "Nat Commun 12: 743-743 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-21060-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33531496", - pubDate: "2021", - abstract: "", - authors: [ - "Osipiuk, J.", - "Azizi, S.A. (0000-0002-9226-9917)", - "Dvorkin, S.", - "Endres, M.", - "Jedrzejczak, R.", - "Jones, K.A. (0000-0003-0711-5516)", - "Kang, S.", - "Kathayat, R.S. (0000-0002-9159-2413)", - "Kim, Y.", - "Lisnyak, V.G. (0000-0002-4406-8440)", - "Maki, S.L. (0000-0001-6917-3602)", - "Nicolaescu, V.", - "Taylor, C.A.", - "Tesar, C.", - "Zhang, Y.A.", - "Zhou, Z. (0000-0002-2792-8429)", - "Randall, G.", - "Michalska, K.", - "Snyder, S.A. (0000-0003-3594-8769)", - "Dickinson, B.C. (0000-0002-9616-1911)", - "Joachimiak, A. (0000-0003-2535-6209)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wrh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wrh", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332", - emdb: null, - pdb: { - dbId: "7VH8", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Main protease, PF-07321332, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VH8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vh8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vh8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Yang, H. (0000-0002-1875-3268)", - "Rao, Z. (0000-0001-9866-2384)", - "Zhao, Y. (0000-0002-2932-2164)", - "Zhang, Q. (0000-0002-6271-9163)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34687004", - title: - "Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332.", - journal: "Protein Cell 13: 689-693 (2022), 1674-8018", - doi: "https://doi.org/10.1007/s13238-021-00883-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34687004", - pubDate: "2022", - abstract: "", - authors: [ - "Zhao, Y. (0000-0002-2932-2164)", - "Fang, C. (0000-0003-4762-7276)", - "Zhang, Q. (0000-0002-6271-9163)", - "Zhang, R. (0000-0002-2518-6185)", - "Zhao, X.", - "Duan, Y. (0000-0002-0544-7413)", - "Wang, H. (0000-0001-8175-5621)", - "Zhu, Y. (0000-0002-7045-4847)", - "Feng, L. (0000-0003-1060-6391)", - "Zhao, J. 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}, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000336438345", - emdb: null, - pdb: { - dbId: "5RSE", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rse_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rse", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QSYGVQIPKLCKAM-MRVPVSSYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rse_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rse", - }, - }, - { - title: - "The 1.95 A Crystal Structure of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "6WQD", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, co-factor for RNA polymerase NSP12, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WQD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wqd_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wqd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 7", - details: "", - altNames: "nsp7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 8", - details: "", - altNames: "nsp8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Wilamowski, M.", - "Godzik, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34197805", - title: - "Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication.", - journal: "Biophys.J. 120: 3152-3165 (2021), 1542-0086", - doi: "https://doi.org/10.1016/j.bpj.2021.06.006", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34197805", - pubDate: "2021", - abstract: "", - authors: [ - "Wilamowski, M.", - "Hammel, M.", - "Leite, W.", - "Zhang, Q.", - "Kim, Y.", - "Weiss, K.L.", - "Jedrzejczak, R.", - "Rosenberg, D.J.", - "Fan, Y.", - "Wower, J.", - "Bierma, J.C.", - "Sarker, A.H.", - "Tsutakawa, S.E.", - "Pingali, S.V.", - "O'Neill, H.M.", - "Joachimiak, A.", - "Hura, G.L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wqd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wqd", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-3", - emdb: null, - pdb: { - dbId: "7VK4", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, SFX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VK4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vk4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vk4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "DeMirci, H. (0000-0002-9135-5397)", - "Buyukdag, C. (0000-0001-9714-4892)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography", - journal: "Crystals 11 (2021), 2073-4352", - doi: "https://doi.org/10.3390/cryst11121579", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Guven, O.", - "Gul, M.", - "Ayan, E.", - "Johnson, J.A.", - "Cakilkaya, B.", - "Usta, G.", - "Ertem, F.B.", - "Tokay, N.", - "Yuksel, B.", - "Gocenler, O.", - "Buyukdag, C.", - "Botha, S.", - "Ketawala, G.", - "Su, Z.", - "Hayes, B.", - "Poitevin, F.", - "Batyuk, A.", - "Yoon, C.H.", - "Kupitz, C.", - "Durdagi, S.", - "Sierra, R.G.", - "DeMirci, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vk4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vk4", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000158650", - emdb: null, - pdb: { - dbId: "5RSR", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsr_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAJLTMBBAVVMQO-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0001-8287-0269)", - "Knecht, W. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rf2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rf2", - }, - }, - { - title: - "Crystal structure of the L452R mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-75 and COVOX-253 Fabs", - emdb: null, - pdb: { - dbId: "7ORB", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, B.1.617 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ORB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7orb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7orb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-253 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-253 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-75 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-75 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PQYJRMFWJJONBO-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "OWMVSZAMULFTJU-UHFFFAOYSA-N", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34242578", - title: - "Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.", - journal: "Cell 184: 4220-4236.e13 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.06.020", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34242578", - pubDate: "2021", - abstract: "", - authors: [ - "Liu, C.", - "Ginn, H.M.", - "Dejnirattisai, W.", - "Supasa, P.", - "Wang, B.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Zhou, D.", - "Mentzer, A.J.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Costa Clemens, S.A.", - "Gomes Naveca, F.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Temperton, N.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Malik, T.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Baillie, V.", - "Serafin, N.", - "Ditse, Z.", - "Da Silva, K.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Madhi, S.", - "Nunes, M.C.", - "Goulder, P.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7orb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7orb", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z4444621910 (Mpro-x2569)", - emdb: null, - pdb: { - dbId: "5RGW", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RGW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rgw_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rgw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DQOFNGNCBXHENB-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgw", - }, - }, - { - title: "Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL", - emdb: null, - pdb: { - dbId: "7MKB", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, CD8+, epitope, HLA, human major histocompatibility complex, MHC-I, YLQPRTFLL, HLA-A2, HLA-A*02:01 IMMUNE SYSTEM-VIRAL PROTEIN complex, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7MKB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mkb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mkb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Nyovanie, S.T.", "Patskovsky, Y.", "Krogsgaard, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL", - journal: "To be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Nyovanie, S.T.", "Patskovsky, Y.", "Krogsgaard, M."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mkb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mkb", - }, - }, - { - title: "Crystal structure of 2019-nCoV nucleocapsid C-terminal domain (CTD) protein", - emdb: null, - pdb: { - dbId: "7CE0", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, RNA binding, nucleocapsid, 2019-nCoV, dimerization, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CE0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ce0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ce0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Qi, J.", "Gao, G.F.", "Song, H.", "Peng, Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32914439", - title: - "Structures of the SARS-CoV-2 nucleocapsid and their perspectives for drug design.", - journal: "Embo J. 39: e105938-e105938 (2020), 1460-2075", - doi: "https://doi.org/10.15252/embj.2020105938", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32914439", - pubDate: "2020", - abstract: "", - authors: [ - "Peng, Y.", - "Du, N.", - "Lei, Y.", - "Dorje, S. (0000-0002-1885-3007)", - "Qi, J.", - "Luo, T.", - "Gao, G.F. (0000-0002-3869-615X)", - "Song, H. (0000-0002-2811-0370)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ce0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ce0", - }, - }, - { - title: "THSC20.HVTR26 Fab bound to SARS-CoV-2 Receptor Binding Domain", - emdb: null, - pdb: { - dbId: "7Z0X", - method: "X-RAY DIFFRACTION", - keywords: - "Neutralizing antibody, SARS-CoV-2, Spike, RBD, ANTIVIRAL PROTEIN, IMMUNOLOGY", - refModels: [ - { - emdbId: null, - pdbId: "7Z0X", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7z0x_final.pdb", - externalLink: "https://pdb-redo.eu/db/7z0x", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "THSC20.HVTR26 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "THSC20.HVTR26 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JKMHFZQWWAIEOD-UHFFFAOYSA-N"], - dbauthors: ["Wibmer, C.K. (0000-0003-2329-2280)"], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35482816", - title: - "A combination of potently neutralizing monoclonal antibodies isolated from an Indian convalescent donor protects against the SARS-CoV-2 Delta variant.", - journal: "Plos Pathog. 18: e1010465-e1010465 (2022), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1010465", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35482816", - pubDate: "2022", - abstract: "", - authors: [ - "Hingankar, N.", - "Deshpande, S.", - "Das, P.", - "Rizvi, Z.A.", - "Wibmer, C.K.", - "Mashilo, P.", - "Ansari, M.Y.", - "Burns, A.", - "Barman, S.", - "Zhao, F.", - "Mukherjee, S.", - "Torres, J.L.", - "Chattopadhyay, S.", - "Mehdi, F.", - "Sutar, J.", - "Rathore, D.K.", - "Pargai, K.", - "Singh, J.", - "Sonar, S.", - "Jakhar, K.", - "Dandotiya, J.", - "Bhattacharyya, S.", - "Mani, S.", - "Samal, S.", - "Singh, S.", - "Kshetrapal, P.", - "Thiruvengadam, R.", - "Batra, G.", - "Medigeshi, G.", - "Ward, A.B.", - "Bhatnagar, S.", - "Awasthi, A.", - "Sok, D.", - "Bhattacharya, J. (0000-0002-1531-3822)", - "Bhattacharya, J.", - ], - }, - { - pmID: "", - title: - "A combination of potently neutralizing monoclonal antibodies isolated from an Indian convalescent donor protects against the SARS-CoV-2 delta variant", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.12.25.474152", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Hingankar, N.", - "Deshpande, S.", - "Das, P.", - "Rizvi, Z.A.", - "Wibmer, C.K.", - "Mashilo, P.", - "Ansari, M.Y.", - "Burns, A.", - "Barman, S.", - "Zhao, F.", - "Mukherjee, S.", - "Torres, J.L.", - "Chattopadhyay, S.", - "Mehdi, F.", - "Sutar, J.", - "Rathore, D.K.", - "Pargai, K.", - "Singh, J.", - "Sonar, S.", - "Jakhar, K.", - "Dandotiya, J.", - "Bhattacharyya, S.", - "Mani, S.", - "Samal, S.", - "Singh, S.", - "Kshetrapal, P.", - "Thiruvengadam, R.", - "Batra, G.", - "Medigeshi, G.", - "Ward, A.B.", - "Bhatnagar, S.", - "Awasthi, A.", - "Sok, D.", - "Bhattacharya, J. (0000-0002-1531-3822)", - "Bhattacharya, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z0x_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z0x", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z4438424255 (Mpro-x2776)", - emdb: null, - pdb: { - dbId: "5RH9", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RH9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rh9_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rh9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "QDPHPMZTNKBBHJ-AFMDSPMNSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rh9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rh9", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 21c", - emdb: null, - pdb: { - dbId: "7M04", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7M04", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m04_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m04", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VNVWDEQECYLCMA-AYUSFXAWSA-N", - "VNVWDEQECYLCMA-JJDHJZHUSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Miller, M.J.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Perera, K.D.", - "Rathnayake, A.D.", - "Jesri, A.R.M.", - "Baird, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34865476", - title: - "Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.", - journal: "J.Med.Chem. 64: 17846-17865 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34865476", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Jesri, A.M.", - "Nguyen, H.N.", - "Miller, M.J.", - "Thurman, H.A.", - "Zheng, J.", - "Kashipathy, M.M.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Kim, Y.", - "Groutas, W.C.", - "Chang, K.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m04_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m04", - }, - }, - { - title: - "Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98", - emdb: null, - pdb: { - dbId: "7VPH", - method: "X-RAY DIFFRACTION", - keywords: - "Complex, Coronavirus, RNA nuclear export, Protein binding, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VPH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vph_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vph", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P78406", - organism: "9606", - name: "mRNA export factor", - details: "", - altNames: "Rae1 protein homolog,mRNA-associated protein mrnp 41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P52948", - organism: "9606", - name: "Isoform 3 of Nuclear pore complex protein Nup98-Nup96", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC6", - organism: "2697049", - name: "ORF6 protein", - details: "", - altNames: - "ORF6,Accessory protein 6,Non-structural protein 6,ns6,Protein X3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Guo, H.", - "Ji, X. (0000-0002-0801-8825)", - "Yang, T.", - "Wen, Y.", - "Li, T. (0000-0002-7931-5907)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35096974", - title: - "Molecular Mechanism of SARS-CoVs Orf6 Targeting the Rae1-Nup98 Complex to Compete With mRNA Nuclear Export.", - journal: "Front Mol Biosci 8: 813248-813248 (2021), 2296-889X", - doi: "https://doi.org/10.3389/fmolb.2021.813248", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35096974", - pubDate: "2021", - abstract: "", - authors: [ - "Li, T.", - "Wen, Y.", - "Guo, H.", - "Yang, T.", - "Yang, H.", - "Ji, X.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vph_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vph", - }, - }, - { - title: "The crystal structure of the SARS-CoV-2 ORF7a ectodomain", - emdb: null, - pdb: { - dbId: "7CI3", - method: "X-RAY DIFFRACTION", - keywords: - "Ig-like fold, type-I transmembrane protein, ER membrane, accessory protein, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CI3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ci3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ci3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "A0A6C0X2S1", - organism: "2697049", - name: "Orf7a protein", - details: "", - altNames: "Nonstructural protein NS7a", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhou, Z. (0000-0002-6801-4180)", - "Zhou, Z. (0000-0002-4057-7512)", - "Chen, S. (0000-0002-7634-2141)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33615195", - title: - "Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14 + monocytes.", - journal: "Iscience 24: 102187-102187 (2021), 2589-0042", - doi: "https://doi.org/10.1016/j.isci.2021.102187", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33615195", - pubDate: "2021", - abstract: "", - authors: [ - "Zhou, Z.", - "Huang, C.", - "Huang, Z.", - "Su, L.", - "Kang, S.", - "Chen, X.", - "Chen, Q.", - "He, S.", - "Rong, X.", - "Xiao, F.", - "Chen, J.", - "Chen, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ci3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ci3", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with FMOOA000509a", - emdb: null, - pdb: { - dbId: "5S4K", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S4K", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s4k_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s4k", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QCWXHFWRNWEAIH-LQJRIPTKSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4k_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4k", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with FUZS-5", - emdb: null, - pdb: { - dbId: "5S71", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5S71", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s71_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s71", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "CPEAGKYEYPXTSP-XLPZGREQSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Bege, M.", - "Keseru, G.M.", - "Bajusz, D.", - "BorbAs, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s71_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s71", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 nsp10/nsp16 in complex with the WZ16 inhibitor", - emdb: null, - pdb: { - dbId: "7R1U", - method: "X-RAY DIFFRACTION", - keywords: "methyltransferase, nsp10, nsp16, inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7R1U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7r1u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7r1u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase nsp16", - details: "", - altNames: "Non-structural protein 16,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "CPUNUFGYWFHFOF-TVDBPQCTSA-N", - "QQOHNVHGNZYSBP-XPWFQUROSA-O", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Li, F.", - "Klima, M. (0000-0002-9083-509X)", - "Boura, E. (0000-0002-9652-4065)", - "Yazdi, A.K.", - "Vedadi, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36040262", - title: - "Crystal structure of SARS-CoV-2 nsp10-nsp16 in complex with small molecule inhibitors, SS148 and WZ16.", - journal: "Protein Sci. 31: e4395-e4395 (2022), 1469-896X", - doi: "https://doi.org/10.1002/pro.4395", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36040262", - pubDate: "2022", - abstract: "", - authors: [ - "Klima, M.", - "Khalili Yazdi, A.", - "Li, F.", - "Chau, I.", - "Hajian, T.", - "Bolotokova, A.", - "Kaniskan, H.U.", - "Han, Y.", - "Wang, K.", - "Li, D.", - "Luo, M.", - "Jin, J.", - "Boura, E. (0000-0002-9652-4065)", - "Vedadi, M. (0000-0002-0574-0169)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7r1u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7r1u", - }, - }, - { - title: "X-ray structure of SCoV2-PLpro in complex with small molecule inhibitor", - emdb: null, - pdb: { - dbId: "7NT4", - method: "X-RAY DIFFRACTION", - keywords: "Drug repurposing, SCoV2-PLpro inhibitor, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7NT4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nt4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nt4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "WDVSHHCDHLJJJR-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: [ - "Napolitano, V.", - "Mourao, A.", - "Bostock, M.", - "Matsuda, A.", - "Czarna, A.", - "Popowicz, G.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35021060", - title: - "Acriflavine, a clinically approved drug, inhibits SARS-CoV-2 and other betacoronaviruses.", - journal: "Cell Chem Biol 29 (2022), 2451-9456", - doi: "https://doi.org/10.1016/j.chembiol.2021.11.006", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35021060", - pubDate: "2022", - abstract: "", - authors: [ - "Napolitano, V.", - "Dabrowska, A.", - "Schorpp, K.", - "Mourao, A.", - "Barreto-Duran, E.", - "Benedyk, M.", - "Botwina, P.", - "Brandner, S.", - "Bostock, M.", - "Chykunova, Y.", - "Czarna, A.", - "Dubin, G.", - "Frohlich, T.", - "Holscher, M.", - "Jedrysik, M.", - "Matsuda, A.", - "Owczarek, K.", - "Pachota, M.", - "Plettenburg, O.", - "Potempa, J.", - "Rothenaigner, I.", - "Schlauderer, F.", - "Slysz, K.", - "Szczepanski, A.", - "Greve-Isdahl Mohn, K.", - "Blomberg, B.", - "Sattler, M.", - "Hadian, K.", - "Popowicz, G.M.", - "Pyrc, K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nt4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nt4", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21)", - emdb: null, - pdb: { - dbId: "7L8I", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, SARS2, COVID19, PROTEASE, PROTEASE INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, RUPINTRIVIR, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7L8I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l8i_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l8i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LMIUALQNZXJHOG-IFILWLFVSA-N"], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Henes, M. (0000-0001-8667-541X)", - "Lee, J.M.", - "Timm, J. (0000-0001-9750-3293)", - "Nalivaika, E.A.", - "Yilmaz, N.K. (0000-0002-5036-676X)", - "Thompson, P.R. (0000-0002-1621-3372)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34506130", - title: - "Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode.", - journal: "Biochemistry 60: 2925-2931 (2021), 0006-2960", - doi: "https://doi.org/10.1021/acs.biochem.1c00414", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34506130", - pubDate: "2021", - abstract: "", - authors: [ - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Henes, M.", - "Lee, J.M.", - "Timm, J. (0000-0001-9750-3293)", - "Nalivaika, E.A.", - "Thompson, P.R. (0000-0002-1621-3372)", - "Kurt Yilmaz, N. (0000-0002-5036-676X)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l8i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l8i", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2856434783", - emdb: null, - pdb: { - dbId: "5SA6", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SA6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sa6_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sa6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SXZSRGKJZKOZRP-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sa6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sa6", - }, - }, - { - title: "Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor SH-5", - emdb: null, - pdb: { - dbId: "7E19", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 3CL protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7E19", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e19_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e19", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KSCRVOKQPYZBHZ-IXPOFIJOSA-N"], - dbauthors: [ - "Senda, M. (0000-0003-3863-4503)", - "Konno, S.", - "Hayashi, Y.", - "Senda, T. (0000-0002-5153-928X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34313428", - title: - "3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.", - journal: "J.Med.Chem. 65: 2926-2939 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34313428", - pubDate: "2022", - abstract: "", - authors: [ - "Konno, S.", - "Kobayashi, K.", - "Senda, M.", - "Funai, Y.", - "Seki, Y.", - "Tamai, I.", - "Schakel, L.", - "Sakata, K.", - "Pillaiyar, T.", - "Taguchi, A.", - "Taniguchi, A.", - "Gutschow, M.", - "Muller, C.E.", - "Takeuchi, K.", - "Hirohama, M.", - "Kawaguchi, A.", - "Kojima, M.", - "Senda, T.", - "Shirasaka, Y.", - "Kamitani, W.", - "Hayashi, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e19_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e19", - }, - }, - { - title: "SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83", - emdb: null, - pdb: { - dbId: "7LLF", - method: "X-RAY DIFFRACTION", - keywords: - "papain-like protease, coronavirus inhibitor, SARS-CoV-2, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LLF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7llf_final.pdb", - externalLink: "https://pdb-redo.eu/db/7llf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "KGBXLFKZBHKPEV-UHFFFAOYSA-N", - "IGVYCVBUHQMNRZ-QNIAMRLHSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Ratia, K.M. (0000-0002-4834-9207)", - "Xiong, R. (0000-0002-6350-9037)", - "Thatcher, G.R. (0000-0002-7757-1739)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33594371", - title: - "Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.02.13.431008", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33594371", - pubDate: "2021", - abstract: "", - authors: [ - "Shen, Z.", - "Ratia, K.", - "Cooper, L.", - "Kong, D.", - "Lee, H.", - "Kwon, Y.", - "Li, Y.", - "Alqarni, S.", - "Huang, F.", - "Dubrovskyi, O.", - "Rong, L.", - "Thatcher, G.R.", - "Xiong, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7llf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7llf", - }, - }, - { - title: "Structure of the SARS-COV-2 main protease with EN102 inhibitor", - emdb: null, - pdb: { - dbId: "7WYP", - method: "X-RAY DIFFRACTION", - keywords: - "Structure of the SARS-COV-2 main protease with EN102 inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WYP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wyp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wyp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UIQVVKYYEHVSIZ-UHFFFAOYSA-N"], - dbauthors: ["Gao, X.", "Qin, B.", "Cui, S.", "Hou, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35702321", - title: - "Acrylamide fragment inhibitors that induce unprecedented conformational distortions in enterovirus 71 3C and SARS-CoV-2 main protease.", - journal: "Acta Pharm Sin B 12: 3924-3933 (2022), 2211-3835", - doi: "https://doi.org/10.1016/j.apsb.2022.06.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35702321", - pubDate: "2022", - abstract: "", - authors: [ - "Qin, B.", - "Craven, G.B.", - "Hou, P.", - "Chesti, J.", - "Lu, X.", - "Child, E.S.", - "Morgan, R.M.L.", - "Niu, W.", - "Zhao, L.", - "Armstrong, A.", - "Mann, D.J.", - "Cui, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wyp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wyp", - }, - }, - { - title: "Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N316-324", - emdb: null, - pdb: { - dbId: "7KGP", - method: "X-RAY DIFFRACTION", - keywords: - "HLA-A*0201, T cell, SARS-CoV-2, COVID-19, viral peptide, TCR, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7KGP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kgp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kgp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "WLZRMCYVCSSEQC-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Gras, S.", - "Chatzileontiadou, D.S.M.", - "Szeto, C.", - "Riboldi-Tunnicliffe, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33521593", - title: - "The presentation of SARS-CoV-2 peptides by the common HLA-A * 02:01 molecule.", - journal: "Iscience 24: 102096-102096 (2021), 2589-0042", - doi: "https://doi.org/10.1016/j.isci.2021.102096", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33521593", - pubDate: "2021", - abstract: "", - authors: [ - "Szeto, C.", - "Chatzileontiadou, D.S.M.", - "Nguyen, A.T.", - "Sloane, H.", - "Lobos, C.A.", - "Jayasinghe, D.", - "Halim, H.", - "Smith, C.", - "Riboldi-Tunnicliffe, A.", - "Grant, E.J.", - "Gras, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kgp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kgp", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2033637875", - emdb: null, - pdb: { - dbId: "5SMC", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SMC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5smc_final.pdb", - externalLink: "https://pdb-redo.eu/db/5smc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "BCFQGXBWVPWHCV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5smc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5smc", - }, - }, - { - title: - "Crystal structure of the K417N mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs", - emdb: null, - pdb: { - dbId: "7NX7", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7NX7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nx7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nx7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "KRKNYBCHXYNGOX-UHFFFAOYSA-N", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33852911", - title: "Antibody evasion by the P.1 strain of SARS-CoV-2.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.03.055", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33852911", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - { - pmID: "", - title: "Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.12.435194", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nx7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nx7", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z32400357", - emdb: null, - pdb: { - dbId: "5SLG", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slg_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "VSYPROQBASLXDK-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slg", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FD-5D Fab", - emdb: null, - pdb: { - dbId: "7PR0", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 antibody, receptor-binding-domain, RBD, spike, neutralisation, FI-3A, FD-11A, FD-5D, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7PR0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7pr0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7pr0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "FD-5D Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "FD-5D Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "NHNBFGGVMKEFGY-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34987630", - title: - "Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2.", - journal: "Theranostics 12: 1-17 (2022), 1838-7640", - doi: "https://doi.org/10.7150/thno.65563", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34987630", - pubDate: "2022", - abstract: "", - authors: [ - "Huang, K.A.", - "Zhou, D.", - "Tan, T.K.", - "Chen, C.", - "Duyvesteyn, H.M.E.", - "Zhao, Y.", - "Ginn, H.M.", - "Qin, L.", - "Rijal, P.", - "Schimanski, L.", - "Donat, R.", - "Harding, A.", - "Gilbert-Jaramillo, J.", - "James, W.", - "Tree, J.A.", - "Buttigieg, K.", - "Carroll, M.", - "Charlton, S.", - "Lien, C.E.", - "Lin, M.Y.", - "Chen, C.P.", - "Cheng, S.H.", - "Chen, X.", - "Lin, T.Y.", - "Fry, E.E.", - "Ren, J.", - "Ma, C.", - "Townsend, A.R.", - "Stuart, D.I.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7pr0_deposited_chain_front_image-200x200.png", - 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}, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z373768898", - emdb: null, - pdb: { - dbId: "5SLP", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slp_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "GXDSBWMCMQHCOL-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slp", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000302059710 - (R) isomer", - emdb: null, - pdb: { - dbId: "5SOK", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sok_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sok", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SILGAHKEYSAGRL-SNVBAGLBSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sok_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sok", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1273312153", - emdb: null, - pdb: { - dbId: "5SL1", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SL1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sl1_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sl1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "OKVUYVXDTGOYRU-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sl1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sl1", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 B.1.351 variant Spike glycoprotein in complex with COVOX-222 and EY6A Fabs", - emdb: null, - pdb: { - dbId: "7NXA", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7NXA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nxa_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nxa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - 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abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - { - pmID: "", - title: "Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.12.435194", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nxa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nxa", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-38", - emdb: null, - pdb: { - dbId: "7PS4", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-COV-2 B.1.1.7 (Alpha) VARIANT, B.1.351 (Beta) VARIANT, P.1 (Gamma) VARIANT, B.1.617.2 (Delta) VARIANT, ANTIBODY, RECEPTOR-BINDING-DOMAIN, SPIKE, NEUTRALISATION, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7PS4", - source: "PDB-REDO", - 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journal: "Cell Host Microbe 30 (2022), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2021.11.013", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34921776", - pubDate: "2022", - abstract: "", - authors: [ - "Liu, C.", - "Zhou, D.", - "Nutalai, R.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Dejnirattisai, W.", - "Supasa, P.", - "Mentzer, A.J.", - "Wang, B.", - "Case, J.B.", - "Zhao, Y.", - "Skelly, D.T.", - "Chen, R.E.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Malik, T.", - "Temperton, N.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Clare, D.K.", - "Howe, A.", - "Goulder, P.J.R.", - "Fry, E.E.", - "Diamond, M.S.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Afonine, P.V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ps4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ps4", - }, - }, - { - title: - "Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2", - emdb: null, - pdb: { - dbId: "6VYO", - method: "X-RAY DIFFRACTION", - keywords: - "CSGID, COVID-19, RNA binding domain, nucleocapsid protein, nucleoprotein, Structural Genomics, Center for Structural Genomics of Infectious Diseases, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6VYO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6vyo_final.pdb", - externalLink: "https://pdb-redo.eu/db/6vyo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Godzik, A.", - "Chang, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Chang, C.", - "Michalska, K.", - "Jedrzejczak, R.", - "Maltseva, N.", - "Endres, M.", - "Godzik, A.", - "Kim, Y.", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6vyo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6vyo", - }, - }, - { - title: - "Structure of SARS-CoV-2 spike receptor-binding domain complexed with its receptor equine ACE2", - emdb: null, - pdb: { - dbId: "7W6U", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7W6U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7w6u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7w6u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "G1TEF4", - organism: "9986", - name: "Angiotensin-converting enzyme", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Han, P.", "Qi, J.X.", "Liu, K.F.", "Xu, Z.P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses", - journal: "Nat Commun 13 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-31276-6", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Xu, Z.", - "Kang, X.", - "Han, P.", - "Du, P.", - "Li, L.", - "Zheng, A.", - "Deng, C.", - "Qi, J.", - "Zhao, X.", - "Wang, Q.", - "Liu, K.", - "Gao, G.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7w6u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7w6u", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)", - emdb: null, - pdb: { - dbId: "7KR0", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7KR0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kr0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kr0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Young, I.D. (0000-0003-4713-9504)", - "Thompson, M.C. (0000-0002-6099-2027)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kr0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kr0", - }, - }, - { - title: "Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2.", - emdb: null, - pdb: { - dbId: "6VWW", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus, endonuclease, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6VWW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6vww_final.pdb", - externalLink: "https://pdb-redo.eu/db/6vww", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Godzik, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32304108", - title: - "Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.", - journal: "Protein Sci. 29: 1596-1605 (2020), 1469-896X", - doi: "https://doi.org/10.1002/pro.3873", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32304108", - pubDate: "2020", - abstract: "", - authors: [ - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Wilamowski, M.", - "Endres, M.", - "Godzik, A.", - "Michalska, K.", - "Joachimiak, A.", - ], - }, - { - pmID: "", - title: - "Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.03.02.968388", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Wilamowski, M.", - "Endres, M.", - "Godzik, A.", - "Michalska, K.", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6vww_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6vww", - }, - }, - { - title: "HLA peptide complex", - emdb: null, - pdb: { - dbId: "7N6D", - method: "X-RAY DIFFRACTION", - keywords: "peptide HLA complex, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7N6D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n6d_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n6d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Rossjohn, J. (0000-0002-2020-7522)", - "Chaurasia, P. (0000-0003-4249-3678)", - "Petersen, J. (0000-0002-2045-6342)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34384783", - title: - "Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein.", - journal: "J.Biol.Chem. 297: 101065-101065 (2021), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2021.101065", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34384783", - pubDate: "2021", - abstract: "", - authors: [ - "Chaurasia, P.", - "Nguyen, T.H.O.", - "Rowntree, L.C.", - "Juno, J.A.", - "Wheatley, A.K.", - "Kent, S.J.", - "Kedzierska, K.", - "Rossjohn, J.", - "Petersen, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n6d_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n6d", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 NendoU in complex with CSC000178569", - emdb: null, - pdb: { - dbId: "7N7W", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7N7W", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n7w_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n7w", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KCHHKGGVOQEHPF-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n7w_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n7w", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2125.", - emdb: null, - pdb: { - dbId: "7N4L", - method: "X-RAY DIFFRACTION", - keywords: - "Neutralizing antibody, SARS-CoV-2, WRAIR-2125, receptor binding domain, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7N4L", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n4l_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n4l", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2125 antibody Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2125 antibody Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Sankhala, R.S. 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(0000-0002-5416-5789)", - "Zhang, Q.", - "Coates, L. (0000-0003-2342-049X)", - "Louis, J.M.", - "Kovalevsky, A. 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(0000-0001-6235-6502)", - "Jacobs, L.M.C. (0000-0002-9939-653X)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36119652", - title: - "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.28.497978", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36119652", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, Y.", - "Lewandowski, E.M.", - "Tan, H.", - "Zhang, X.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Butler, S.G.", - "Gongora, M.V.", - "Choy, J.", - "Deng, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dfe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dfe", - }, - }, - { - title: - "Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with 3'-uridinemonophosphate", - emdb: null, - pdb: { - dbId: "6X4I", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus 2, endoribonuclease, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6X4I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6x4i_final.pdb", - externalLink: "https://pdb-redo.eu/db/6x4i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FOGRQMPFHUHIGU-XVFCMESISA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Chang, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33564093", - title: - "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.", - journal: "Commun Biol 4: 193-193 (2021), 2399-3642", - doi: "https://doi.org/10.1038/s42003-021-01735-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33564093", - pubDate: "2021", - abstract: "", - authors: [ - "Kim, Y.", - "Wower, J. (0000-0001-8096-7745)", - "Maltseva, N. (0000-0002-2871-465X)", - "Chang, C.", - "Jedrzejczak, R.", - "Wilamowski, M.", - "Kang, S.", - "Nicolaescu, V.", - "Randall, G.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Wower, J.", - "Maltseva, N.", - "Nicolaescu,, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - { - pmID: "", - title: - "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.06.26.173872", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Kim, Y.", - "Wower, J. (0000-0001-8096-7745)", - "Maltseva, N. (0000-0002-2871-465X)", - "Chang, C.", - "Jedrzejczak, R.", - "Wilamowski, M.", - "Kang, S.", - "Nicolaescu, V.", - "Randall, G.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Wower, J.", - "Maltseva, N.", - "Nicolaescu,, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6x4i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6x4i", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1849009686", - emdb: null, - pdb: { - dbId: "5SLC", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slc_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "NSTXYAFVZNXQTB-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slc", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000043461211", - emdb: null, - pdb: { - dbId: "5SOX", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sox_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sox", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CIFSVKGWWCXKQT-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sox_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sox", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2092370954", - emdb: null, - pdb: { - dbId: "5SMG", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SMG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5smg_final.pdb", - externalLink: "https://pdb-redo.eu/db/5smg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "URNKFNQWYLXELN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5smg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5smg", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FI-3A Fab", - 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(0000-0002-5085-8027)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34534459", - title: - "Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies.", - journal: "Cell Rep 36: 109760-109760 (2021), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2021.109760", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34534459", - pubDate: "2021", - abstract: "", - authors: [ - "Jette, C.A.", - "Cohen, A.A.", - "Gnanapragasam, P.N.P.", - "Muecksch, F.", - "Lee, Y.E.", - "Huey-Tubman, K.E.", - "Schmidt, F.", - "Hatziioannou, T.", - "Bieniasz, P.D.", - "Nussenzweig, M.C.", - "West Jr., A.P.", - "Keeffe, J.R.", - "Bjorkman, P.J.", - "Barnes, C.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rku_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rku", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with beta-24 Fabs", - emdb: null, - pdb: { - dbId: "7PS0", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 alpha variant, beta variant, gamma variant, delta variant, B.1.1.7, B.1.351, P.1, B.1.617.2, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7PS0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ps0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ps0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-24 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - 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"Skelly, D.T.", - "Chen, R.E.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Malik, T.", - "Temperton, N.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Clare, D.K.", - "Howe, A.", - "Goulder, P.J.R.", - "Fry, E.E.", - "Diamond, M.S.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Afonine, P.V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ps0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ps0", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z32014663", - emdb: null, - pdb: { - dbId: "5SL5", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SL5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sl5_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sl5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "KJFNIMLMIUNQSJ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sl5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sl5", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000897286891 - (R) isomer", - emdb: null, - pdb: { - dbId: "5SOO", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5soo_final.pdb", - externalLink: "https://pdb-redo.eu/db/5soo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XUBYDFCDYPJZTA-SNVBAGLBSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. 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}, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "NPBRDFPBRHOBAK-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slt", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with UAW241", - 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"https://www.ebi.ac.uk/pdbe/static/entry/6xa4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xa4", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z68277692", - emdb: null, - pdb: { - dbId: "5SM1", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SM1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sm1_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sm1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - 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(0000-0001-7090-2112)", - "Wang, Y. (0000-0001-8300-0847)", - "Pan, L. (0000-0002-9229-6288)", - "Xu, X. (0000-0003-0092-5313)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33979649", - title: - "Development of potent and selective inhibitors targeting the papain-like protease of SARS-CoV-2.", - journal: "Cell Chem Biol 28 (2021), 2451-9456", - doi: "https://doi.org/10.1016/j.chembiol.2021.04.020", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33979649", - pubDate: "2021", - abstract: "", - authors: [ - "Shan, H.", - "Liu, J.", - "Shen, J.", - "Dai, J.", - "Xu, G.", - "Lu, K.", - "Han, C.", - "Wang, Y.", - "Xu, X.", - "Tong, Y.", - "Xiang, H.", - "Ai, Z.", - "Zhuang, G.", - "Hu, J.", - "Zhang, Z.", - "Li, Y.", - "Pan, L.", - "Tan, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e35_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e35", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z425449682", - emdb: null, - pdb: { - dbId: "5SAD", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SAD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sad_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sad", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AQZLTCXQTOKUAA-UHFFFAOYSA-O"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sad_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sad", - }, - }, - { - title: "Crystal structure of ligand-free SARS-CoV-2 main protease", - emdb: null, - pdb: { - dbId: "7BAJ", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, COVID19, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7BAJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7baj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7baj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Main Protease", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Amporndanai, K. (0000-0001-8527-9394)", - "O'Neill, P.M. (0000-0003-4338-0317)", - "Hasnain, S.S. (0000-0002-2854-4718)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34031399", - title: - "Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives.", - journal: "Nat Commun 12: 3061-3061 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23313-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34031399", - pubDate: "2021", - abstract: "", - authors: [ - "Amporndanai, K.", - "Meng, X. (0000-0002-7774-2075)", - "Shang, W.", - "Jin, Z. (0000-0001-6448-820X)", - "Rogers, M.", - "Zhao, Y.", - "Rao, Z. (0000-0001-9866-2384)", - "Liu, Z.J. (0000-0001-7279-2893)", - "Yang, H. (0000-0002-1875-3268)", - "Zhang, L. (0000-0002-2593-2571)", - "O'Neill, P.M. (0000-0003-4338-0317)", - "Samar Hasnain, S. (0000-0002-2854-4718)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7baj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7baj", - }, - }, - { - title: - "SARS-CoV-2 3CLPro in complex with 2-(benzotriazol-1-yl)-N-[4-(1H-imidazol-4-yl)phenyl]-N-(3-thienylmethyl)acetamide", - emdb: null, - pdb: { - dbId: "7LMF", - method: "X-RAY DIFFRACTION", - keywords: - "3CLPro, SARS-CoV-2 Main Protease, SARS-CoV-2 3CLPro, Inhibitor Complex, Protease, VIRAL PROTEIN, Hydrolase-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7LMF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lmf_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lmf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XZJQABWECIWHRU-UHFFFAOYSA-N"], - dbauthors: [ - "Goins, C.M. (0000-0002-6617-4877)", - "Stauffer, S.R. (0000-0002-6332-1827)", - "Arya, T. (0000-0001-8690-6425)", - "Macdonald, J.D. (0000-0002-6360-2768)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34347470", - title: - "Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro ).", - journal: "J.Med.Chem. 65: 2880-2904 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00598", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34347470", - pubDate: "2022", - abstract: "", - authors: [ - "Han, S.H.", - "Goins, C.M.", - "Arya, T.", - "Shin, W.J.", - "Maw, J.", - "Hooper, A.", - "Sonawane, D.P.", - "Porter, M.R.", - "Bannister, B.E.", - "Crouch, R.D.", - "Lindsey, A.A.", - "Lakatos, G.", - "Martinez, S.R.", - "Alvarado, J.", - "Akers, W.S.", - "Wang, N.S.", - "Jung, J.U.", - "Macdonald, J.D.", - "Stauffer, S.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lmf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lmf", - }, - }, - { - title: "Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor", - emdb: null, - pdb: { - dbId: "7RFR", - method: "X-RAY DIFFRACTION", - keywords: - "Protease SARS-CoV-2 Covalent complex inhibitor, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RFR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rfr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rfr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CVWZBMVWUPHSSU-AJEOIHGXSA-N"], - dbauthors: ["Ferre, R.A.", "Liu, W.", "Stewart, A.E.", "Gajiwala, K.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34726479", - title: - "An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19.", - journal: "Science 374: 1586-1593 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abl4784", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34726479", - pubDate: "2021", - abstract: "", - authors: [ - "Owen, D.R.", - "Allerton, C.M.N.", - "Anderson, A.S.", - "Aschenbrenner, L.", - "Avery, M.", - "Berritt, S.", - "Boras, B.", - "Cardin, R.D.", - "Carlo, A.", - "Coffman, K.J.", - "Dantonio, A.", - "Di, L.", - "Eng, H.", - "Ferre, R.", - "Gajiwala, K.S.", - "Gibson, S.A.", - "Greasley, S.E.", - "Hurst, B.L.", - "Kadar, E.P.", - "Kalgutkar, A.S.", - "Lee, J.C.", - "Lee, J.", - "Liu, W.", - "Mason, S.W.", - "Noell, S.", - "Novak, J.J.", - "Obach, R.S.", - "Ogilvie, K.", - "Patel, N.C.", - "Pettersson, M.", - "Rai, D.K.", - "Reese, M.R.", - "Sammons, M.F.", - "Sathish, J.G.", - "Singh, R.S.P.", - "Steppan, C.M.", - "Stewart, A.E.", - "Tuttle, J.B.", - "Updyke, L.", - "Verhoest, P.R.", - "Wei, L.", - "Yang, Q.", - "Zhu, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rfr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rfr", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z56866006", - emdb: null, - pdb: { - dbId: "5S49", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S49", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s49_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s49", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s49_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s49", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to UNC-2327", - emdb: null, - pdb: { - dbId: "7AQE", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-19, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AQE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aqe_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aqe", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "MYTRGTBDVGKKRO-UHFFFAOYSA-N", - ], - dbauthors: ["Reinke, P.", "Guenther, S.", "Meents, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7aqe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7aqe", - }, - }, - { - title: "SARS-CoV-2 main protease in complex with nsp8/9 substrate peptide", - emdb: null, - pdb: { - dbId: "7MGR", - method: "X-RAY DIFFRACTION", - keywords: "protease, 3C-like protease, VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7MGR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mgr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mgr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "ALA-VAL-LYS-LEU-GLN-ASN-ASN-GLU", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Windsor, I.W.", - "MacDonald, E.A. (0000-0002-5873-6809)", - "Hinshaw, S.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34437808", - title: - "Recognition of Divergent Viral Substrates by the SARS-CoV-2 Main Protease.", - journal: "Acs Infect Dis. 7: 2591-2595 (2021), 2373-8227", - doi: "https://doi.org/10.1021/acsinfecdis.1c00237", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34437808", - pubDate: "2021", - abstract: "", - authors: [ - "MacDonald, E.A.", - "Frey, G.", - "Namchuk, M.N.", - "Harrison, S.C.", - "Hinshaw, S.M.", - "Windsor, I.W.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mgr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mgr", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 RBD in complex with BD-236 Fab and BD-368-2 Fab", - emdb: null, - pdb: { - dbId: "7CHE", - method: "X-RAY DIFFRACTION", - keywords: "mAb, ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7CHE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7che_final.pdb", - externalLink: "https://pdb-redo.eu/db/7che", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "BD-236 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-236 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-368-2 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-368-2 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Xiao, J. (0000-0003-1822-1701)", "Zhu, Q. (0000-0001-7020-2044)"], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32970990", - title: - "Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.", - journal: "Cell 183: 1013-1023.e13 (2020), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2020.09.035", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32970990", - pubDate: "2020", - abstract: "", - authors: [ - "Du, S.", - "Cao, Y.", - "Zhu, Q.", - "Yu, P.", - "Qi, F.", - "Wang, G.", - "Du, X.", - "Bao, L.", - "Deng, W.", - "Zhu, H.", - "Liu, J.", - "Nie, J.", - "Zheng, Y.", - "Liang, H.", - "Liu, R.", - "Gong, S.", - "Xu, H.", - "Yisimayi, A.", - "Lv, Q.", - "Wang, B.", - "He, R.", - "Han, Y.", - "Zhao, W.", - "Bai, Y.", - "Qu, Y.", - "Gao, X.", - "Ji, C.", - "Wang, Q.", - "Gao, N.", - "Huang, W.", - "Wang, Y.", - "Xie, X.S.", - "Su, X.D.", - "Xiao, J.", - "Qin, C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7che_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7che", - }, - }, - { - title: - "Crystal structure of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2", - emdb: null, - pdb: { - dbId: "6WIQ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, co-factor for RNA polymerase NSP12, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WIQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wiq_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wiq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 7", - details: "", - altNames: "nsp7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 8", - details: "", - altNames: "nsp8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Wilamowski, M.", - "Godzik, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34197805", - title: - "Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication.", - journal: "Biophys.J. 120: 3152-3165 (2021), 1542-0086", - doi: "https://doi.org/10.1016/j.bpj.2021.06.006", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34197805", - pubDate: "2021", - abstract: "", - authors: [ - "Wilamowski, M.", - "Hammel, M.", - "Leite, W.", - "Zhang, Q.", - "Kim, Y.", - "Weiss, K.L.", - "Jedrzejczak, R.", - "Rosenberg, D.J.", - "Fan, Y.", - "Wower, J.", - "Bierma, J.C.", - "Sarker, A.H.", - "Tsutakawa, S.E.", - "Pingali, S.V.", - "O'Neill, H.M.", - "Joachimiak, A.", - "Hura, G.L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wiq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wiq", - }, - }, - { - title: "SARS CoV-2 PLpro in complex with GRL0617", - emdb: null, - pdb: { - dbId: "7CJM", - method: "X-RAY DIFFRACTION", - keywords: "Plpro-C111S, GRL0617, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7CJM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cjm_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cjm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UVERBUNNCOKGNZ-CQSZACIVSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: ["Huang, H.", "Fu, Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33473130", - title: - "The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery.", - journal: "Nat Commun 12: 488-488 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-20718-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33473130", - pubDate: "2021", - abstract: "", - authors: [ - "Fu, Z.", - "Huang, B.", - "Tang, J.", - "Liu, S.", - "Liu, M.", - "Ye, Y. (0000-0003-3951-5709)", - "Liu, Z.", - "Xiong, Y.", - "Zhu, W.", - "Cao, D.", - "Li, J.", - "Niu, X.", - "Zhou, H.", - "Zhao, Y.J.", - "Zhang, G. (0000-0002-3617-5449)", - "Huang, H. (0000-0001-7836-2894)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cjm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cjm", - }, - }, - { - title: "SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein", - emdb: null, - pdb: { - dbId: "7THH", - method: "X-RAY DIFFRACTION", - keywords: - "Covid-19, coronavirus, SARS, CoV-2, nsp3, SARS coronavirus-unique domain, SUD-C, ubiquitin-like domain, Ubl2, CSGID-IDP51000, CSGID-IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7THH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7thh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7thh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - 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externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7thh", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 13c", - emdb: null, - pdb: { - dbId: "7M00", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7M00", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m00_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m00", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AFVXFMYQWMALEA-JWWIWJDOSA-N", "AFVXFMYQWMALEA-VERUCKTNSA-N"], - dbauthors: [ - "Miller, M.J.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Perera, K.D.", - "Rathnayake, A.D.", - "Jesri, A.R.M.", - "Baird, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34865476", - title: - "Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.", - journal: "J.Med.Chem. 64: 17846-17865 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34865476", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Jesri, A.M.", - "Nguyen, H.N.", - "Miller, M.J.", - "Thurman, H.A.", - "Zheng, J.", - "Kashipathy, M.M.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Kim, Y.", - "Groutas, W.C.", - 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(0000-0002-9078-6697)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33242394", - title: - "Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity.", - journal: "Immunity 53 (2020), 1074-7613", - doi: "https://doi.org/10.1016/j.immuni.2020.10.023", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33242394", - pubDate: "2020", - abstract: "", - authors: [ - "Liu, H.", - "Wu, N.C.", - "Yuan, M.", - "Bangaru, S.", - "Torres, J.L.", - "Caniels, T.G.", - "van Schooten, J.", - "Zhu, X.", - "Lee, C.D.", - "Brouwer, P.J.M.", - "van Gils, M.J.", - "Sanders, R.W.", - "Ward, A.B.", - "Wilson, I.A.", - ], - }, - { - pmID: "32793906", - title: - "Cross-neutralization of a SARS-CoV-2 antibody to a functionally conserved site is mediated by avidity.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.08.02.233536", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32793906", - pubDate: "2020", - abstract: "", - authors: [ - "Liu, H.", - "Wu, N.C.", - "Yuan, M.", - "Bangaru, S.", - "Torres, J.L.", - "Caniels, T.G.", - "van Schooten, J.", - "Zhu, X.", - "Lee, C.D.", - "Brouwer, P.J.M.", - "van Gils, M.J.", - "Sanders, R.W.", - "Ward, A.B.", - "Wilson, I.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jmw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jmw", - }, - }, - { - title: "Nonstructural protein 7 and 8 complex of SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7DCD", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, NSP7, NSP8, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7DCD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dcd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dcd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 7", - details: "", - altNames: "nsp7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 8", - details: "", - altNames: "nsp8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Li, L.", "Zhang, C.H.", "Su, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33594727", - title: "Nonstructural protein 7 and 8 complexes of SARS-CoV-2.", - journal: "Protein Sci. 30: 873-881 (2021), 1469-896X", - doi: "https://doi.org/10.1002/pro.4046", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33594727", - pubDate: "2021", - abstract: "", - authors: ["Zhang, C.", "Li, L.", "He, J.", "Chen, C.", "Su, D."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dcd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dcd", - }, - }, - { - title: "Macro domain of SARS-CoV-2 in complex with ADP-ribose", - emdb: null, - pdb: { - dbId: "7C33", - method: "X-RAY DIFFRACTION", - keywords: "COVID-19, SARS-CoV-2, macro domain, ADP-ribose, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7C33", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c33_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c33", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-KEOHHSTQSA-N"], - dbauthors: ["Lin, M.H.", "Hsu, C.H. (0000-0002-0008-7383)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32946224", - title: - "Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain.", - journal: "Acs Infect Dis. 6: 2970-2978 (2020), 2373-8227", - doi: "https://doi.org/10.1021/acsinfecdis.0c00441", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32946224", - pubDate: "2020", - abstract: "", - authors: [ - "Lin, M.H.", - "Chang, S.C.", - "Chiu, Y.C.", - "Jiang, B.C.", - "Wu, T.H.", - "Hsu, C.H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7c33_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7c33", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) at 298 K and High Humidity", - emdb: null, - pdb: { - dbId: "7MHJ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Coronavirus, main protease, 3CLpro, Mpro, 298 K, hydrolase, ambient temperature, room temperature, humidity, high humidity, 99.5% RH, temperature, temperature series, multitemperature, multiconformer", - refModels: [ - { - emdbId: null, - pdbId: "7MHJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mhj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mhj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36071812", - title: - "The tem-per-ature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).", - journal: "Iucrj 9: 682-694 (2022), 2052-2525", - doi: "https://doi.org/10.1107/S2052252522007497", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36071812", - pubDate: "2022", - abstract: "", - authors: [ - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - "Ebrahim, A.", - "Riley, B.T.", - "Andi, B.", - "Fuchs, M.R.", - "McSweeney, S.", - "Keedy, D.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mhj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mhj", - }, - }, - { - title: "The crystal structure of SARS-CoV-2 papain-like protease in apo form", - emdb: null, - pdb: { - dbId: "7D7K", - method: "X-RAY DIFFRACTION", - keywords: "protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7D7K", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7d7k_final.pdb", - externalLink: "https://pdb-redo.eu/db/7d7k", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "RYYVLZVUVIJVGH-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: [ - "Sun, L. (0000-0001-8741-0202)", - "Zhao, Y. (0000-0002-2932-2164)", - "Yang, H.T. (0000-0002-1875-3268)", - "Rao, Z.H. (0000-0001-9866-2384)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33864621", - title: - "High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors.", - journal: "Protein Cell 12: 877-888 (2021), 1674-8018", - doi: "https://doi.org/10.1007/s13238-021-00836-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33864621", - pubDate: "2021", - abstract: "", - authors: [ - "Zhao, Y.", - "Du, X.", - "Duan, Y.", - "Pan, X.", - "Sun, Y.", - "You, T.", - "Han, L.", - "Jin, Z.", - "Shang, W.", - "Yu, J.", - "Guo, H.", - "Liu, Q.", - "Wu, Y.", - "Peng, C.", - "Wang, J.", - "Zhu, C.", - "Yang, X.", - "Yang, K.", - "Lei, Y.", - "Guddat, L.W.", - "Xu, W.", - "Xiao, G.", - "Sun, L.", - "Zhang, L.", - "Rao, Z.", - "Yang, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7d7k_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7d7k", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with NCL-00025058", - emdb: null, - pdb: { - dbId: "5RG2", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RG2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rg2_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rg2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "STYVOOMPCLDYII-HTRCEHHLSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rel_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rel", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102243", - emdb: null, - pdb: { - dbId: "5RFW", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfw_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "PEHVQKQLQOREKN-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rfw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rfw", - }, - }, - { - title: - "Structure of SARS-CoV-2 Papain-like protease PLpro in complex with p-hydroxybenzaldehyde", - emdb: null, - pdb: { - dbId: "7OFT", - method: "X-RAY DIFFRACTION", - keywords: - "Papain-like protease SARS-CoV-2 Hydrolase Zinc binding protein, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7OFT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7oft_final.pdb", - externalLink: "https://pdb-redo.eu/db/7oft", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "RGHHSNMVTDWUBI-UHFFFAOYSA-N", - "NPYPAHLBTDXSSS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Wang, M.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Turk, D.", - "Hinrichs, W.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "Brognaro, H.", - "Brings, L.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Ginn, H.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Ullah, N.", - "Andaleeb, H.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Saouane, S.", - "Wolf, M.", - "Lieske, J.", - "Ewert, W.", - "Srinivasan, V. (0000-0002-8895-5885)", - "Sprenger, J.", - "Perk, A.", - "Wahab, A.", - "Choudary, I.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35953531", - title: - "Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.", - journal: "Commun Biol 5: 805-805 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03737-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35953531", - pubDate: "2022", - abstract: "", - authors: [ - "Srinivasan, V. (0000-0002-8895-5885)", - "Brognaro, H.", - "Prabhu, P.R.", - "de Souza, E.E.", - "Gunther, S. (0000-0002-7329-6653)", - "Reinke, P.Y.A.", - "Lane, T.J. (0000-0003-2627-4432)", - "Ginn, H.", - "Han, H.", - "Ewert, W. (0000-0001-8626-4864)", - "Sprenger, J.", - "Koua, F.H.M. (0000-0001-8371-9587)", - "Falke, S.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N. (0000-0003-0900-5927)", - "Franca, B.A.", - "Wang, M.", - "Barra, A.L.C. (0000-0003-0457-7758)", - "Perbandt, M. (0000-0001-7517-8522)", - "Schwinzer, M.", - "Schmidt, C. (0000-0002-6662-1294)", - "Brings, L.", - "Lorenzen, K.", - "Schubert, R. (0000-0002-6213-2872)", - "Machado, R.R.G.", - "Candido, E.D. (0000-0002-9132-569X)", - "Oliveira, D.B.L. (0000-0002-0534-0886)", - "Durigon, E.L.", - "Niebling, S. (0000-0001-6582-5984)", - "Garcia, A.S.", - "Yefanov, O.", - "Lieske, J. (0000-0002-5439-5082)", - "Gelisio, L. (0000-0001-7832-6201)", - "Domaracky, M. (0000-0003-4624-023X)", - "Middendorf, P.", - "Groessler, M.", - "Trost, F. (0000-0001-5628-598X)", - "Galchenkova, M.", - "Mashhour, A.R.", - "Saouane, S. (0000-0002-7260-9021)", - "Hakanpaa, J.", - "Wolf, M.", - "Alai, M.G.", - "Turk, D. (0000-0003-0205-6609)", - "Pearson, A.R. (0000-0001-8499-7490)", - "Chapman, H.N.", - "Hinrichs, W. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rs7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rs7", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-6", - emdb: null, - pdb: { - dbId: "7VK0", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, SFX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VK0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vk0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vk0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "DeMirci, H. (0000-0002-9135-5397)", - "Cakilkaya, B. 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(0000-0001-8078-4113)", - "Xia, A.J. (0000-0002-2695-3024)", - "Hou, Y.", - "Zeng, R.", - "Liu, X.L.", - "Lin, G.F.", - "Qiao, J.X.", - "Li, W.P.", - "Wang, F.L.", - "Wang, K.", - "Zhou, R.J.", - "Yuen, T.T.", - "Chen, M.X.", - "Yoon, C.", - "Wu, M.", - "Zhang, S.Y.", - "Huang, C.", - "Wang, Y.F.", - "Yang, W.", - "Tian, C.", - "Li, W.M. (0000-0003-0985-0311)", - "Wei, Y.Q.", - "Yuen, K.Y. (0000-0002-2083-1552)", - "Chan, J.F. (0000-0001-6336-6657)", - "Lei, J. (0000-0001-9326-0554)", - "Chu, H. (0000-0003-2855-9837)", - "Yang, S. 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(0000-0001-9283-080X)", - "Wang, B. (0000-0002-3380-4473)", - "Zhao, T.N.", - "Liang, Z.T.", - "Peng, T.B.", - "Song, X.H.", - "Wu, J.J.", - "Wang, Y.C. (0000-0001-9769-5141)", - "Su, X.D. 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"HCOXBSXZYFWFSP-WUXMJOGZSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Reinke, P.", - "Hinrichs, W.", - "Han, H.", - "Srinivasan, V.", - "Lorenzen, K.", - "Betzel, C.", - "Meents, A.", - "Falke, S.", - "Gunther, S.", - "Lieske, J.", - "Ewert, W.", - "Niebling, S.", - "Miglioli, F.", - "Carcelli, M.", - "Guenther, C.", - "Garcia-Alai, M.", - "Rogolino, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35480391", - title: - "Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease.", - journal: "Front Chem 10: 832431-832431 (2022), 2296-2646", - doi: "https://doi.org/10.3389/fchem.2022.832431", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35480391", - pubDate: "2022", - abstract: "", - authors: [ - 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refModels: [ - { - emdbId: null, - pdbId: "7JW8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jw8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jw8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GENYQFMDDNZIRG-UCWBBBRQSA-N", "OWMVSZAMULFTJU-UHFFFAOYSA-N"], - dbauthors: [ - "Liu, H.", - "Ho, D.D.", - "Forouhar, F.", - "Iketani, S.", - "Hong, S.J.", - "Nair, M.S.", - "Chavez, A.", - "Stockwell, B.R.", - "Zask, A.", - "Lin, F.-Y.", - "Xing, L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33795671", - title: - "Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors.", - journal: "Nat Commun 12: 2016-2016 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-22362-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33795671", - pubDate: "2021", - abstract: "", - authors: [ - "Iketani, S. (0000-0002-3733-9556)", - "Forouhar, F.", - "Liu, H. (0000-0002-5214-1572)", - "Hong, S.J.", - "Lin, F.Y. (0000-0003-0103-0167)", - "Nair, M.S. (0000-0002-5994-3957)", - "Zask, A.", - "Huang, Y. (0000-0001-6270-1644)", - "Xing, L. (0000-0002-9056-7996)", - "Stockwell, B.R. (0000-0002-3532-3868)", - "Chavez, A. (0000-0001-5626-7140)", - "Ho, D.D. (0000-0003-1627-149X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jw8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jw8", - }, - }, - { - title: - "Crystallographic structure of two neutralizing antibodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)", - emdb: null, - pdb: { - dbId: "7FCP", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, RBD, neutralizing antibodies, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FCP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fcp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fcp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P14-44 antibody Fab fragment heavy chain", - details: "", - 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"Ultrapotent neutralizing antibodies against SARS-CoV-2 with a high degree of mutation resistance.", - journal: "J.Clin.Invest. 132 (2022), 0021-9738", - doi: "https://doi.org/10.1172/JCI154987", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35108220", - pubDate: "2022", - abstract: "", - authors: [ - "Zou, J.", - "Li, L.", - "Zheng, P.", - "Liang, W.", - "Hu, S.", - "Zhou, S.", - "Wang, Y.", - "Zhao, J.", - "Yuan, D.", - "Liu, L.", - "Wu, D.", - "Xu, M.", - "Zhang, F.", - "Zhu, M.", - "Wu, Z.", - "Cao, X.", - "Ni, M.", - "Ling, X.", - "Wu, Y.", - "Kuang, Z.", - "Hu, M.", - "Li, J.", - "Li, X.", - "Guo, X.", - "Xu, T.", - "Jiang, H.", - "Gao, C.", - "Yu, M.", - "Liu, J.", - "Zhong, N.", - "Zhou, J.", - "Huang, J.A.", - "Jin, T.", - "He, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fcp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fcp", - }, - }, - { - title: - "Structure of SARS-CoV-2 Papain-like Protease bound to N-(2,4-dihydroxybenzylidene)-thiosemicarbazone", - emdb: null, - pdb: { - dbId: "7QCJ", - method: "X-RAY DIFFRACTION", - keywords: - "Cystein-Protease, Inhibitor, SARS-CoV-2, Thiosemicarbazone, Deubiquitination, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7QCJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qcj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qcj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "DZTQPWJXTVXKJK-ONNFQVAWSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Reinke, P.", - "Hinrichs, W.", - "Han, H.", - "Srinivasan, V.", - "Lorenzen, K.", - "Betzel, C.", - "Meents, A.", - "Falke, S.", - "Gunther, S.", - "Lieske, J.", - "Ewert, W.", - "Niebling, S.", - "Miglioli, F.", - "Carcelli, M.", - "Guenther, C.", - "Garcia-Alai, M.", - "Rogolino, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35480391", - title: - "Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease.", - journal: "Front Chem 10: 832431-832431 (2022), 2296-2646", - doi: "https://doi.org/10.3389/fchem.2022.832431", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35480391", - pubDate: "2022", - abstract: "", - authors: [ - "Ewert, W.", - "Gunther, S.", - "Miglioli, F.", - "Falke, S.", - "Reinke, P.Y.A.", - "Niebling, S.", - "Gunther, C.", - "Han, H.", - "Srinivasan, V.", - "Brognaro, H.", - "Lieske, J.", - "Lorenzen, K.", - "Garcia-Alai, M.M.", - "Betzel, C.", - "Carcelli, M.", - "Hinrichs, W.", - "Rogolino, D.", - "Meents, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qcj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qcj", - }, - }, - { - title: "SARS-CoV-2 S protein RBD in complex with A8-1 Fab", - emdb: null, - pdb: { - dbId: "7F7H", - method: "X-RAY DIFFRACTION", - keywords: "Antibody, SARS-CoV-2, VIRUS, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7F7H", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f7h_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f7h", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of A8-1 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of A8-1 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wang, K.", "Wang, X.", "Liu, P.", "Dou, Y.", "Lu, B."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "High throughput isolation of potent neutralizing antibodies from convalescent COVID-19 patients.", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Dou, Y.", "Jia, Z.", "Deng, Y.", "Lan, J.", "Liu, H."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7f7h_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7f7h", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor Leupeptin", - emdb: null, - pdb: { - dbId: "7MRR", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Main Protease, 3CLpro/Mpro, Leupeptin, VIRAL PROTEIN, Inhibitor, HYDROLASE-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MRR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mrr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mrr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "LEUPEPTIN", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Shi, W.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "McSweeney, S. (0000-0002-3758-3161)", - "Kreitler, D.F.", - "Soares, A.S.", - "Jakoncic, J.", - "Keereetaweep, J.", - "Shanklin, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35842458", - title: - "Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.", - journal: "Sci Rep 12: 12197-12197 (2022), 2045-2322", - doi: "https://doi.org/10.1038/s41598-022-15930-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35842458", - pubDate: "2022", - abstract: "", - authors: [ - "Andi, B.", - "Kumaran, D.", - "Kreitler, D.F.", - "Soares, A.S.", - "Keereetaweep, J.", - "Jakoncic, J.", - "Lazo, E.O.", - "Shi, W.", - "Fuchs, M.R.", - "Sweet, R.M.", - "Shanklin, J.", - "Adams, P.D.", - "Schmidt, J.G.", - "Head, M.S.", - "McSweeney, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mrr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mrr", - }, - }, - { - title: - "Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 with 7-methyl-GpppA and S-adenosyl-L-homocysteine in the Active Site and Sulfates in the mRNA Binding Groove.", - emdb: null, - pdb: { - dbId: "6WRZ", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, 7-methyl-GpppA, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WRZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wrz_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wrz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "QQOHNVHGNZYSBP-XPWFQUROSA-O", - "JOPOQPCBCUIPFX-UHFFFAOYSA-L", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Brunzelle, J.S.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32994211", - title: - "High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design.", - journal: "Sci.Signal. 13 (2020), 1937-9145", - doi: "https://doi.org/10.1126/scisignal.abe1202", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32994211", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsw", - }, - }, - { - title: "SARS-CoV-2 Mpro mutant (H41A) in complex with nsp14|15 peptidyl substrate", - emdb: null, - pdb: { - dbId: "7DW6", - method: "X-RAY DIFFRACTION", - keywords: "protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7DW6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dw6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dw6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "nsp14/15 peptidyl substrate", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Liu, X.", "Yang, H.", "Rao, Z.", "Zhao, Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35380892", - title: - "Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2117142119-e2117142119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2117142119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35380892", - pubDate: "2022", - abstract: "", - authors: [ - "Zhao, Y. (0000-0002-2932-2164)", - "Zhu, Y. (0000-0002-7045-4847)", - "Liu, X. (0000-0001-5498-6942)", - "Jin, Z. (0000-0001-6448-820X)", - "Duan, Y.", - "Zhang, Q. (0000-0002-6271-9163)", - "Wu, C. (0000-0001-9178-7467)", - "Feng, L. (0000-0003-1060-6391)", - "Du, X.", - "Zhao, J. (0000-0002-5119-359X)", - "Shao, M. (0000-0002-9762-8608)", - "Zhang, B. (0000-0001-8556-8049)", - "Yang, X. (0000-0003-3443-9815)", - "Wu, L. (0000-0002-2253-0497)", - "Ji, X. (0000-0002-0801-8825)", - "Guddat, L.W. (0000-0002-8204-8408)", - "Yang, K.", - "Rao, Z. (0000-0001-9866-2384)", - "Yang, H. (0000-0002-1875-3268)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dw6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dw6", - }, - }, - { - title: "STRUCTURE OF THE SARS-CoV-2 ORF8 ENCODED ACCESSORY PROTEIN", - emdb: null, - pdb: { - dbId: "7JX6", - method: "X-RAY DIFFRACTION", - keywords: - "Immunoglobulin-like, disulfide-linked dimer, viral protein, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID", - refModels: [ - { - emdbId: null, - pdbId: "7JX6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jx6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jx6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC8", - organism: "2697049", - name: "ORF8 protein", - details: "", - altNames: "ORF8, Non-structural protein 8, ns8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Fremont, D.H. (0000-0002-8544-2689)", - "Hall, P.D. (0000-0002-2799-4506)", - "Nelson, C.A. (0000-0001-8730-4768)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Crystal Structure of the SARS-CoV-2 ORF8 Protein", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Nelson, C.A. (0000-0001-8730-4768)", - "Hall, P.D. (0000-0002-2799-4506)", - "Fremont, D.H. (0000-0002-8544-2689)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jx6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jx6", - }, - }, - { - title: - "Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, methyl ester", - emdb: null, - pdb: { - dbId: "7OFU", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE Papain-like protease PLpro Complex, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7OFU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ofu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ofu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "CUFLZUDASVUNOE-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Wang, M.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Turk, D.", - "Hinrichs, W.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "Brognaro, H.", - "Brings, L.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Ginn, H.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Ullah, N.", - "Andaleeb, H.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Saouane, S.", - "Hakanpaeae, J.", - "Wolf, M.", - "Lieske, J.", - "Ewert, W.", - "Srinivasan, V. 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(0000-0002-0435-4565)", - "Wrenger, C. (0000-0001-5987-1749)", - "Meents, A. (0000-0001-6078-4095)", - "Betzel, C. (0000-0002-3879-5019)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ofu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ofu", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102306", - emdb: null, - pdb: { - dbId: "5RFV", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfv_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "VSORHSQQVYIMDG-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0001-5774-8202)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Lukacik, P.", - "Strain-Damerell, C.", - "Horrell, S. (0000-0001-6355-8640)", - "Gildae, R.J. (0000-0001-5038-6958)", - "Axford, D.", - "Owen, R.L. (0000-0002-2104-7057)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35647922", - title: "xia2.multiplex: a multi-crystal data-analysis pipeline.", - journal: - "Acta Crystallogr D Struct Biol 78: 752-769 (2022), 2059-7983", - doi: "https://doi.org/10.1107/S2059798322004399", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35647922", - pubDate: "2022", - abstract: "", - authors: [ - "Gildea, R.J. (0000-0001-5038-6958)", - "Beilsten-Edmands, J.", - "Axford, D. (0000-0001-7694-8525)", - "Horrell, S. (0000-0001-6355-8640)", - "Aller, P. (0000-0002-1793-7030)", - "Sandy, J. (0000-0002-6271-2084)", - "Sanchez-Weatherby, J. (0000-0001-5893-9641)", - "Owen, C.D.", - "Lukacik, P.", - "Strain-Damerell, C.", - "Owen, R.L. (0000-0002-2104-7057)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Winter, G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qt5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qt5", - }, - }, - { - title: "SARS-CoV-2 main protease in complex with N-terminal autoprocessing substrate", - emdb: null, - pdb: { - dbId: "7MGS", - method: "X-RAY DIFFRACTION", - keywords: "protease, 3C-like protease, VIRAL PROTEIN, hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7MGS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mgs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mgs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "SER-ALA-VAL-LEU-GLN-SER-GLY-PHE", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Windsor, I.W.", - "MacDonald, E.A. (0000-0002-5873-6809)", - "Hinshaw, S.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34437808", - title: - "Recognition of Divergent Viral Substrates by the SARS-CoV-2 Main Protease.", - journal: "Acs Infect Dis. 7: 2591-2595 (2021), 2373-8227", - doi: "https://doi.org/10.1021/acsinfecdis.1c00237", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34437808", - pubDate: "2021", - abstract: "", - authors: [ - "MacDonald, E.A.", - "Frey, G.", - "Namchuk, M.N.", - "Harrison, S.C.", - "Hinshaw, S.M.", - "Windsor, I.W.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mgs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mgs", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-63", - emdb: null, - pdb: { - dbId: "7TIZ", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TIZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tiz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tiz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SOKKEQHRVRNCKI-VERUCKTNSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "ZMZDMBWJUHKJPS-UHFFFAOYSA-M", - ], - dbauthors: [ - "Liu, H.", - "Huang, Y.", - "Li, W.", - "Lee, S.", - "Ho, D.D.", - "Hurst, B.", - "Forouhar, F.", - "Iketani, S.", - "Zack, A.", - "Khanizeman, N.", - "Bednarova, E.", - "Fowler, B.", - "Hong, S.J.", - "Mohri, H.", - "Nair, M.S.", - "Tay, N.E.S.", - "Karan, C.", - "Resnick, S.J.", - "Quinn, C.", - "Shion, H.", - "Jurtschenko, C.", - "Lauber, M.A.", - "McDonald, T.", - "Rovis, T.", - "Chavez, A.", - "Stockwell, B.R.", - "Stokes, M.E.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35393402", - title: - "Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19.", - journal: "Nat Commun 13: 1891-1891 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-29413-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35393402", - pubDate: "2022", - abstract: "", - authors: [ - "Liu, H. 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(0000-0002-3532-3868)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tiz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tiz", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z1741982125", - emdb: null, - pdb: { - dbId: "5S48", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S48", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s48_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s48", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UBQKCCHYAOITMY-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s48_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s48", - }, - }, - { - title: "Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor", - emdb: null, - pdb: { - dbId: "7RFS", - method: "X-RAY DIFFRACTION", - keywords: - "Protease SARS-CoV-2 Covalent complex inhibitor, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RFS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rfs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rfs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Greasley, S.E.", "Ferre, R.A.", "Liu, W.", "Stewart, A.E."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34726479", - title: - "An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19.", - journal: "Science 374: 1586-1593 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abl4784", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34726479", - pubDate: "2021", - abstract: "", - authors: [ - "Owen, D.R.", - "Allerton, C.M.N.", - "Anderson, A.S.", - "Aschenbrenner, L.", - "Avery, M.", - "Berritt, S.", - "Boras, B.", - "Cardin, R.D.", - "Carlo, A.", - "Coffman, K.J.", - "Dantonio, A.", - "Di, L.", - "Eng, H.", - "Ferre, R.", - "Gajiwala, K.S.", - "Gibson, S.A.", - "Greasley, S.E.", - "Hurst, B.L.", - "Kadar, E.P.", - "Kalgutkar, A.S.", - "Lee, J.C.", - "Lee, J.", - "Liu, W.", - "Mason, S.W.", - "Noell, S.", - "Novak, J.J.", - "Obach, R.S.", - "Ogilvie, K.", - "Patel, N.C.", - "Pettersson, M.", - "Rai, D.K.", - "Reese, M.R.", - "Sammons, M.F.", - "Sathish, J.G.", - "Singh, R.S.P.", - "Steppan, C.M.", - "Stewart, A.E.", - "Tuttle, J.B.", - "Updyke, L.", - "Verhoest, P.R.", - "Wei, L.", - "Yang, Q.", - "Zhu, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rfs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rfs", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 main protease treated with ebselen", - emdb: null, - pdb: { - dbId: "7BAK", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, COVID19, ebselen, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7BAK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bak_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bak", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Main Protease", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BUGBHKTXTAQXES-UHFFFAOYSA-N"], - dbauthors: [ - "Amporndanai, K. (0000-0001-8527-9394)", - "O'Neill, P.M. (0000-0003-4338-0317)", - "Hasnain, S.S. (0000-0002-2854-4718)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34031399", - title: - "Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives.", - journal: "Nat Commun 12: 3061-3061 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23313-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34031399", - pubDate: "2021", - abstract: "", - authors: [ - "Amporndanai, K.", - "Meng, X. (0000-0002-7774-2075)", - "Shang, W.", - "Jin, Z. (0000-0001-6448-820X)", - "Rogers, M.", - "Zhao, Y.", - "Rao, Z. (0000-0001-9866-2384)", - "Liu, Z.J. (0000-0001-7279-2893)", - "Yang, H. (0000-0002-1875-3268)", - "Zhang, L. (0000-0002-2593-2571)", - "O'Neill, P.M. (0000-0003-4338-0317)", - "Samar Hasnain, S. (0000-0002-2854-4718)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bak_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bak", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z3219959731", - emdb: null, - pdb: { - dbId: "5SAE", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SAE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sae_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sae", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "AAILEWXSEQLMNI-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sae_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sae", - }, - }, - { - title: - "PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain", - emdb: null, - pdb: { - dbId: "5S74", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S74", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s74_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s74", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Schuller, M.", - "Rangel, V.L.", - "Douangamath, A.", - "Aimon, A.", - "Powell, A.J.", - "Dias, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Gorrie-Stone, T.J.", - "Thompson, W.", - "Krojer, T.", - "Rack, J.G.M.", - "Zhu, K.", - "Ahel, I.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s74_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s74", - }, - }, - { - title: "Crystal structure of SARS CoV2 main protease in complex with FSP007", - emdb: null, - pdb: { - dbId: "7NT1", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Complex, Covalent, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NT1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nt1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nt1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "UWYXREXKBLOKIU-OAHLLOKOSA-N"], - dbauthors: [ - "Oerlemans, R. (0000-0001-7114-3736)", - "Eris, D.", - "Wang, M. (0000-0002-5340-3036)", - "Sharpe, M.", - "Groves, M.R.", - "Domling, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34097796", - title: - "Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.", - journal: - "Angew.Chem.Int.Ed.Engl. 60: 18231-18239 (2021), 1521-3773", - doi: "https://doi.org/10.1002/anie.202105584", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34097796", - pubDate: "2021", - abstract: "", - authors: [ - "Sutanto, F.", - "Shaabani, S. (0000-0001-5546-7140)", - "Oerlemans, R.", - "Eris, D.", - "Patil, P.", - "Hadian, M.", - "Wang, M.", - "Sharpe, M.E.", - "Groves, M.R.", - "Domling, A. (0000-0002-9923-8873)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nt1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nt1", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z32665176", - emdb: null, - pdb: { - dbId: "5SM0", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SM0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sm0_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sm0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5soy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5soy", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z744930860", - emdb: null, - pdb: { - dbId: "5SLB", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slb_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "ZDAUOJUKQPYKAC-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slb", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 NSP3 macrodomain (P43 crystal form)", - emdb: null, - pdb: { - dbId: "7KQO", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7KQO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kqo_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kqo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Young, I.D. (0000-0003-4713-9504)", - "Thompson, M.C. (0000-0002-6099-2027)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. 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(0000-0001-8639-5290)", - "Joyce, M.G. (0000-0002-6808-7232)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34716452", - title: - "Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations.", - journal: "Nat.Immunol. 22: 1503-1514 (2021), 1529-2916", - doi: "https://doi.org/10.1038/s41590-021-01068-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34716452", - pubDate: "2021", - abstract: "", - authors: [ - "Dussupt, V. (0000-0002-8579-6356)", - "Sankhala, R.S.", - "Mendez-Rivera, L.", - "Townsley, S.M.", - "Schmidt, F.", - "Wieczorek, L.", - "Lal, K.G.", - "Donofrio, G.C.", - "Tran, U.", - "Jackson, N.D. (0000-0002-9654-6926)", - "Zaky, W.I.", - "Zemil, M. (0000-0002-1700-6658)", - "Tritsch, S.R.", - "Chen, W.H.", - "Martinez, E.J.", - "Ahmed, A. (0000-0003-3093-4982)", - "Choe, M.", - "Chang, W.C. (0000-0003-4967-6426)", - "Hajduczki, A.", - "Jian, N.", - "Peterson, C.E.", - "Rees, P.A.", - "Rutkowska, M.", - "Slike, B.M. (0000-0003-4132-4637)", - "Selverian, C.N. (0000-0002-1047-4336)", - "Swafford, I. (0000-0001-8638-2772)", - "Teng, I.T.", - "Thomas, P.V.", - "Zhou, T. (0000-0002-3935-4637)", - "Smith, C.J.", - "Currier, J.R. (0000-0002-5696-0268)", - "Kwong, P.D. (0000-0003-3560-232X)", - "Rolland, M. (0000-0003-3650-8490)", - "Davidson, E.", - "Doranz, B.J. (0000-0002-8245-3083)", - "Mores, C.N. (0000-0001-6678-9049)", - "Hatziioannou, T.", - "Reiley, W.W.", - "Bieniasz, P.D. (0000-0002-2368-3719)", - "Paquin-Proulx, D. (0000-0003-1407-3414)", - "Gromowski, G.D.", - "Polonis, V.R.", - "Michael, N.L. (0000-0001-5882-5548)", - "Modjarrad, K.", - "Joyce, M.G. (0000-0002-6808-7232)", - "Krebs, S.J. 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(0000-0002-1875-3268)", - "Rao, Z. (0000-0001-9866-2384)", - "Zhao, Y. (0000-0002-2932-2164)", - "Liu, X. (0000-0001-5498-6942)", - "Zhang, B. (0000-0001-8556-8049)", - "Jin, Z. (0000-0002-5993-1999)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32382072", - title: - "Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur.", - journal: "Nat.Struct.Mol.Biol. 27: 529-532 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0440-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32382072", - pubDate: "2020", - abstract: "", - authors: [ - "Jin, Z. (0000-0001-6448-820X)", - "Zhao, Y.", - "Sun, Y. (0000-0001-8244-7436)", - "Zhang, B.", - "Wang, H.", - "Wu, Y.", - "Zhu, Y.", - "Zhu, C.", - "Hu, T.", - "Du, X. (0000-0002-8415-8686)", - "Duan, Y.", - "Yu, J.", - "Yang, X.", - "Yang, K.", - "Liu, X. (0000-0001-5498-6942)", - "Guddat, L.W.", - "Xiao, G.", - "Zhang, L. (0000-0002-2593-2571)", - "Yang, H. (0000-0002-1875-3268)", - "Rao, Z.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7buy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7buy", - }, - }, - { - title: "TCR peptide HLA-A2 complex", - emdb: null, - pdb: { - dbId: "7N6E", - method: "X-RAY DIFFRACTION", - keywords: - "T cell receptor, Human Leucocyte Antigen, SARS-CoV-2, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7N6E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n6e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n6e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "TRAV12-1 TCR-alpha", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "TRBV19 TCR beta", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Rossjohn, J. (0000-0002-2020-7522)", - "Chaurasia, P. (0000-0003-4249-3678)", - "Petersen, J. (0000-0002-2045-6342)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34384783", - title: - "Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein.", - journal: "J.Biol.Chem. 297: 101065-101065 (2021), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2021.101065", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34384783", - pubDate: "2021", - abstract: "", - authors: [ - "Chaurasia, P.", - "Nguyen, T.H.O.", - "Rowntree, L.C.", - "Juno, J.A.", - "Wheatley, A.K.", - "Kent, S.J.", - "Kedzierska, K.", - "Rossjohn, J.", - "Petersen, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n6e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n6e", - }, - }, - { - title: "SARS-CoV-2 Macrodomain in complex with ADP-HPM", - emdb: null, - pdb: { - dbId: "6Z72", - method: "X-RAY DIFFRACTION", - keywords: - "Viral Macrodomain, ADP-ribose binding module, ADP-ribosylhydrolase, ADP-ribosylation, VIRAL PROTEIN, ADP-HPM", - refModels: [ - { - emdbId: null, - pdbId: "6Z72", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6z72_final.pdb", - externalLink: "https://pdb-redo.eu/db/6z72", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PHEYQOBMMIEFLO-IBCGMDAMSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "BJEPYKJPYRNKOW-UWTATZPHSA-N", - ], - dbauthors: [ - "Ahel, I. (0000-0002-9446-3756)", - "Zorzini, V. (0000-0002-8727-309X)", - "Rack, J. (0000-0001-8341-6439)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33202171", - title: - "Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential.", - journal: "Open Biology 10: 200237-200237 (2020), 2046-2441", - doi: "https://doi.org/10.1098/rsob.200237", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33202171", - pubDate: "2020", - abstract: "", - authors: [ - "Rack, J.G.M.", - "Zorzini, V.", - "Zhu, Z.", - "Schuller, M.", - "Ahel, D.", - "Ahel, I.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6z72_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6z72", - }, - }, - { - title: "Crystal Structure of the N-terminus of Nonstructural protein 1 from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7EQ4", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Nsp1, protein translation, ribosome, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7EQ4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7eq4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7eq4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Host translation inhibitor nsp1", - details: "", - altNames: "Leader protein,Non-structural protein 1,nsp1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Liu, Y. (0000-0002-5983-0151)", - "Ke, Z.", - "Hu, H.", - "Zhao, K. (0000-0002-0261-1599)", - "Xiao, J. (0000-0002-8074-5963)", - "Xia, Y. (0000-0001-8460-3893)", - "Li, Y. (0000-0003-1963-839X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34132580", - title: - "Structural Basis and Function of the N Terminus of SARS-CoV-2 Nonstructural Protein 1.", - journal: "Microbiol Spectr 9: e0016921-e0016921 (2021), 2165-0497", - doi: "https://doi.org/10.1128/Spectrum.00169-21", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34132580", - pubDate: "2021", - abstract: "", - authors: [ - "Zhao, K. (0000-0002-0261-1599)", - "Ke, Z.", - "Hu, H.", - "Liu, Y.", - "Li, A.", - "Hua, R.", - "Guo, F.", - "Xiao, J.", - "Zhang, Y.", - "Duan, L.", - "Yan, X.F.", - "Gao, Y.G.", - "Liu, B.", - "Xia, Y. (0000-0001-8460-3893)", - "Li, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7eq4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7eq4", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Q192T Mutant in Complex with Inhibitor GC376", - emdb: null, - pdb: { - dbId: "8DGB", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DGB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dgb_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dgb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-OGNFBWPZSA-N"], - dbauthors: [ - "Lewandowski, E.M. 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(0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36119652", - title: - "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.28.497978", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36119652", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, Y.", - "Lewandowski, E.M.", - "Tan, H.", - "Zhang, X.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Butler, S.G.", - "Gongora, M.V.", - "Choy, J.", - "Deng, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dgb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dgb", - }, - }, - { - title: - "Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody", - emdb: null, - pdb: { - dbId: "7BZ5", - method: "X-RAY DIFFRACTION", - keywords: "covid-19 antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7BZ5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bz5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bz5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of B38", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of B38", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Qi, J.", - "Wu, Y. 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(0000-0003-2778-4290)", - "Tan, W. (0000-0002-5963-1136)", - "Lu, X.", - "Fan, C. (0000-0001-5556-2025)", - "Wang, Q.", - "Liu, Y.", - "Zhang, C.", - "Qi, J.", - "Gao, G.F. (0000-0002-3869-615X)", - "Gao, F. (0000-0002-0670-010X)", - "Liu, L. 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(0000-0002-3618-9226)", - "Christie, M. (0000-0002-0955-665X)", - "Mackay, J.P. (0000-0001-7508-8033)", - "Passioura, T. (0000-0002-6089-5067)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34230894", - title: - "Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein Using mRNA Display.", - journal: "Acs Cent.Sci. 7: 1001-1008 (2021), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.0c01708", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34230894", - pubDate: "2021", - abstract: "", - authors: [ - "Norman, A.", - "Franck, C.", - "Christie, M.", - "Hawkins, P.M.E.", - "Patel, K.", - "Ashhurst, A.S.", - "Aggarwal, A.", - "Low, J.K.K.", - "Siddiquee, R.", - "Ashley, C.L.", - "Steain, M.", - "Triccas, J.A.", - "Turville, S.", - "Mackay, J.P.", - "Passioura, T. (0000-0002-6089-5067)", - "Payne, R.J. (0000-0002-3618-9226)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l4z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l4z", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z274575916", - emdb: null, - pdb: { - dbId: "5SMD", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SMD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5smd_final.pdb", - externalLink: "https://pdb-redo.eu/db/5smd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "NARMKNJWXHFJFF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5smd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5smd", - }, - }, - { - title: "SARS CoV-2 PLpro in complex with ubiquitin propargylamide", - emdb: null, - pdb: { - dbId: "6XAA", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, papain-like protease, ubiquitin activity based probe, COVID19, HYDROLASE-SUBSTRATE complex", - refModels: [ - { - emdbId: null, - pdbId: "6XAA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xaa_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xaa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "J3QS39", - organism: "9606", - name: "Ubiquitin-propargylamide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Klemm, T. (0000-0002-2847-3550)", - "Calleja, D.J. (0000-0002-8306-0900)", - "Richardson, L.W. (0000-0001-8877-1376)", - "Lechtenberg, B.C. (0000-0002-5674-6894)", - "Komander, D. (0000-0002-8092-4320)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32845033", - title: - "Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2.", - journal: "Embo J. 39: e106275-e106275 (2020), 1460-2075", - doi: "https://doi.org/10.15252/embj.2020106275", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32845033", - pubDate: "2020", - abstract: "", - authors: [ - "Klemm, T. (0000-0002-2847-3550)", - "Ebert, G.", - "Calleja, D.J. (0000-0002-8306-0900)", - "Allison, C.C.", - "Richardson, L.W. (0000-0001-8877-1376)", - "Bernardini, J.P. (0000-0002-5767-7624)", - "Lu, B.G. (0000-0001-8044-9710)", - "Kuchel, N.W.", - "Grohmann, C.", - "Shibata, Y.", - "Gan, Z.Y. (0000-0001-5755-7780)", - "Cooney, J.P. (0000-0003-3680-4644)", - "Doerflinger, M. (0000-0001-9159-3021)", - "Au, A.E. (0000-0003-3656-2673)", - "Blackmore, T.R. (0000-0001-7079-676X)", - "van der Heden van Noort, G.J. (0000-0001-5955-6431)", - "Geurink, P.P.", - "Ovaa, H.", - "Newman, J. (0000-0003-2666-3219)", - "Riboldi-Tunnicliffe, A. (0000-0003-2244-2486)", - "Czabotar, P.E.", - "Mitchell, J.P.", - "Feltham, R.", - "Lechtenberg, B.C. (0000-0002-5674-6894)", - "Lowes, K.N.", - "Dewson, G. (0000-0003-4251-8898)", - "Pellegrini, M. (0000-0003-3627-3126)", - "Lessene, G. (0000-0002-1193-8147)", - "Komander, D. (0000-0002-8092-4320)", - "Adams, P.D.", - "Afonine, P.V.", - "Bunkoczi, G.", - "Chen, V.B.", - "Davis, I.W.", - "Echols, N.", - "Headd, J.J.", - "Hung, L.W.", - "Kapral, G.J.", - "Grosse-Kunstleve, R.W.", - "McCoy, A.J.", - "Moriarty, N.W.", - "Oeffner, R.", - "Read, R.J.", - "Richardson, D.C.", - "Richardson, J.S.", - "Terwilliger, T.C.", - "Zwart, P.H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xaa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xaa", - }, - }, - { - title: "Crystal structure from SARS-CoV-2 NendoU NSP15", - emdb: null, - pdb: { - dbId: "7KEH", - method: "X-RAY DIFFRACTION", - keywords: - "NSP15, NendoU, covid-19, covid, sars, sars-cov-2, endoribonuclease, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7KEH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7keh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7keh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["HHKZCCWKTZRCCL-UHFFFAOYSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Oliveira, K.I.Z.", - "Pereira, H.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. 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emdb: null, - pdb: { - dbId: "5SL6", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SL6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sl6_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sl6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "IFLKEBSJTZGCJG-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sl6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sl6", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000910475722 - (S,R) isomer", - emdb: null, - pdb: { - dbId: "5SOL", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sol_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sol", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VUGBTOAPDMYPIQ-BMIGLBTASA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sol_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sol", - }, - }, - { - title: "SARS-CoV-2 spike Protein TM domain", - emdb: null, - pdb: { - dbId: "7LC8", - method: "SOLUTION NMR", - keywords: - "Coronavirus, SARS, COVID 19, Severe acute respiratory syndrome coronavirus 2, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Fu, Q. (0000-0002-7445-2355)", "Chou, J.J. (0000-0002-4442-0344)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34086443", - title: - "A Trimeric Hydrophobic Zipper Mediates the Intramembrane Assembly of SARS-CoV-2 Spike.", - journal: "J.Am.Chem.Soc. 143: 8543-8546 (2021), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c02394", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34086443", - pubDate: "2021", - abstract: "", - authors: ["Fu, Q.", "Chou, J.J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lc8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lc8", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1310876699", - emdb: null, - pdb: { - dbId: "5SLW", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slw_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "HQJMILNSKHZGJL-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slw", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and Manganese (Mn).", - emdb: null, - pdb: { - dbId: "7L6R", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, VIRAL PROTEIN, SAH, Cap-1, VIRAL PROTEIN-RNA complex", - refModels: [ - { - emdbId: null, - pdbId: "7L6R", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l6r_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l6r", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*UP*AP*A)-3')", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PWHULOQIROXLJO-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "DHMQDGOQFOQNFH-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "LKDRXBCSQODPBY-ARQDHWQXSA-N", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Brunzelle, J.S.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34131072", - title: - "Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16.", - journal: "Sci.Signal. 14 (2021), 1937-9145", - doi: "https://doi.org/10.1126/scisignal.abh2071", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34131072", - pubDate: "2021", - abstract: "", - authors: [ - "Minasov, G. (0000-0001-5460-3462)", - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Brunzelle, J.S. (0000-0001-9197-0018)", - "Daczkowski, C.M.", - "Hoover, P.", - "Mesecar, A.D. (0000-0002-1241-2577)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l6r_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l6r", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-1605072", - emdb: null, - pdb: { - dbId: "5SAG", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SAG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sag_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sag", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["HQNOODJDSFSURF-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sag_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sag", - }, - }, - { - title: "Crystal structure of SARS CoV2 main protease in complex with FSCU015", - emdb: null, - pdb: { - dbId: "7NT3", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NT3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nt3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nt3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "BMXUYKHPBOFWRQ-NRFANRHFSA-N"], - dbauthors: [ - "Oerlemans, R. (0000-0001-7114-3736)", - "Eris, D.", - "Wang, M. (0000-0002-5340-3036)", - "Sharpe, M.", - "Domling, A. (0000-0002-9923-8873)", - "Groves, M.R. (0000-0001-9859-5177)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34097796", - title: - "Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.", - journal: - "Angew.Chem.Int.Ed.Engl. 60: 18231-18239 (2021), 1521-3773", - doi: "https://doi.org/10.1002/anie.202105584", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34097796", - pubDate: "2021", - abstract: "", - authors: [ - "Sutanto, F.", - "Shaabani, S. (0000-0001-5546-7140)", - "Oerlemans, R.", - "Eris, D.", - "Patil, P.", - "Hadian, M.", - "Wang, M.", - "Sharpe, M.E.", - "Groves, M.R.", - "Domling, A. (0000-0002-9923-8873)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nt3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nt3", - }, - }, - { - title: - "SARS-CoV-2 3CLPro in complex with N-[4-[[2-(benzotriazol-1-yl)acetyl]-(3-thienylmethyl)amino]phenyl]cyclopropanecarboxamide", - emdb: null, - pdb: { - dbId: "7LME", - method: "X-RAY DIFFRACTION", - keywords: - "3CLPro, SARS-CoV-2 Main Protease, SARS-CoV-2 3CLPro, Inhibitor Complex, Protease, VIRAL PROTEIN, Hydrolase-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7LME", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lme_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lme", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OCKMJWOFMCSMEX-UHFFFAOYSA-N"], - dbauthors: [ - "Goins, C.M. (0000-0002-6617-4877)", - "Stauffer, S.R. (0000-0002-6332-1827)", - "Arya, T. (0000-0001-8690-6425)", - "Macdonald, J.D. (0000-0002-6360-2768)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34347470", - title: - "Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro ).", - journal: "J.Med.Chem. 65: 2880-2904 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00598", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34347470", - pubDate: "2022", - abstract: "", - authors: [ - "Han, S.H.", - "Goins, C.M.", - "Arya, T.", - "Shin, W.J.", - "Maw, J.", - "Hooper, A.", - "Sonawane, D.P.", - "Porter, M.R.", - "Bannister, B.E.", - "Crouch, R.D.", - "Lindsey, A.A.", - "Lakatos, G.", - "Martinez, S.R.", - "Alvarado, J.", - "Akers, W.S.", - "Wang, N.S.", - "Jung, J.U.", - "Macdonald, J.D.", - "Stauffer, S.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lme_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lme", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 RBD in complex with BD-604 Fab and BD-368-2 Fab", - emdb: null, - pdb: { - dbId: "7CHF", - method: "X-RAY DIFFRACTION", - keywords: "mAb, ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7CHF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7chf_final.pdb", - externalLink: "https://pdb-redo.eu/db/7chf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "BD-604 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-604 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-368-2 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-368-2 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Xiao, J. (0000-0003-1822-1701)", "Zhu, Q. 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(0000-0002-1510-7412)", - "Ling-Hu, T.", - "Minasov, G.", - "Wiersum, G.", - "Rosas-Lemus, M.", - "Shuvalova, L.", - "Achenbach, C.J. (0000-0003-4847-7249)", - "Hultquist, J.F. (0000-0001-6424-4280)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Bachta, K.E.R. 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(0000-0002-5214-1572)", - "Iketani, S. (0000-0002-3733-9556)", - "Zask, A.", - "Khanizeman, N.", - "Bednarova, E.", - "Forouhar, F.", - "Fowler, B.", - "Hong, S.J.", - "Mohri, H.", - "Nair, M.S. (0000-0002-5994-3957)", - "Huang, Y. (0000-0001-6270-1644)", - "Tay, N.E.S.", - "Lee, S.", - "Karan, C.", - "Resnick, S.J.", - "Quinn, C.", - "Li, W.", - "Shion, H.", - "Xia, X.", - "Daniels, J.D.", - "Bartolo-Cruz, M.", - "Farina, M.", - "Rajbhandari, P.", - "Jurtschenko, C.", - "Lauber, M.A.", - "McDonald, T.", - "Stokes, M.E.", - "Hurst, B.L. (0000-0003-1025-5878)", - "Rovis, T. (0000-0001-6287-8669)", - "Chavez, A. (0000-0001-5626-7140)", - "Ho, D.D. (0000-0003-1627-149X)", - "Stockwell, B.R. (0000-0002-3532-3868)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tix_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tix", - }, - }, - { - title: - "Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2, form 2", - emdb: null, - pdb: { - dbId: "7TI9", - method: "X-RAY DIFFRACTION", - keywords: - "VIRAL PROTEIN, SARS-COV-2, NON-STRUCTURAL PROTEIN, NSP3, UBIQUITIN-LIKE DOMAIN, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, NIAID", - refModels: [ - { - emdbId: null, - pdbId: "7TI9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ti9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ti9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Satchell, K.J.F.", - "Stogios, P.J.", - "Skarina, T.", - "Di Leo, R.", - "Savchenko, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2, form 2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Stogios, P.J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ti9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ti9", - }, - }, - { - title: - "Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a neutralizing antibody, CV2-75 Fab", - emdb: null, - pdb: { - dbId: "7M3I", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, Antibody, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7M3I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m3i_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m3i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "CV2-75 Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV2-75 Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Hurlburt, N.K. (0000-0001-9891-916X)", - "Pancera, M. (0000-0001-9217-6270)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34237283", - title: - "Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects.", - journal: "Cell Rep 36: 109353-109353 (2021), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2021.109353", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34237283", - pubDate: "2021", - abstract: "", - authors: [ - "Jennewein, M.F.", - "MacCamy, A.J.", - "Akins, N.R.", - "Feng, J.", - "Homad, L.J.", - "Hurlburt, N.K.", - "Seydoux, E.", - "Wan, Y.H.", - "Stuart, A.B.", - "Edara, V.V.", - "Floyd, K.", - "Vanderheiden, A.", - "Mascola, J.R.", - "Doria-Rose, N.", - "Wang, L.", - "Yang, E.S.", - "Chu, H.Y.", - "Torres, J.L.", - "Ozorowski, G.", - "Ward, A.B.", - "Whaley, R.E.", - "Cohen, K.W.", - "Pancera, M.", - "McElrath, M.J.", - "Englund, J.A.", - "Finzi, A.", - 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"Nutalai, R.", - "Zhou, D.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Supasa, P.", - "Liu, C.", - "Huo, J.", - "Mentzer, A.J.", - "Duyvesteyn, H.M.E.", - "Dijokaite-Guraliuc, A.", - "Skelly, D.", - "Ritter, T.G.", - "Amini, A.", - "Bibi, S.", - "Adele, S.", - "Johnson, S.A.", - "Constantinides, B.", - "Webster, H.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Goulder, P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Mongkolsapaya, J.", - "Fry, E.E.", - "Dejnirattisai, W.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zf9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zf9", - }, - }, - { - title: "Room temperature In-situ SARS-CoV-2 MPRO with bound Z4439011520", - emdb: null, - pdb: { - dbId: "7QT7", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Main protease, SARS-CoV-2, VIRAL PROTEIN", - 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(0000-0001-5774-8202)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Lukacik, P.", - "Strain-Damerell, C.", - "Horrell, S. (0000-0001-6355-8640)", - "Gildae, R.J. (0000-0001-5038-6958)", - "Axford, D.", - "Owen, R.L. (0000-0002-2104-7057)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35647922", - title: "xia2.multiplex: a multi-crystal data-analysis pipeline.", - journal: - "Acta Crystallogr D Struct Biol 78: 752-769 (2022), 2059-7983", - doi: "https://doi.org/10.1107/S2059798322004399", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35647922", - pubDate: "2022", - abstract: "", - authors: [ - "Gildea, R.J. (0000-0001-5038-6958)", - "Beilsten-Edmands, J.", - "Axford, D. (0000-0001-7694-8525)", - "Horrell, S. (0000-0001-6355-8640)", - "Aller, P. (0000-0002-1793-7030)", - "Sandy, J. (0000-0002-6271-2084)", - "Sanchez-Weatherby, J. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rfc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rfc", - }, - }, - { - title: - "Non-structural protein 10 (nsp10) from SARS CoV-2 in complex with fragment VT00022", - emdb: null, - pdb: { - dbId: "7ORR", - method: "X-RAY DIFFRACTION", - keywords: "Fragment, complex, small molecule, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ORR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7orr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7orr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "XHLKOHSAWQPOFO-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Wang, Q.", - "Lou, J.", - "Kozielski, F.", - "Shi, X.", - "Krojer, T.", - "Talibov, V.O.", - "Sele, C.", - "Dong, D.", - "Nyblom, M.", - "Rogstam, A.", - "Knecht, W.", - "Fisher, S.Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35128408", - title: - "Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16.", - journal: "Rsc Chem Biol 3: 44-55 (2022), 2633-0679", - doi: "https://doi.org/10.1039/d1cb00135c", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35128408", - pubDate: "2022", - abstract: "", - authors: [ - "Kozielski, F.", - "Sele, C.", - "Talibov, V.O.", - "Lou, J.", - "Dong, D.", - "Wang, Q.", - "Shi, X.", - "Nyblom, M.", - "Rogstam, A.", - "Krojer, T.", - "Fisher, Z. (0000-0001-8287-0269)", - "Knecht, W. (0000-0001-9530-7598)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7orr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7orr", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102287", - emdb: null, - pdb: { - dbId: "5REX", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5REX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rex_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rex", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "OCMXSYZDVBVSSV-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgp", - }, - }, - { - title: - "The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with Beta-55 and EY6A Fabs", - emdb: null, - pdb: { - dbId: "7QNX", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, beta variant, Omicron variant, B.1.351, B.1.1.529, antibody, RBD, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7QNX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qnx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qnx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "EY6A heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-55 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-55 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "A0A7S6Y2X1", - organism: "2697049", - name: "Surface glycoprotein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35081335", - title: - "SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.", - journal: "Cell 185: 467-484.e15 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.12.046", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35081335", - pubDate: "2022", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Huo, J.", - "Zhou, D.", - "Zahradnik, J.", - "Supasa, P.", - "Liu, C.", - "Duyvesteyn, H.M.E.", - "Ginn, H.M.", - "Mentzer, A.J.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Dijokaite, A.", - "Khan, S.", - "Avinoam, O.", - "Bahar, M.", - "Skelly, D.", - "Adele, S.", - "Johnson, S.A.", - "Amini, A.", - "Ritter, T.G.", - "Mason, C.", - "Dold, C.", - "Pan, D.", - "Assadi, S.", - "Bellass, A.", - "Omo-Dare, N.", - "Koeckerling, D.", - "Flaxman, A.", - "Jenkin, D.", - "Aley, P.K.", - "Voysey, M.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Baillie, V.", - "Serafin, N.", - "Kwatra, G.", - "Da Silva, K.", - "Madhi, S.A.", - "Nunes, M.C.", - "Malik, T.", - "Openshaw, P.J.M.", - "Baillie, J.K.", - "Semple, M.G.", - "Townsend, A.R.", - "Huang, K.A.", - "Tan, T.K.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Constantinides, B.", - "Webster, H.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Schreiber, G.", - "Stuart, D.I.", - "Screaton, G.R.", - "Ritter, T.", - "Voysey, M. (0000-0001-6324-6559)", - "Resende, P.C. (0000-0002-2884-3662)", - "Ditse, Z.", - "Silva, K.D.", - "Madhi, S.", - "Openshaw, P.J. (0000-0002-7220-2555)", - "Baillie, J.K. (0000-0001-5258-793X)", - "Semple, M.G. (0000-0001-9700-0418)", - "Townsend, A.R. (0000-0002-3702-0107)", - "Tan, T.K. (0000-0001-8746-8308)", - "Stuart, D.I. (0000-0002-3426-4210)", - "Duyvesteyn, H.M.", - "Openshaw, P.J.", - "Huang, K.Y.A.", - ], - }, - { - pmID: "34981049", - title: - "Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.", - journal: "Biorxiv (2021), 2692-8205", - doi: "https://doi.org/10.1101/2021.12.03.471045", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34981049", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Huo, J.", - "Zhou, D.", - "Zahradnik, J.", - "Supasa, P.", - "Liu, C.", - "Duyvesteyn, H.M.E.", - "Ginn, H.M.", - "Mentzer, A.J.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Dijokaite, A.", - "Khan, S.", - "Avinoam, O.", - "Bahar, M.", - "Skelly, D.", - "Adele, S.", - "Johnson, S.A.", - "Amini, A.", - "Ritter, T.G.", - "Mason, C.", - "Dold, C.", - "Pan, D.", - "Assadi, S.", - "Bellass, A.", - "Omo-Dare, N.", - "Koeckerling, D.", - "Flaxman, A.", - "Jenkin, D.", - "Aley, P.K.", - "Voysey, M.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Baillie, V.", - "Serafin, N.", - "Kwatra, G.", - "Da Silva, K.", - "Madhi, S.A.", - "Nunes, M.C.", - "Malik, T.", - "Openshaw, P.J.M.", - "Baillie, J.K.", - "Semple, M.G.", - "Townsend, A.R.", - "Huang, K.A.", - "Tan, T.K.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Constantinides, B.", - "Webster, H.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Schreiber, G.", - "Stuart, D.I.", - "Screaton, G.R.", - "Ritter, T.", - "Voysey, M. (0000-0001-6324-6559)", - "Resende, P.C. (0000-0002-2884-3662)", - "Ditse, Z.", - "Silva, K.D.", - "Madhi, S.", - "Openshaw, P.J. (0000-0002-7220-2555)", - "Baillie, J.K. (0000-0001-5258-793X)", - "Semple, M.G. (0000-0001-9700-0418)", - "Townsend, A.R. (0000-0002-3702-0107)", - "Tan, T.K. (0000-0001-8746-8308)", - "Stuart, D.I. (0000-0002-3426-4210)", - "Duyvesteyn, H.M.", - "Openshaw, P.J.", - "Huang, K.Y.A.", - ], - }, - { - pmID: "", - title: - "SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses", - journal: "Cell(Cambridge,Mass.) (2022), 0092-8674", - doi: "https://doi.org/10.1016/j.cell.2021.12.046", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Huo, J.", - "Zhou, D.", - "Zahradnik, J.", - "Supasa, P.", - "Liu, C.", - "Duyvesteyn, H.M.E.", - "Ginn, H.M.", - "Mentzer, A.J.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Dijokaite, A.", - "Khan, S.", - "Avinoam, O.", - "Bahar, M.", - "Skelly, D.", - "Adele, S.", - "Johnson, S.A.", - "Amini, A.", - "Ritter, T.G.", - "Mason, C.", - "Dold, C.", - "Pan, D.", - "Assadi, S.", - "Bellass, A.", - "Omo-Dare, N.", - "Koeckerling, D.", - "Flaxman, A.", - "Jenkin, D.", - "Aley, P.K.", - "Voysey, M.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Baillie, V.", - "Serafin, N.", - "Kwatra, G.", - "Da Silva, K.", - "Madhi, S.A.", - "Nunes, M.C.", - "Malik, T.", - "Openshaw, P.J.M.", - "Baillie, J.K.", - "Semple, M.G.", - "Townsend, A.R.", - "Huang, K.A.", - "Tan, T.K.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Constantinides, B.", - "Webster, H.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Schreiber, G.", - "Stuart, D.I.", - "Screaton, G.R.", - "Ritter, T.", - "Voysey, M. 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(0000-0002-3426-4210)", - "Duyvesteyn, H.M.", - "Openshaw, P.J.", - "Huang, K.Y.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qnx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qnx", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000001674697", - emdb: null, - pdb: { - dbId: "5RSB", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsb_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KSOREMDAQHJJKY-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsb", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-2", - emdb: null, - pdb: { - dbId: "7VK3", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, SFX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VK3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vk3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vk3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["DeMirci, H. (0000-0002-9135-5397)", "Guven, O. (0000-0003-2388-5297)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography", - journal: "Crystals 11 (2021), 2073-4352", - doi: "https://doi.org/10.3390/cryst11121579", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Guven, O.", - "Gul, M.", - "Ayan, E.", - "Johnson, J.A.", - "Cakilkaya, B.", - "Usta, G.", - "Ertem, F.B.", - "Tokay, N.", - "Yuksel, B.", - "Gocenler, O.", - "Buyukdag, C.", - "Botha, S.", - "Ketawala, G.", - "Su, Z.", - "Hayes, B.", - "Poitevin, F.", - "Batyuk, A.", - "Yoon, C.H.", - "Kupitz, C.", - "Durdagi, S.", - "Sierra, R.G.", - "DeMirci, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vk3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vk3", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000002055", - emdb: null, - pdb: { - dbId: "5RSU", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsu_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SKZKKFZAGNVIMN-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsu", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 3CL protease in complex with compound 4", - emdb: null, - pdb: { - dbId: "7JT7", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 3CL protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JT7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jt7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jt7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GENYQFMDDNZIRG-UCWBBBRQSA-N"], - dbauthors: [ - "Liu, H.", - "Huang, Y.", - "Ho, D.D.", - "Forouhar, F.", - "Iketani, S.", - "Hong, S.J.", - "Nair, M.S.", - "Chavez, A.", - "Stockwell, B.R.", - "Zask, A.", - "Lin, F.-Y.", - "Xing, L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33795671", - title: - "Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors.", - journal: "Nat Commun 12: 2016-2016 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-22362-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33795671", - pubDate: "2021", - abstract: "", - authors: [ - "Iketani, S. (0000-0002-3733-9556)", - "Forouhar, F.", - "Liu, H. (0000-0002-5214-1572)", - "Hong, S.J.", - "Lin, F.Y. (0000-0003-0103-0167)", - "Nair, M.S. (0000-0002-5994-3957)", - "Zask, A.", - "Huang, Y. (0000-0001-6270-1644)", - "Xing, L. (0000-0002-9056-7996)", - "Stockwell, B.R. (0000-0002-3532-3868)", - "Chavez, A. (0000-0001-5626-7140)", - "Ho, D.D. (0000-0003-1627-149X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jt7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jt7", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 main protease in complex with Y180", - emdb: null, - pdb: { - dbId: "7FAZ", - method: "X-RAY DIFFRACTION", - keywords: "coronavirus, protease, inhibitor, complex., VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FAZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7faz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7faz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZZPWEZVCHNBBBZ-DORSKGMSSA-N", "FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: ["Zeng, R.", "Lei, J.", "Quan, B.X.", "Liu, X.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35477751", - title: - "An orally available M pro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron.", - journal: "Nat Microbiol 7: 716-725 (2022), 2058-5276", - doi: "https://doi.org/10.1038/s41564-022-01119-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35477751", - pubDate: "2022", - abstract: "", - authors: [ - "Quan, B.X.", - "Shuai, H. (0000-0001-8078-4113)", - "Xia, A.J. (0000-0002-2695-3024)", - "Hou, Y.", - "Zeng, R.", - "Liu, X.L.", - "Lin, G.F.", - "Qiao, J.X.", - "Li, W.P.", - "Wang, F.L.", - "Wang, K.", - "Zhou, R.J.", - "Yuen, T.T.", - "Chen, M.X.", - "Yoon, C.", - "Wu, M.", - "Zhang, S.Y.", - "Huang, C.", - "Wang, Y.F.", - "Yang, W.", - "Tian, C.", - "Li, W.M. (0000-0003-0985-0311)", - "Wei, Y.Q.", - "Yuen, K.Y. (0000-0002-2083-1552)", - "Chan, J.F. (0000-0001-6336-6657)", - "Lei, J. (0000-0001-9326-0554)", - "Chu, H. (0000-0003-2855-9837)", - "Yang, S. (0000-0001-5147-3746)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7faz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7faz", - }, - }, - { - title: "the complex of SARS-CoV2 3cl and NB2B4", - emdb: null, - pdb: { - dbId: "7VFB", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, 3cl, nanobody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7VFB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vfb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vfb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9837", - name: "nb2b4", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wang, L.", "Geng, Y.", "Sun, Z.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35324337", - title: - "An extended conformation of SARS-CoV-2 main protease reveals allosteric targets.", - journal: "Proc.Natl.Acad.Sci.USA 119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2120913119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35324337", - pubDate: "2022", - abstract: "", - authors: [ - "Sun, Z.", - "Wang, L.", - "Li, X.", - "Fan, C.", - "Xu, J.", - "Shi, Z.", - "Qiao, H.", - "Lan, Z.", - "Zhang, X.", - "Li, L.", - "Zhou, X.", - "Geng, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vfb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vfb", - }, - }, - { - title: - "Structure of SARS-CoV-2 Papain-like Protease bound to N-(3,5-dimethoxy-4-hydroxybenzyliden)thiosemicarbazone", - emdb: null, - pdb: { - dbId: "7QCH", - method: "X-RAY DIFFRACTION", - keywords: - "Cystein-Protease, Inhibitor, SARS-CoV-2, Thiosemicarbazone, Deubiquitination, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7QCH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qch_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qch", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VQIQQYLIOAABJK-LFYBBSHMSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Reinke, P.", - "Hinrichs, W.", - "Han, H.", - "Srinivasan, V.", - "Lorenzen, K.", - "Betzel, C.", - "Meents, A.", - "Falke, S.", - "Gunther, S.", - "Lieske, J.", - "Ewert, W.", - "Niebling, S.", - "Miglioli, F.", - "Carcelli, M.", - "Guenther, C.", - "Garcia-Alai, M.", - "Rogolino, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35480391", - title: - "Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease.", - journal: "Front Chem 10: 832431-832431 (2022), 2296-2646", - doi: "https://doi.org/10.3389/fchem.2022.832431", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35480391", - pubDate: "2022", - abstract: "", - authors: [ - "Ewert, W.", - "Gunther, S.", - "Miglioli, F.", - "Falke, S.", - "Reinke, P.Y.A.", - "Niebling, S.", - "Gunther, C.", - "Han, H.", - "Srinivasan, V.", - "Brognaro, H.", - "Lieske, J.", - "Lorenzen, K.", - "Garcia-Alai, M.M.", - "Betzel, C.", - "Carcelli, M.", - "Hinrichs, W.", - "Rogolino, D.", - "Meents, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qch_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qch", - }, - }, - { - title: "Complex Structure of antibody BD-503 and RBD-E484K of COVID-19", - emdb: null, - pdb: { - dbId: "7F6Y", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, Neutralization Antibody, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7F6Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f6y_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f6y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy Chain of BD-503", - 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(2022), 0092-8674", - doi: "https://doi.org/10.1016/j.cell.2021.12.046", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Huo, J.", - "Zhou, D.", - "Zahradnik, J.", - "Supasa, P.", - "Liu, C.", - "Duyvesteyn, H.M.E.", - "Ginn, H.M.", - "Mentzer, A.J.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Dijokaite, A.", - "Khan, S.", - "Avinoam, O.", - "Bahar, M.", - "Skelly, D.", - "Adele, S.", - "Johnson, S.A.", - "Amini, A.", - "Ritter, T.G.", - "Mason, C.", - "Dold, C.", - "Pan, D.", - "Assadi, S.", - "Bellass, A.", - "Omo-Dare, N.", - "Koeckerling, D.", - "Flaxman, A.", - "Jenkin, D.", - "Aley, P.K.", - "Voysey, M.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Baillie, V.", - "Serafin, N.", - "Kwatra, G.", - "Da Silva, K.", - "Madhi, S.A.", - "Nunes, M.C.", - "Malik, T.", - "Openshaw, P.J.M.", - "Baillie, J.K.", - "Semple, M.G.", - "Townsend, A.R.", - "Huang, K.A.", - "Tan, T.K.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Constantinides, B.", - "Webster, H.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Schreiber, G.", - "Stuart, D.I.", - "Screaton, G.R.", - "Ritter, T.", - "Voysey, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgq", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102535", - emdb: null, - pdb: { - dbId: "5RG0", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RG0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rg0_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rg0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "NBQBICYRKOTWRR-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. 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(0000-0003-4175-3714)", - "Aihara, H. (0000-0001-7508-6230)", - "Esler, M.A.", - "Harris, R.S. (0000-0002-9034-9112)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35471084", - title: - "Gain-of-Signal Assays for Probing Inhibition of SARS-CoV-2 M pro /3CL pro in Living Cells.", - journal: "Mbio 13: e0078422-e0078422 (2022), 2150-7511", - doi: "https://doi.org/10.1128/mbio.00784-22", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35471084", - pubDate: "2022", - abstract: "", - authors: [ - "Moghadasi, S.A.", - "Esler, M.A.", - "Otsuka, Y.", - "Becker, J.T.", - "Moraes, S.N.", - "Anderson, C.B.", - "Chamakuri, S.", - "Belica, C.", - "Wick, C.", - "Harki, D.A.", - "Young, D.W.", - "Scampavia, L.", - "Spicer, T.P.", - "Shi, K.", - "Aihara, H.", - "Brown, W.L.", - "Harris, R.S. 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(0000-0001-5774-8202)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Lukacik, P.", - "Strain-Damerell, C.", - "Horrell, S. (0000-0001-6355-8640)", - "Gildae, R.J. (0000-0001-5038-6958)", - "Axford, D.", - "Owen, R.L. (0000-0002-2104-7057)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35647922", - title: "xia2.multiplex: a multi-crystal data-analysis pipeline.", - journal: - "Acta Crystallogr D Struct Biol 78: 752-769 (2022), 2059-7983", - doi: "https://doi.org/10.1107/S2059798322004399", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35647922", - pubDate: "2022", - abstract: "", - authors: [ - "Gildea, R.J. (0000-0001-5038-6958)", - "Beilsten-Edmands, J.", - "Axford, D. (0000-0001-7694-8525)", - "Horrell, S. (0000-0001-6355-8640)", - "Aller, P. (0000-0002-1793-7030)", - "Sandy, J. (0000-0002-6271-2084)", - "Sanchez-Weatherby, J. 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(0000-0002-3544-1389)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7chp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7chp", - }, - }, - { - title: "SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab", - emdb: null, - pdb: { - dbId: "7ZF8", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Omicron, BA.1, BA.2, RBD, antibody, Fab, COVOX-150, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZF8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zf8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zf8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-150 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-150 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I.", "Huo, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35662412", - title: - "Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.", - journal: "Cell 185: 2116-2131.e18 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.05.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35662412", - pubDate: "2022", - abstract: "", - authors: [ - "Nutalai, R.", - "Zhou, D.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Supasa, P.", - "Liu, C.", - "Huo, J.", - "Mentzer, A.J.", - "Duyvesteyn, H.M.E.", - "Dijokaite-Guraliuc, A.", - "Skelly, D.", - "Ritter, T.G.", - "Amini, A.", - "Bibi, S.", - "Adele, S.", - "Johnson, S.A.", - "Constantinides, B.", - "Webster, H.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Goulder, P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Mongkolsapaya, J.", - "Fry, E.E.", - "Dejnirattisai, W.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zf8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zf8", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 3CL in complex with inhibitor NK01-48", - emdb: null, - pdb: { - dbId: "7TIY", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TIY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tiy_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tiy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "UQJSPTNSSUFGMT-IREPMIDKSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Liu, H.", - "Huang, Y.", - "Li, W.", - "Lee, S.", - "Ho, D.D.", - "Hurst, B.", - "Forouhar, F.", - "Iketani, S.", - "Zack, A.", - "Khanizeman, N.", - "Bednarova, E.", - "Fowler, B.", - "Hong, S.J.", - "Mohri, H.", - "Nair, M.S.", - "Tay, N.E.S.", - "Karan, C.", - "Resnick, S.J.", - "Quinn, C.", - "Shion, H.", - "Jurtschenko, C.", - "Lauber, M.A.", - "McDonald, T.", - "Rovis, T.", - "Chavez, A.", - "Stockwell, B.R.", - "Stokes, M.E.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35393402", - title: - "Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19.", - journal: "Nat Commun 13: 1891-1891 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-29413-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35393402", - pubDate: "2022", - abstract: "", - authors: [ - "Liu, H. (0000-0002-5214-1572)", - "Iketani, S. (0000-0002-3733-9556)", - "Zask, A.", - "Khanizeman, N.", - "Bednarova, E.", - "Forouhar, F.", - "Fowler, B.", - "Hong, S.J.", - "Mohri, H.", - "Nair, M.S. (0000-0002-5994-3957)", - "Huang, Y. (0000-0001-6270-1644)", - "Tay, N.E.S.", - "Lee, S.", - "Karan, C.", - "Resnick, S.J.", - "Quinn, C.", - "Li, W.", - "Shion, H.", - "Xia, X.", - "Daniels, J.D.", - "Bartolo-Cruz, M.", - "Farina, M.", - "Rajbhandari, P.", - "Jurtschenko, C.", - "Lauber, M.A.", - "McDonald, T.", - "Stokes, M.E.", - "Hurst, B.L. (0000-0003-1025-5878)", - "Rovis, T. (0000-0001-6287-8669)", - "Chavez, A. (0000-0001-5626-7140)", - "Ho, D.D. (0000-0003-1627-149X)", - "Stockwell, B.R. (0000-0002-3532-3868)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tiy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tiy", - }, - }, - { - title: - "Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 at 1.6A resolution (spacegroup P2(1)2(1)2(1))", - emdb: null, - pdb: { - dbId: "7BB2", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7BB2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bb2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bb2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P.", "Giabbai, B."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34769210", - title: - "Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L.", - journal: "Int J Mol Sci 22 (2021), 1422-0067", - doi: "https://doi.org/10.3390/ijms222111779", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34769210", - pubDate: "2021", - abstract: "", - authors: [ - "Costanzi, E.", - "Kuzikov, M. (0000-0001-8771-1865)", - "Esposito, F. (0000-0001-9725-7977)", - "Albani, S. (0000-0002-3560-4539)", - "Demitri, N.", - "Giabbai, B.", - "Camasta, M.", - "Tramontano, E. (0000-0002-4849-0980)", - "Rossetti, G. (0000-0002-2032-4630)", - "Zaliani, A. (0000-0002-1740-8390)", - "Storici, P. (0000-0002-2590-3332)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bb2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bb2", - }, - }, - { - title: - "SARS-CoV-2 3CLPro in complex with 2-(benzotriazol-1-yl)-N-[4-(1H-pyrazol-4-yl)phenyl]-N-(3-thienylmethyl)acetamide", - emdb: null, - pdb: { - dbId: "7LMD", - method: "X-RAY DIFFRACTION", - keywords: - "3CLPro, SARS-CoV-2 Main Protease, SARS-CoV-2 3CLPro, Inhibitor Complex, Protease, VIRAL PROTEIN, hydrolase-Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7LMD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lmd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lmd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PYVQFTGANJRGEP-UHFFFAOYSA-N"], - dbauthors: [ - "Goins, C.M. (0000-0002-6617-4877)", - "Stauffer, S.R. (0000-0002-6332-1827)", - "Arya, T. (0000-0001-8690-6425)", - "Macdonald, J.D. (0000-0002-6360-2768)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34347470", - title: - "Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro ).", - journal: "J.Med.Chem. 65: 2880-2904 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00598", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34347470", - pubDate: "2022", - abstract: "", - authors: [ - "Han, S.H.", - "Goins, C.M.", - "Arya, T.", - "Shin, W.J.", - "Maw, J.", - "Hooper, A.", - "Sonawane, D.P.", - "Porter, M.R.", - "Bannister, B.E.", - "Crouch, R.D.", - "Lindsey, A.A.", - "Lakatos, G.", - "Martinez, S.R.", - "Alvarado, J.", - "Akers, W.S.", - "Wang, N.S.", - "Jung, J.U.", - "Macdonald, J.D.", - "Stauffer, S.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lmd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lmd", - }, - }, - { - title: "NMR structure of the N-terminal domain of Nsp8 from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7YWR", - method: "SOLUTION NMR", - keywords: "SARS-CoV-2, non-structural protein, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "A0A8B1JQ63", - organism: "2697049", - name: "ORF1a polyprotein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Mompean, M.", "Laurents, D.V.", "Pantoja-Uceda, D.", "Trevino, M.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "NMR structure of the N-terminal domain of Nsp8 from SARS-CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - 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isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "DLNUNWNLBKOMMX-WUOGMODZSA-O", - "DLNUNWNLBKOMMX-PGIRCJHISA-O", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Madden, T.K.", - "Kim, Y.", - "Nguyen, H.N.", - "Machen, A.J.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - "Picard, H.R.", - "Thruman, H.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36654747", - title: - "Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.", - journal: "Acs Pharmacol Transl Sci 6: 181-194 (2023), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00206", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36654747", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Nguyen, H.N.", - 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(0000-0001-7114-3736)", - "Eris, D.", - "Wang, M. (0000-0002-5340-3036)", - "Sharpe, M.", - "Groves, M.R.", - "Domling, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34097796", - title: - "Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.", - journal: - "Angew.Chem.Int.Ed.Engl. 60: 18231-18239 (2021), 1521-3773", - doi: "https://doi.org/10.1002/anie.202105584", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34097796", - pubDate: "2021", - abstract: "", - authors: [ - "Sutanto, F.", - "Shaabani, S. (0000-0001-5546-7140)", - "Oerlemans, R.", - "Eris, D.", - "Patil, P.", - "Hadian, M.", - "Wang, M.", - "Sharpe, M.E.", - "Groves, M.R.", - "Domling, A. 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(0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5saf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5saf", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2856434942", - emdb: null, - pdb: { - dbId: "5SLV", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slv_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "XUHKVJOCQINJLO-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slv", - }, - }, - { - title: "Crystal Structure of NSP1 from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7K3N", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV2, NSP1, Non-structural protein 1, COVID19, viral protein", - refModels: [ - { - emdbId: null, - pdbId: "7K3N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k3n_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k3n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Host translation inhibitor nsp1", - details: "", - altNames: "Leader protein,Non-structural protein 1,nsp1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Chang, C.", - "Savchenko, A.", - "Semper, C.", - "Watanabe, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33319167", - title: - "Structural characterization of nonstructural protein 1 from SARS-CoV-2.", - journal: "Iscience 24: 101903-101903 (2021), 2589-0042", - doi: "https://doi.org/10.1016/j.isci.2020.101903", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33319167", - pubDate: "2021", - abstract: "", - authors: ["Semper, C.", "Watanabe, N.", "Savchenko, A."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k3n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k3n", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000835985505 - (S) isomer", - emdb: null, - pdb: { - dbId: "5SOM", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5som_final.pdb", - externalLink: "https://pdb-redo.eu/db/5som", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BBSKBVDQKLCENN-AWEZNQCLSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5som_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5som", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1186029914", - emdb: null, - pdb: { - dbId: "5SL7", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SL7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sl7_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sl7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "LXSCPIWTZCIAIQ-SECBINFHSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sl7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sl7", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-29 and Beta-53 Fabs", - emdb: null, - pdb: { - dbId: "7PS2", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-COV-2 B.1.1.7 (Alpha) VARIANT, B.1.351 (Beta) VARIANT, P.1 (Gamma) VARIANT, B.1.617.2 (Delta) VARIANT, ANTIBODY, RECEPTOR-BINDING-DOMAIN, SPIKE, NEUTRALISATION, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7PS2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ps2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ps2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Beta-29 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-29 Fab heavy chain", - details: "", - 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dbId: "5SM3", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SM3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sm3_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sm3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "NSZUGQROUUTGGI-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sm3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sm3", - }, - }, - { - title: - "Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex with Leupeptin", - emdb: null, - pdb: { - dbId: "6XCH", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 Main Protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "6XCH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xch_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xch", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - 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(0000-0002-5416-5789)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. 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(0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. 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(0000-0002-4090-5176)", - "Khan, M.B. (0000-0002-4164-9573)", - "Lemieux, M.J. 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externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lco", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1003207278", - emdb: null, - pdb: { - dbId: "5SLA", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sla_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sla", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "PFWYRMPHHJKJBB-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sla_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sla", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z437584380", - emdb: null, - pdb: { - dbId: "5SME", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SME", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sme_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sme", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "PIZZAODWSORPSH-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sme_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sme", - }, - }, - { - title: - "Soaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex.", - emdb: null, - pdb: { - dbId: "6ZLR", - method: "X-RAY DIFFRACTION", - keywords: "SARS-COV-2, VIRAL PROTEIN COMPLEX, ANTIBODY, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6ZLR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6zlr_final.pdb", - externalLink: "https://pdb-redo.eu/db/6zlr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CR3022 FAB HEAVY CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CR3022 FAB LIGHT CHAIN", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "de Nicola, G.F. (0000-0003-4649-9452)", - "Nichols, C.E. (0000-0002-2159-371X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33381049", - title: - "A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex-An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface.", - journal: "Front Pharmacol 11: 615211-615211 (2020), 1663-9812", - doi: "https://doi.org/10.3389/fphar.2020.615211", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33381049", - pubDate: "2020", - abstract: "", - authors: [ - "Nichols, C.", - "Ng, J.", - "Keshu, A.", - "Fraternali, F.", - "De Nicola, G.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zlr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zlr", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) S144L Mutant in Complex with Inhibitor GC376", - emdb: null, - pdb: { - dbId: "8DD9", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DD9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dd9_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dd9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-OGNFBWPZSA-N"], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Jacobs, L.M.C. (0000-0002-9939-653X)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36119652", - title: - "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.28.497978", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36119652", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, Y.", - "Lewandowski, E.M.", - "Tan, H.", - "Zhang, X.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Butler, S.G.", - "Gongora, M.V.", - "Choy, J.", - "Deng, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dd9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dd9", - }, - }, - { - title: "SARS-CoV-2 Main Protease in mature form", - emdb: null, - pdb: { - dbId: "7KPH", - method: "X-RAY DIFFRACTION", - keywords: "mpro, sars-cov-2, covid-19, protease, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7KPH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kph_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kph", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Noske, G.D.", - "Oliva, G.", - "Godoy, A.S.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Lima, G.M.A.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34174328", - title: - "A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.", - journal: "J.Mol.Biol. 433: 167118-167118 (2021), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2021.167118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34174328", - pubDate: "2021", - abstract: "", - authors: [ - "Noske, G.D.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Lima, G.M.A.", - "Rosa, H.V.D.", - "Pereira, H.D.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "Freire, M.C.L.C.", - "Fearon, D.", - "Douangamath, A.", - "von Delft, F.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kph_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kph", - }, - }, - { - title: - "Structure of SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a", - emdb: null, - pdb: { - dbId: "7PKU", - method: "SOLUTION NMR", - keywords: - "SARS-Cov-2; nucleoprotein; nsp3; NMR; intrinsically disordered protein; chaperone; replication; nucleocapsid; RNA; SAXS, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Bessa, L.M.", - "Guseva, S.", - "Camacho-Zarco, A.R.", - "Salvi, N.", - "Blackledge, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35044811", - title: - "The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a.", - journal: "Sci Adv 8: eabm4034-eabm4034 (2022), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abm4034", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35044811", - pubDate: "2022", - abstract: "", - authors: [ - "Bessa, L.M. 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(0000-0003-0935-721X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7pku_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7pku", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 5c", - emdb: null, - pdb: { - dbId: "7LZZ", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LZZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lzz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lzz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GQBZOCZYIKJBAR-FUDCQAQESA-N", "GQBZOCZYIKJBAR-WXCIZVPBSA-N"], - dbauthors: [ - "Miller, M.J.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Perera, K.D.", - "Rathnayake, A.D.", - "Jesri, A.R.M.", - "Baird, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34865476", - title: - "Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.", - journal: "J.Med.Chem. 64: 17846-17865 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34865476", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Jesri, A.M.", - "Nguyen, H.N.", - "Miller, M.J.", - "Thurman, H.A.", - "Zheng, J.", - "Kashipathy, M.M.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Kim, Y.", - "Groutas, W.C.", - "Chang, K.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lzz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lzz", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 NendoU in complex with LIZA-7", - emdb: null, - pdb: { - dbId: "7N7U", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7N7U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n7u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n7u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [""], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n7u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n7u", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z4718398515 - (R,S) isomer", - emdb: null, - pdb: { - dbId: "5SPH", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SPH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sph_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sph", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BAKOSBATOMEZBB-HOTGVXAUSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sph_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sph", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINCnt000006kx7L", - emdb: null, - pdb: { - dbId: "5SS2", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SS2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5ss2_final.pdb", - externalLink: "https://pdb-redo.eu/db/5ss2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BORZWBYDXGSJEW-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5ss2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5ss2", - }, - }, - { - title: - "YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01", - emdb: null, - pdb: { - dbId: "7RTR", - method: "X-RAY DIFFRACTION", - keywords: - "human leukocyte antigen, major histocompatibility complex, HLA-A2, HLA-A*02:01, YLQPRTFLL, T cell receptor, TCR, TCRpMHC, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7RTR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rtr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rtr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q53Z42", - organism: "9606", - name: "HLA class I antigen", - details: "", - altNames: - "HLA class I histocompatibility antigen,HLA class I histocompatibility antigen A alpha chain,A alpha chain,MHC class I antigen,MHC class I protein,MHC class I protein (HLA-A)", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "YLQ-SG3 TCR alpha chain (TRAV12-2)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "YLQ-SG3 TCR beta chain (TRBV7-9)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: ["Szeto, C. (0000-0003-3784-5210)", "Gras, S. (0000-0001-7416-038X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34685626", - title: - "Molecular Basis of a Dominant SARS-CoV-2 Spike-Derived Epitope Presented by HLA-A*02:01 Recognised by a Public TCR.", - journal: "Cells 10 (2021), 2073-4409", - doi: "https://doi.org/10.3390/cells10102646", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34685626", - pubDate: "2021", - abstract: "", - authors: [ - "Szeto, C. (0000-0003-3784-5210)", - "Nguyen, A.T.", - "Lobos, C.A.", - "Chatzileontiadou, D.S.M.", - "Jayasinghe, D.", - "Grant, E.J.", - "Riboldi-Tunnicliffe, A.", - "Smith, C.", - "Gras, S. (0000-0001-7416-038X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rtr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rtr", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI11", - emdb: null, - pdb: { - dbId: "7RVM", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, main protease, reversible covalent inhibitors, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RVM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rvm_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rvm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NMNHQNPORDVBGU-CMOCDZPBSA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. 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(0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33786375", - title: - "Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations.", - journal: "Acs Cent.Sci. 7: 467-475 (2021), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.1c00039", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33786375", - pubDate: "2021", - abstract: "", - authors: [ - "Zhang, C.H.", - "Stone, E.A.", - "Deshmukh, M.", - "Ippolito, J.A.", - "Ghahremanpour, M.M.", - "Tirado-Rives, J.", - "Spasov, K.A.", - "Zhang, S.", - "Takeo, Y.", - "Kudalkar, S.N.", - "Liang, Z.", - "Isaacs, F.", - "Lindenbach, B.", - "Miller, S.J.", - "Anderson, K.S.", - "Jorgensen, W.L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l11_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l11", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-71", - emdb: null, - pdb: { - dbId: "7RNK", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RNK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rnk_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rnk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LOQJVSKMCQMDKR-UHFFFAOYSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34705466", - title: - "Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.", - journal: "J.Med.Chem. 64: 17366-17383 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01475", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34705466", - pubDate: "2021", - abstract: "", - authors: [ - "Kneller, D.W. 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(0000-0002-7666-639X)", - "Shi, W.", - "McSweeney, S. (0000-0002-3758-3161)", - "Fuchs, M.R.", - "Soares, A.S.", - "Jakoncic, J.", - "Keereetaweep, J.", - "Shanklin, J.", - "Kreitler, D.F. (0000-0003-4758-7913)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35842458", - title: - "Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.", - journal: "Sci Rep 12: 12197-12197 (2022), 2045-2322", - doi: "https://doi.org/10.1038/s41598-022-15930-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35842458", - pubDate: "2022", - abstract: "", - authors: [ - "Andi, B.", - "Kumaran, D.", - "Kreitler, D.F.", - "Soares, A.S.", - "Keereetaweep, J.", - "Jakoncic, J.", - "Lazo, E.O.", - "Shi, W.", - "Fuchs, M.R.", - "Sweet, R.M.", - "Shanklin, J.", - "Adams, P.D.", - "Schmidt, J.G.", - "Head, M.S.", - "McSweeney, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k6e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k6e", - }, - }, - { - title: - "Structure of the SARS-CoV-2 RBD in complex with neutralizing antibody C099 and CR3022", - emdb: null, - pdb: { - dbId: "7R8L", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, receptor binding domain, RBD, neutralizing antibody, COVID-19, spike, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7R8L", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7r8l_final.pdb", - externalLink: "https://pdb-redo.eu/db/7r8l", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "C099 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "C099 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - 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"Muecksch, F.", - "Weisblum, Y.", - "Barnes, C.O.", - "Schmidt, F.", - "Schaefer-Babajew, D.", - "Wang, Z.", - "C Lorenzi, J.C.", - "Flyak, A.I.", - "DeLaitsch, A.T.", - "Huey-Tubman, K.E.", - "Hou, S.", - "Schiffer, C.A.", - "Gaebler, C.", - "Da Silva, J.", - "Poston, D.", - "Finkin, S.", - "Cho, A.", - "Cipolla, M.", - "Oliveira, T.Y.", - "Millard, K.G.", - "Ramos, V.", - "Gazumyan, A.", - "Rutkowska, M.", - "Caskey, M.", - "Nussenzweig, M.C.", - "Bjorkman, P.J.", - "Hatziioannou, T.", - "Bieniasz, P.D.", - "Lorenzi, J.C.C.", - ], - }, - { - pmID: "33758864", - title: - "Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.07.434227", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33758864", - pubDate: "2021", - abstract: "", - authors: [ - "Muecksch, F.", - "Weisblum, Y.", - "Barnes, C.O.", - "Schmidt, F.", - "Schaefer-Babajew, D.", - "Wang, Z.", - "C Lorenzi, J.C.", - "Flyak, A.I.", - "DeLaitsch, A.T.", - "Huey-Tubman, K.E.", - "Hou, S.", - "Schiffer, C.A.", - "Gaebler, C.", - "Da Silva, J.", - "Poston, D.", - "Finkin, S.", - "Cho, A.", - "Cipolla, M.", - "Oliveira, T.Y.", - "Millard, K.G.", - "Ramos, V.", - "Gazumyan, A.", - "Rutkowska, M.", - "Caskey, M.", - "Nussenzweig, M.C.", - "Bjorkman, P.J.", - "Hatziioannou, T.", - "Bieniasz, P.D.", - "Lorenzi, J.C.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7r8l_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7r8l", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs", - emdb: null, - pdb: { - dbId: "7BEP", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, antibody, germline, V-gene, receptor-binding-domain, spike, neutralisation, protection, glycosylation, valency, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s1q_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s1q", - }, - }, - { - title: - "1.50 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 2k", - emdb: null, - pdb: { - dbId: "7LKT", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LKT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lkt_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lkt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "AFONNBAHWVWJGI-XKEITGKGSA-N", - "AFONNBAHWVWJGI-SHBYJIAFSA-N", - "RFHAOTPXVQNOHP-UHFFFAOYSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Rathnayake, A.D.", - "Baird, M.A.", - "Shadipeni, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34213885", - title: - "Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease.", - journal: "J.Med.Chem. 64: 10047-10058 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00319", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34213885", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Kim, Y.", - "Bickmeier, N.", - "Rathnayake, A.D.", - "Nguyen, H.N.", - "Zheng, J.", - "Kashipathy, M.M.", - "Baird, M.A.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lkt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lkt", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z287484230", - emdb: null, - pdb: { - dbId: "5S3N", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3n_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JQSGNNVZAVLVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3n", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z285782452", - emdb: null, - pdb: { - dbId: "5RLQ", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RLQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rlq_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rlq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "YLDKGNWSSXYUAH-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rlq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rlq", - }, - }, - { - title: - "PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease covalent inhibitors -- Crystal Structure of SARS-CoV-2 main protease in complex with LON-WEI-adc59df6-2 (Mpro-x3110)", - emdb: null, - pdb: { - dbId: "5RL0", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5RL0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rl0_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rl0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XJCLWVXTCRQIDI-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "London, N.", - "Zaidman, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease covalent inhibitors", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Zaidman, D.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Gorrie-Stone, T.J.", - "Skyner, R.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rl0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rl0", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Clonidine", - emdb: null, - pdb: { - dbId: "7AWW", - method: "X-RAY DIFFRACTION", - keywords: "inhibitor, complex, screen, sars-cov-2, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AWW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aww_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aww", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GJSURZIOUXUGAL-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Reinke, P.Y.A.", - "Lieske, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - 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(0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. 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(0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rmb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rmb", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant Y54F at 1.63 A resolution", - emdb: null, - pdb: { - dbId: "7ZB7", - method: "X-RAY DIFFRACTION", - keywords: "SARS-COV-2, MPRO, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7ZB7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zb7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zb7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Paknia, E. (0000-0002-9228-6215)", - "Rabe von Pappenheim, F. (0000-0002-3925-8127)", - "Funk, L.-M. (0000-0003-2443-691X)", - "Tittmann, K. (0000-0001-7891-7108)", - "Chari, A. (0000-0001-6220-9828)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Redox regulation of the SARS-CoV-2 main protease provides new opportunities for drug design", - journal: "Biorxiv (2022)", - doi: "https://doi.org/10.1101/2022.04.18.487732", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Funk, L.M.", - "Poschmann, G.", - "Chari, A.", - "von Pappenheim, F.R.", - "Stegmann, K.M.", - "Dickmanns, A.", - "Eulig, N.", - "Wensien, M.", - "Paknia, E.", - "Heyne, G.", - "Penka, E.", - "Pearson, A.R.", - "Berndt, C.", - "Fritz, T.", - "Bazzi, S.", - "Uranga, J.", - "Mata, R.A.", - "Dobbelstein, M.", - "Hilgenfeld, R.", - "Curth, U.", - "Tittmann, K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zb7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zb7", - }, - }, - { - title: "X-ray Structure of SARS-CoV-2 main protease bound to Boceprevir at 1.45 A", - emdb: null, - pdb: { - dbId: "6WNP", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Covid-19, main protease, 3CL-protease, Boceprevir, FDA Drug, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WNP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wnp_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wnp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FEBWCINGHXXUCV-GFLQDLJJSA-N"], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Anson, B. (0000-0003-2670-974X)", - "Mesecar, A. (0000-0002-1241-2577)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "X-ray Structure of SARS-CoV-2 main protease bound to Boceprevir at 1.45 A", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Anson, B. (0000-0003-2670-974X)", - "Mesecar, A. (0000-0002-1241-2577)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wnp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wnp", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with PF-07321332", - emdb: null, - pdb: { - dbId: "7SI9", - method: "X-RAY DIFFRACTION", - keywords: "cysteine protease, inhibitor complex, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7SI9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7si9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7si9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35477935", - title: - "Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease", - journal: "Nat Commun 13 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-29915-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35477935", - pubDate: "2022", - abstract: "", - authors: [ - "Kneller, D.W.", - "Li, H.", - "Phillips, G.", - "Weiss, K.L.", - "Zhang, Q.", - "Arnould, M.A.", - "Jonsson, C.B.", - "Surendranathan, S.", - "Parvathareddy, J.", - "Blakeley, M.P.", - "Coates, L.", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A.", - "Kneller, D.", - "Phillips, G. (0000-0001-5858-3825)", - "Weiss, K. (0000-0002-6486-8007)", - "Arnould, M. (0000-0003-0172-8311)", - "Jonsson, C.", - "Blakeley, M. (0000-0002-6412-4358)", - "Coates, L. (0000-0003-2342-049X)", - "Louis, J. (0000-0002-0052-1899)", - "Bonnesen, P. (0000-0002-1397-8281)", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Adams, P.D.", - "Mustyakimov, M.", - "Afonine, P.V.", - "Langan, P.", - ], - }, - { - pmID: "35169792", - title: - "Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease: room-temperature X-ray and neutron crystallography, binding thermodynamics, and antiviral activity.", - journal: "Res Sq (2022), 2693-5015", - doi: "https://doi.org/10.21203/rs.3.rs-1318037/v1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35169792", - pubDate: "2022", - abstract: "", - authors: [ - "Kneller, D.W.", - "Li, H.", - "Phillips, G.", - "Weiss, K.L.", - "Zhang, Q.", - "Arnould, M.A.", - "Jonsson, C.B.", - "Surendranathan, S.", - "Parvathareddy, J.", - "Blakeley, M.P.", - "Coates, L.", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A.", - "Kneller, D.", - "Phillips, G. (0000-0001-5858-3825)", - "Weiss, K. (0000-0002-6486-8007)", - "Arnould, M. (0000-0003-0172-8311)", - "Jonsson, C.", - "Blakeley, M. (0000-0002-6412-4358)", - "Coates, L. (0000-0003-2342-049X)", - "Louis, J. (0000-0002-0052-1899)", - "Bonnesen, P. (0000-0002-1397-8281)", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Adams, P.D.", - "Mustyakimov, M.", - "Afonine, P.V.", - "Langan, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7si9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7si9", - }, - }, - { - title: - "The co-crystal structure of SARS-CoV-2 main protease with peptidomimetic inhibitor N-((S)-3-methyl-1-(((S)-4-methyl-1-oxo-1-(((S)-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)amino)pentan-2-yl)amino)-1-oxobutan-2-yl)-4-nitrobenzamide", - emdb: null, - pdb: { - dbId: "7DGI", - method: "X-RAY DIFFRACTION", - keywords: "complex, inhibitor, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7DGI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dgi_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dgi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UUOJCIYWLMPKQE-LGGPRVQUSA-N"], - dbauthors: ["Shang, L.Q. (0000-0003-4424-3162)", "Wang, H. (0000-0002-1916-7092)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35635946", - title: - "The structure-based design of peptidomimetic inhibitors against SARS-CoV-2 3C like protease as Potent anti-viral drug candidate.", - journal: "Eur.J.Med.Chem. 238: 114458-114458 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114458", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35635946", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, H.", - "Pei, R.", - "Li, X.", - "Deng, W.", - "Xing, S.", - "Zhang, Y.", - "Zhang, C.", - "He, S.", - "Sun, H.", - "Xiao, S.", - "Xiong, J.", - "Chen, X.", - "Wang, Y.", - "Guo, Y.", - "Zhang, B.", - "Shang, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dgi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dgi", - }, - }, - { - title: "Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 9/10", - emdb: null, - pdb: { - dbId: "7TA4", - method: "X-RAY DIFFRACTION", - keywords: - "Coronavirus, COVID-19, COVID, PROTEASE, DRUG RESISTANCE, COMPLEX, HYDROLASE, DURG DISCOVERY, MAIN PROTEASE, MPRO, SUBSTRATE COMPLEX, NSP 9/10, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TA4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ta4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ta4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Nonstructural protein 9/10", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Shaqra, A.M. (0000-0001-6994-2416)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35729165", - title: - "Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.", - journal: "Nat Commun 13: 3556-3556 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-31210-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35729165", - pubDate: "2022", - abstract: "", - authors: [ - "Shaqra, A.M.", - "Zvornicanin, S.N.", - "Huang, Q.Y.J. (0000-0001-5107-2336)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Knapp, M.", - "Tandeske, L.", - "Bakan, D.T.", - "Flynn, J. (0000-0002-5490-393X)", - "Bolon, D.N.A.", - "Moquin, S.", - "Dovala, D.", - "Kurt Yilmaz, N. (0000-0002-5036-676X)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ta4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ta4", - }, - }, - { - title: "The crystal structure of SARS-CoV-2 main protease in complex with GC376", - emdb: null, - pdb: { - dbId: "7CBT", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, GC376, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CBT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cbt_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cbt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: ["Shi, Y. (0000-0002-9500-6995)", "Peng, G. (0000-0002-7093-4728)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33691601", - title: - "The preclinical inhibitor GS441524 in combination with GC376 efficaciously inhibited the proliferation of SARS-CoV-2 in the mouse respiratory tract.", - journal: "Emerg Microbes Infect 10: 481-492 (2021), 2222-1751", - doi: "https://doi.org/10.1080/22221751.2021.1899770", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33691601", - pubDate: "2021", - abstract: "", - authors: [ - "Shi, Y. (0000-0002-9500-6995)", - "Shuai, L. (0000-0003-2122-8365)", - "Wen, Z. (0000-0003-3112-0243)", - "Wang, C. (0000-0002-3970-9071)", - "Yan, Y. (0000-0001-8385-8827)", - "Jiao, Z. (0000-0002-0250-0565)", - "Guo, F. (0000-0001-8122-0176)", - "Fu, Z.F. (0000-0001-6293-9329)", - "Chen, H. (0000-0003-0680-5953)", - "Bu, Z. (0000-0001-9242-4211)", - "Peng, G. (0000-0001-8813-6663)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cbt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cbt", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C63", - emdb: null, - pdb: { - dbId: "7MLG", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, 3CLpro, covalent inhibitor, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7MLG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mlg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mlg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZCSLMPKXGXMPHB-HSZRJFAPSA-N"], - dbauthors: [ - "Wang, G.", - "Sharon, I.", - "Stille, J.", - "Tjutrins, J.", - "Venegas, F.A.", - "Hennecker, C.", - "Rueda, A.M.", - "Miron, C.E.", - "Pinus, S.", - "Labarre, A.", - "Patrascu, M.B.", - "Vlaho, D.", - "Huot, M.", - "Mittermaier, A.K.", - "Moitessier, N.", - "Schmeing, T.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34995923", - title: - "Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors.", - journal: "Eur.J.Med.Chem. 229: 114046-114046 (2021), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2021.114046", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34995923", - pubDate: "2021", - abstract: "", - authors: [ - "Stille, J.K.", - "Tjutrins, J.", - "Wang, G.", - "Venegas, F.A.", - "Hennecker, C.", - "Rueda, A.M.", - "Sharon, I.", - "Blaine, N.", - "Miron, C.E.", - "Pinus, S.", - "Labarre, A.", - "Plescia, J.", - "Burai Patrascu, M.", - "Zhang, X.", - "Wahba, A.S.", - "Vlaho, D.", - "Huot, M.J.", - "Schmeing, T.M.", - "Mittermaier, A.K.", - "Moitessier, N.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mlg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mlg", - }, - }, - { - title: "Structure of coiled-coil tetramer from SARS-CoV-2 spike stalk region", - emdb: null, - pdb: { - dbId: "7OWX", - method: "X-RAY DIFFRACTION", - keywords: - "spike, sars-cov-2, coiled-coil, tetramer, virus, coronavirus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7OWX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7owx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7owx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2", - details: - "Lysine at N-terminal is used for biochemical assays; two serines were added at N-terminal to increase the peptide solubility in PBS", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: ["Zivic, Z.", "Hadzi, S. (0000-0002-5615-7918)"], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "35157347", - title: - "Structural polymorphism of coiled-coils from the stalk domain of SARS-CoV-2 spike protein.", - journal: "Faseb J. 36: e22199-e22199 (2022), 1530-6860", - doi: "https://doi.org/10.1096/fj.202101670R", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35157347", - pubDate: "2022", - abstract: "", - authors: [ - "Zivic, Z. (0000-0001-9044-3064)", - "Strmsek, Z.", - "Novinec, M.", - "Lah, J.", - "Hadzi, S. (0000-0002-5615-7918)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7owx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7owx", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to AR-42.", - emdb: null, - pdb: { - dbId: "7AXO", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-!9, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AXO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7axo_final.pdb", - externalLink: "https://pdb-redo.eu/db/7axo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "LAMIXXKAWNLXOC-INIZCTEOSA-N"], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Lieske, J.", - "Ewert, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7axo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7axo", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530718726", - emdb: null, - pdb: { - dbId: "7S3K", - method: "X-RAY DIFFRACTION", - keywords: - "enzyme-inhibitor complex, cysteine protease, homodimer, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S3K", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s3k_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s3k", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UFUGOWGYSILVPI-UHFFFAOYSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35434531", - title: - "Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.", - journal: "Acs Pharmacol Transl Sci 5: 255-265 (2022), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00026", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35434531", - pubDate: "2022", - abstract: "", - authors: [ - "Glaser, J. (0000-0003-1852-3849)", - "Sedova, A.", - "Galanie, S. (0000-0001-5712-2568)", - "Kneller, D.W.", - "Davidson, R.B.", - "Maradzike, E.", - "Del Galdo, S.", - "Labbe, A.", - "Hsu, D.J.", - "Agarwal, R.", - "Bykov, D.", - "Tharrington, A.", - "Parks, J.M. (0000-0002-3103-9333)", - "Smith, D.M.A.", - "Daidone, I. (0000-0001-8970-8408)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A.", - "Smith, J.C. (0000-0002-2978-3227)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s3k_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s3k", - }, - }, - { - title: - "Structure of sybody MR17-SR31 fusion in complex with the SARS-CoV-2 S Receptor Binding domain (RBD)", - emdb: null, - pdb: { - dbId: "7D30", - method: "X-RAY DIFFRACTION", - keywords: - "coronavirus, Covid-19, nanobody, neutralizing antibody, receptor binding protein, SARS-CoV-2, S protein, synthetic antibody, VHH., PROTEIN BINDING", - refModels: [ - { - emdbId: null, - pdbId: "7D30", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7d30_final.pdb", - externalLink: "https://pdb-redo.eu/db/7d30", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "32630", - name: "sybody fusion of MR17-SR31 with a GS linker", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: true, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "JLFNLZLINWHATN-UHFFFAOYSA-N", - "PUPZLCDOIYMWBV-BYPYZUCNSA-N", - "WLZRMCYVCSSEQC-UHFFFAOYSA-N", - ], - dbauthors: ["Li, T.", "Li, D.", "Yao, H.", "Cai, H.", "Qin, W."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33657135", - title: - "A high-affinity RBD-targeting nanobody improves fusion partner's potency against SARS-CoV-2.", - journal: "Plos Pathog. 17: e1009328-e1009328 (2021), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1009328", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33657135", - pubDate: "2021", - abstract: "", - authors: [ - "Yao, H. 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(0000-0002-1241-2577)"], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w79_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w79", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000164777", - emdb: null, - pdb: { - dbId: "5RTW", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RTW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rtw_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rtw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CCVYRRGZDBSHFU-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5ru2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5ru2", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease in complex with PF07321332 in spacegroup P1211", - emdb: null, - pdb: { - dbId: "7VLP", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7VLP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vlp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vlp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Replicase polyprotein 1a", - details: "", - altNames: "pp1a,ORF1a polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Zhang, J.", "Li, J.", "Zhou, X.L.", "Zhong, F.L.", "Lin, C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35389231", - title: - "Structural Basis of the Main Proteases of Coronavirus Bound to Drug Candidate PF-07321332.", - journal: "J.Virol. 96: e0201321-e0201321 (2022), 1098-5514", - doi: "https://doi.org/10.1128/jvi.02013-21", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35389231", - pubDate: "2022", - abstract: "", - authors: [ - "Li, J.", - "Lin, C.", - "Zhou, X.", - "Zhong, F.", - "Zeng, P.", - "Yang, Y.", - "Zhang, Y.", - "Yu, B.", - "Fan, X.", - "McCormick, P.J.", - "Fu, R.", - "Fu, Y.", - "Jiang, H. (0000-0002-1895-3040)", - "Zhang, J. (0000-0002-9705-0033)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vlp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vlp", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 6 (P43 crystal form)", - emdb: null, - pdb: { - dbId: "7TWO", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, room temperature diffraction, protein dynamics, water networks, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TWO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7two_final.pdb", - externalLink: "https://pdb-redo.eu/db/7two", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "MNIGYIKCFSPQRJ-UHFFFAOYSA-N"], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 6 (P43 crystal form)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7two_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7two", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 7 (P43 crystal form)", - emdb: null, - pdb: { - dbId: "7TWX", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, room temperature diffraction, protein dynamics, water networks, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TWX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7twx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7twx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-ZQSHOCFMSA-N"], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 7 (P43 crystal form)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7twx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7twx", - }, - }, - { - title: "SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 93", - emdb: null, - pdb: { - dbId: "7MZJ", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, spike, RBD, human antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7MZJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mzj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mzj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "WCSL 129 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WCSL 129 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "PDI 93 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "PDI 93 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Pymm, P. 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(0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33283984", - title: - "A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*.", - journal: "Chemmedchem 16: 942-948 (2021), 1860-7187", - doi: "https://doi.org/10.1002/cmdc.202000924", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33283984", - pubDate: "2021", - abstract: "", - authors: [ - "Yang, K.S.", - "Ma, X.R.", - "Ma, Y.", - "Alugubelli, Y.R.", - "Scott, D.A.", - "Vatansever, E.C.", - "Drelich, A.K.", - "Sankaran, B.", - "Geng, Z.Z.", - "Blankenship, L.R.", - "Ward, H.E.", - "Sheng, Y.J.", - "Hsu, J.C.", - "Kratch, K.C.", - "Zhao, B.", - "Hayatshahi, H.S.", - "Liu, J.", - "Li, P.", - "Fierke, C.A.", - "Tseng, C.K.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jpy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jpy", - }, - }, - { - title: - "The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 7mer dsRNA", - emdb: null, - pdb: { - dbId: "7ACS", - method: "SOLUTION NMR", - keywords: "protein-RNA complex, docking, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "RNA (5'-R(P*CP*AP*CP*UP*GP*AP*C)-3')", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "RNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3')", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Veverka, V. (0000-0003-3782-5279)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33264373", - title: - "Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein.", - journal: "Plos Pathog. 16: e1009100-e1009100 (2020), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1009100", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33264373", - pubDate: "2020", - abstract: "", - authors: [ - "Dinesh, D.C. (0000-0001-9125-4775)", - "Chalupska, D. (0000-0002-9666-4228)", - "Silhan, J.", - "Koutna, E.", - "Nencka, R. (0000-0001-6167-0380)", - "Veverka, V. (0000-0003-3782-5279)", - "Boura, E. (0000-0002-9652-4065)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7acs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7acs", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with HEPES", - emdb: null, - pdb: { - dbId: "6YWK", - method: "X-RAY DIFFRACTION", - keywords: - 'NSP3, macrodomain, ADP-ribose-1"-phosphatase, ADRP, Covid-19, SARS-COV-2, Structural Genomics, Structural Genomics Consortium, SGC, VIRAL PROTEIN', - refModels: [ - { - emdbId: null, - pdbId: "6YWK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6ywk_final.pdb", - externalLink: "https://pdb-redo.eu/db/6ywk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "NSP3 macrodomain", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "JKMHFZQWWAIEOD-UHFFFAOYSA-N", - ], - dbauthors: [ - "Ni, X.", - "Wang, M.", - "Schroeder, M.", - "Olieric, V.", - "Sharpe, E.M.", - "Wojdyla, J.A.", - "Knapp, S.", - "Chaikuad, A.", - "Structural Genomics Consortium (SGC)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33850605", - title: - "Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain.", - journal: "Acs Med.Chem.Lett. 12: 603-609 (2021), 1948-5875", - doi: "https://doi.org/10.1021/acsmedchemlett.0c00684", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33850605", - pubDate: "2021", - abstract: "", - authors: [ - "Ni, X.", - "Schroder, M.", - "Olieric, V.", - "Sharpe, M.E.", - "Hernandez-Olmos, V.", - "Proschak, E.", - "Merk, D.", - "Knapp, S.", - "Chaikuad, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6ywk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6ywk", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000000922", - emdb: null, - pdb: { - dbId: "5RUE", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RUE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rue_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rue", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WUBBRNOQWQTFEX-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rue_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rue", - }, - }, - { - title: - "Ambient-Temperature Serial Femtosecond X-ray Crystal structure of SARS-CoV-2 Main Protease at 2.1 A Resolution (P212121)", - emdb: null, - pdb: { - dbId: "7CWC", - method: "X-RAY DIFFRACTION", - keywords: - "COVID19, SARS-CoV-2, Drug Target, Serial Femtosecond X-ray Crystallography, SFX, XFEL, Virus Protein, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CWC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cwc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cwc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["DeMirci, H. (0000-0002-9135-5397)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34403647", - title: - "Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing.", - journal: "Structure 29: 1382-1396.e6 (2021), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2021.07.007", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34403647", - pubDate: "2021", - abstract: "", - authors: [ - "Durdagi, S.", - "Dag, C.", - "Dogan, B.", - "Yigin, M.", - "Avsar, T.", - "Buyukdag, C.", - "Erol, I.", - "Ertem, F.B.", - "Calis, S.", - "Yildirim, G.", - "Orhan, M.D.", - "Guven, O.", - "Aksoydan, B.", - "Destan, E.", - "Sahin, K.", - "Besler, S.O.", - "Oktay, L.", - "Shafiei, A.", - "Tolu, I.", - "Ayan, E.", - "Yuksel, B.", - "Peksen, A.B.", - "Gocenler, O.", - "Yucel, A.D.", - "Can, O.", - "Ozabrahamyan, S.", - "Olkan, A.", - "Erdemoglu, E.", - "Aksit, F.", - "Tanisali, G.", - "Yefanov, O.M.", - "Barty, A.", - "Tolstikova, A.", - "Ketawala, G.K.", - "Botha, S.", - "Dao, E.H.", - "Hayes, B.", - "Liang, M.", - "Seaberg, M.H.", - "Hunter, M.S.", - "Batyuk, A.", - "Mariani, V.", - "Su, Z.", - "Poitevin, F.", - "Yoon, C.H.", - "Kupitz, C.", - "Sierra, R.G.", - "Snell, E.H.", - "DeMirci, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cwc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cwc", - }, - }, - { - title: "SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 96", - emdb: null, - pdb: { - dbId: "7MZK", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, spike, RBD, human antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7MZK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mzk_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mzk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "WCSL 129 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WCSL 129 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "PDI 96 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "PDI 96 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SVTOYMIYCMHPIV-UHFFFAOYSA-N", - "KRKNYBCHXYNGOX-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Pymm, P. (0000-0003-2722-4621)", - "Tham, W.H. (0000-0001-7950-8699)", - "Chan, L.J. (0000-0002-9439-3487)", - "Tan, L.L. (0000-0003-0606-4446)", - "Dietrich, M.H. 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(0000-0002-6366-6112)", - "Kutateladze, T.G. (0000-0001-7375-6990)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35716662", - title: - "Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection.", - journal: "Structure 30 (2022), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2022.05.020", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35716662", - pubDate: "2022", - abstract: "", - authors: [ - "Vann, K.R.", - "Acharya, A.", - "Jang, S.M.", - "Lachance, C.", - "Zandian, M.", - "Holt, T.A.", - "Smith, A.L.", - "Pandey, K.", - "Durden, D.L.", - "El-Gamal, D.", - "Cote, J.", - "Byrareddy, S.N.", - "Kutateladze, T.G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tuq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tuq", - }, - }, - { - title: "SARS-CoV-2 3CL protease (3CLpro) in complex with 7-O-methyl-dihydromyricetin", - emdb: null, - pdb: { - dbId: "7DPV", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, 3CLpro, inhibitor, complex, myricetin, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7DPV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dpv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dpv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OEYMPTGVGRACKD-CVEARBPZSA-N"], - dbauthors: ["Li, M.J.", "Xie, H.", "Su, H.X.", "Zhao, W.F.", "Xu, Y.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34131140", - title: - "Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease.", - journal: "Nat Commun 12: 3623-3623 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23751-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34131140", - pubDate: "2021", - abstract: "", - authors: [ - "Su, H. (0000-0002-7174-3851)", - "Yao, S.", - "Zhao, W. (0000-0003-2517-4747)", - "Zhang, Y. (0000-0003-0767-1221)", - "Liu, J. (0000-0002-8167-9750)", - "Shao, Q.", - "Wang, Q. (0000-0003-1028-1267)", - "Li, M.", - "Xie, H.", - "Shang, W.", - "Ke, C.", - "Feng, L.", - "Jiang, X.", - "Shen, J. (0000-0001-9679-9934)", - "Xiao, G.", - "Jiang, H. (0000-0003-0656-6315)", - "Zhang, L. (0000-0002-2593-2571)", - "Ye, Y. (0000-0003-1316-5915)", - "Xu, Y. (0000-0002-1581-6155)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dpv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dpv", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab", - emdb: null, - pdb: { - dbId: "6YLA", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 Spike protein, RBD, CR3022, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6YLA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6yla_final.pdb", - externalLink: "https://pdb-redo.eu/db/6yla", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "OFOBLEOULBTSOW-UHFFFAOYSA-L", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "JLFNLZLINWHATN-UHFFFAOYSA-N", - "SBASXUCJHJRPEV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhao, Y.", - "Zhou, D.", - "Ren, J.", - "Stuart, D.I.", - "Ginn, H.M.", - "Huo, J.", - "Fry, E.E.", - "Owens, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.", - journal: "Cell Host Microbe 28: 445-454.e6 (2020), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2020.06.010", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Huo, J.", - "Zhao, Y.", - "Ren, J.", - "Zhou, D.", - "Duyvesteyn, H.M.E.", - "Ginn, H.M.", - "Carrique, L.", - "Malinauskas, T.", - "Ruza, R.R.", - "Shah, P.N.M.", - "Tan, T.K.", - "Rijal, P.", - "Coombes, N.", - "Bewley, K.R.", - "Tree, J.A.", - "Radecke, J.", - "Paterson, N.G.", - "Supasa, P.", - "Mongkolsapaya, J.", - "Screaton, G.R.", - "Carroll, M.", - "Townsend, A.", - "Fry, E.E.", - "Owens, R.J.", - "Stuart, D.I.", - "Duyvesteyn, H.M.E. (0000-0002-4641-5442)", - "Carrique, L. (0000-0001-5332-8593)", - "Ren, J. (0000-0003-4015-1404)", - "Stuart, D.I. (0000-0002-3426-4210)", - "Fry, E.E. (0000-0001-9754-5303)", - "Zhao, Y. (0000-0001-8916-8552)", - "Malinauskas, T. (0000-0002-4847-5529)", - "Zhou, D. (0000-0002-7188-5243)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6yla_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6yla", - }, - }, - { - title: "The crystal structure of Nsp9 RNA binding protein of SARS CoV-2", - emdb: null, - pdb: { - dbId: "6W4B", - method: "X-RAY DIFFRACTION", - keywords: - "replicase, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, REPLICATION, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6W4B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6w4b_final.pdb", - externalLink: "https://pdb-redo.eu/db/6w4b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 9", - details: "", - altNames: "nsp9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Joachimiak, A. (0000-0003-2535-6209)", - "Maltseva, N.", - "Jedrzejczak, R.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Tan, K. (0000-0002-4003-7903)", - "Michalska, K.", - "Kim, Y. (0000-0002-1610-4889)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of Nsp9 replicase protein of COVID-19", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Tan, K. (0000-0002-4003-7903)", - "Kim, Y. (0000-0002-1610-4889)", - "Jedrzejczak, R.", - "Maltseva, N.", - "Endres, M.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w4b_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w4b", - }, - }, - { - title: "Crystal structure of SARS-Cov-2 main protease with narlaprevir", - emdb: null, - pdb: { - dbId: "7D1O", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, MAIN PROTEASE, Narlaprevir, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7D1O", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7d1o_final.pdb", - externalLink: "https://pdb-redo.eu/db/7d1o", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BZXRATSZUNDEEV-FZFXNXQRSA-N"], - dbauthors: ["Feng, Y.", "Qi, J.X.", "Fu, L.F."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33542181", - title: - "Structural basis for the inhibition of the SARS-CoV-2 main protease by the anti-HCV drug narlaprevir.", - journal: "Signal Transduct Target Ther 6: 51-51 (2021), 2059-3635", - doi: "https://doi.org/10.1038/s41392-021-00468-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33542181", - pubDate: "2021", - abstract: "", - authors: [ - "Bai, Y.", - "Ye, F.", - "Feng, Y.", - "Liao, H.", - "Song, H. (0000-0002-2811-0370)", - "Qi, J.", - "Gao, G.F. (0000-0002-3869-615X)", - "Tan, W.", - "Fu, L. (0000-0003-0431-5424)", - "Shi, Y. (0000-0002-3053-2687)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7d1o_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7d1o", - }, - }, - { - title: - "The crystal structure of COVID-19 main protease in complex with an inhibitor Shikonin", - emdb: null, - pdb: { - dbId: "7CA8", - method: "X-RAY DIFFRACTION", - keywords: "Viral protein, Main Protease, inhibitor", - refModels: [ - { - emdbId: null, - pdbId: "7CA8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ca8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ca8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UNNKKUDWEASWDN-SNVBAGLBSA-N"], - dbauthors: ["Zhang, J.", "Li, J.", "Zhou, X.L.", "Zhong, F.L.", "Lin, C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33163253", - title: - "Crystal structure of SARS-CoV-2 main protease in complex with the natural product inhibitor shikonin illuminates a unique binding mode.", - journal: "Sci Bull (Beijing) 66: 661-663 (2021), 2095-9273", - doi: "https://doi.org/10.1016/j.scib.2020.10.018", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33163253", - pubDate: "2021", - abstract: "", - authors: [ - "Li, J.", - "Zhou, X.", - "Zhang, Y.", - "Zhong, F.", - "Lin, C.", - "McCormick, P.J.", - "Jiang, F.", - "Luo, J.", - "Zhou, H.", - "Wang, Q.", - "Fu, Y.", - "Duan, J.", - "Zhang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ca8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ca8", - }, - }, - { - title: - "The co-crystal structure of SARS-CoV-2 main protease with peptidomimetic inhibitor N-((S)-3-methyl-1-(((S)-4-methyl-1-oxo-1-(((S)-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)amino)pentan-2-yl)amino)-1-oxobutan-2-yl)-2-naphthamide", - emdb: null, - pdb: { - dbId: "7DGH", - method: "X-RAY DIFFRACTION", - keywords: "Complex, inhibitor, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7DGH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dgh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dgh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VUMQTHGFOAZOLH-GKXKVECMSA-N"], - dbauthors: ["Shang, L.Q. (0000-0003-4424-3162)", "Wang, H. (0000-0002-1916-7092)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35635946", - title: - "The structure-based design of peptidomimetic inhibitors against SARS-CoV-2 3C like protease as Potent anti-viral drug candidate.", - journal: "Eur.J.Med.Chem. 238: 114458-114458 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114458", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35635946", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, H.", - "Pei, R.", - "Li, X.", - "Deng, W.", - "Xing, S.", - "Zhang, Y.", - "Zhang, C.", - "He, S.", - "Sun, H.", - "Xiao, S.", - "Xiong, J.", - "Chen, X.", - "Wang, Y.", - "Guo, Y.", - "Zhang, B.", - "Shang, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dgh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dgh", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C7", - emdb: null, - pdb: { - dbId: "7MLF", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, 3CLpro, covalent inhibitor, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7MLF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mlf_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mlf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FMBPORSTYBRWAD-HSZRJFAPSA-N"], - dbauthors: [ - "Wang, G.", - "Sharon, I.", - "Stille, J.", - "Tjutrins, J.", - "Venegas, F.A.", - "Hennecker, C.", - "Rueda, A.M.", - "Miron, C.E.", - "Pinus, S.", - "Labarre, A.", - "Patrascu, M.B.", - "Vlaho, D.", - "Huot, M.", - "Mittermaier, A.K.", - "Moitessier, N.", - "Schmeing, T.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34995923", - title: - "Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors.", - journal: "Eur.J.Med.Chem. 229: 114046-114046 (2021), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2021.114046", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34995923", - pubDate: "2021", - abstract: "", - authors: [ - "Stille, J.K.", - "Tjutrins, J.", - "Wang, G.", - "Venegas, F.A.", - "Hennecker, C.", - "Rueda, A.M.", - "Sharon, I.", - "Blaine, N.", - "Miron, C.E.", - "Pinus, S.", - "Labarre, A.", - "Plescia, J.", - "Burai Patrascu, M.", - "Zhang, X.", - "Wahba, A.S.", - "Vlaho, D.", - "Huot, M.J.", - "Schmeing, T.M.", - "Mittermaier, A.K.", - "Moitessier, N.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mlf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mlf", - }, - }, - { - title: - "Structure of sybody MR17-K99Y in complex with the SARS-CoV-2 S Receptor-binding domain (RBD)", - emdb: null, - pdb: { - dbId: "7CAN", - method: "X-RAY DIFFRACTION", - keywords: - "coronavirus, Covid-19, nanobody, neutralizing antibody, receptor binding protein, SARS-CoV-2, S protein, synthetic antibody, VHH., PROTEIN BINDING", - refModels: [ - { - emdbId: null, - pdbId: "7CAN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7can_final.pdb", - externalLink: "https://pdb-redo.eu/db/7can", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "32630", - name: "sybody MR17-K99Y", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: true, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Li, T.", "Li, D.", "Yao, H.", "Cai, H.", "Qin, W."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34330908", - title: - "A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection.", - journal: "Nat Commun 12: 4635-4635 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-24905-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34330908", - pubDate: "2021", - abstract: "", - authors: [ - "Li, T. (0000-0003-3146-2761)", - "Cai, H. (0000-0001-7221-8330)", - "Yao, H. (0000-0002-8588-5877)", - "Zhou, B. (0000-0002-7753-4065)", - "Zhang, N.", - "van Vlissingen, M.F. (0000-0003-2213-5910)", - "Kuiken, T. (0000-0001-5501-9049)", - "Han, W.", - "GeurtsvanKessel, C.H. (0000-0002-7678-314X)", - "Gong, Y.", - "Zhao, Y. (0000-0001-7738-6181)", - "Shen, Q.", - "Qin, W.", - "Tian, X.X.", - "Peng, C. (0000-0002-6814-2676)", - "Lai, Y.", - "Wang, Y.", - "Hutter, C.A.J. (0000-0002-8920-3343)", - "Kuo, S.M. (0000-0002-4437-689X)", - "Bao, J.", - "Liu, C.", - "Richard, A.S. (0000-0002-0207-0139)", - "Raoul, H. (0000-0002-4241-3255)", - "Lan, J.", - "Seeger, M.A. (0000-0003-1761-8571)", - "Cong, Y. (0000-0002-7164-8694)", - "Rockx, B. (0000-0003-2463-027X)", - "Wong, G. (0000-0002-9044-8153)", - "Bi, Y. (0000-0002-5595-363X)", - "Lavillette, D. (0000-0002-4706-1519)", - "Li, D. (0000-0003-4729-4678)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7can_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7can", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant C44S at 2.12 A resolution", - emdb: null, - pdb: { - dbId: "7ZB6", - method: "X-RAY DIFFRACTION", - keywords: "SARS-COV-2, MPRO, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7ZB6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zb6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zb6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Paknia, E. (0000-0002-9228-6215)", - "Rabe von Pappenheim, F. (0000-0002-3925-8127)", - "Funk, L.-M. (0000-0003-2443-691X)", - "Tittmann, K. (0000-0001-7891-7108)", - "Chari, A. (0000-0001-6220-9828)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Redox regulation of the SARS-CoV-2 main protease provides new opportunities for drug design", - journal: "Biorxiv (2022)", - doi: "https://doi.org/10.1101/2022.04.18.487732", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Funk, L.M.", - "Poschmann, G.", - "Chari, A.", - "von Pappenheim, F.R.", - "Stegmann, K.M.", - "Dickmanns, A.", - "Eulig, N.", - "Wensien, M.", - "Paknia, E.", - "Heyne, G.", - "Penka, E.", - "Pearson, A.R.", - "Berndt, C.", - "Fritz, T.", - "Bazzi, S.", - "Uranga, J.", - "Mata, R.A.", - "Dobbelstein, M.", - "Hilgenfeld, R.", - "Curth, U.", - "Tittmann, K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zb6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zb6", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z24758179", - emdb: null, - pdb: { - dbId: "5RMC", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RMC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rmc_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rmc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "UQIOKJVVJMHUTP-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. 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(0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. 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(0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rlp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rlp", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder496 inhibitor", - emdb: null, - pdb: { - dbId: "7KOL", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7KOL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kol_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kol", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "UTAGJMUNTWRPTE-IKMPRTQCSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder496", - journal: "to be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Lisnyak, V.", - "Maki, S.", - "Taylor, C.", - "Zhang, Y.", - "Zhou, Z.", - "Azizi, S.A.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - "Dickinson, B.C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kol_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kol", - }, - }, - { - title: - "Crystal structure of synthetic nanobody (Sb45+Sb68) complexes with SARS-CoV-2 receptor binding domain", - emdb: null, - pdb: { - dbId: "7KLW", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Spike Protein, Receptor Binding Domain, RBD, Antibody, Nanobody, Sybody, Complex, Neutralization, VIRAL PROTEIN, Epitope", - refModels: [ - { - emdbId: null, - pdbId: "7KLW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7klw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7klw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "32630", - name: "SB45, Synthetic Nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: true, - }, - { - uniprotAcc: null, - organism: "32630", - name: "SB68, Synthetic nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: true, - }, - ], - ligands: [], - dbauthors: [ - "Jiang, J. (0000-0003-0964-5481)", - "Ahmad, J. (0000-0002-3269-1518)", - "Natarajan, K. (0000-0002-6295-2571)", - "Boyd, L.F. (0000-0002-5126-6250)", - "Margulies, D.H. (0000-0001-8530-7375)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34537245", - title: - "Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.", - journal: "J.Biol.Chem. 297: 101202-101202 (2021), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2021.101202", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34537245", - pubDate: "2021", - abstract: "", - authors: [ - "Ahmad, J.", - "Jiang, J.", - "Boyd, L.F.", - "Zeher, A.", - "Huang, R.", - "Xia, D.", - "Natarajan, K.", - "Margulies, D.H.", - "Ahmad, J. (0000-0002-3269-1518)", - "Jiang, J. (0000-0003-0964-5481)", - "Boyd, L.F. (0000-0002-5126-6250)", - "Natarajan, K. (0000-0002-6295-2571)", - "Margulies, D.H. (0000-0001-8530-7375)", - ], - }, - { - pmID: "33532775", - title: - "Synthetic nanobody-SARS-CoV-2 receptor-binding domain structures identify distinct epitopes.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.01.27.428466", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33532775", - pubDate: "2021", - abstract: "", - authors: [ - "Ahmad, J.", - "Jiang, J.", - "Boyd, L.F.", - "Zeher, A.", - "Huang, R.", - "Xia, D.", - "Natarajan, K.", - "Margulies, D.H.", - "Ahmad, J. (0000-0002-3269-1518)", - "Jiang, J. (0000-0003-0964-5481)", - "Boyd, L.F. (0000-0002-5126-6250)", - "Natarajan, K. (0000-0002-6295-2571)", - "Margulies, D.H. (0000-0001-8530-7375)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7klw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7klw", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z102768020", - emdb: null, - pdb: { - dbId: "5S3O", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3O", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3o_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3o", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SZXULAAYIBSASF-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3o_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3o", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z445856640", - emdb: null, - pdb: { - dbId: "5S2K", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S2K", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s2k_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s2k", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RMWFRPZNASSVCZ-MRVPVSSYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s2k_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s2k", - }, - }, - { - title: - "1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 3b (deuterated analog of inhibitor 2a)", - emdb: null, - pdb: { - dbId: "7LKU", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LKU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lku_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lku", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PGYROSRJIVXTOE-HATFLPCOSA-N", "PGYROSRJIVXTOE-HCKQHCFMSA-N"], - dbauthors: [ - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Rathnayake, A.D.", - "Baird, M.A.", - "Shadipeni, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34213885", - title: - "Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease.", - journal: "J.Med.Chem. 64: 10047-10058 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00319", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34213885", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Kim, Y.", - "Bickmeier, N.", - "Rathnayake, A.D.", - "Nguyen, H.N.", - "Zheng, J.", - "Kashipathy, M.M.", - "Baird, M.A.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lku_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lku", - }, - }, - { - title: "Viral protease", - emdb: null, - pdb: { - dbId: "7E6K", - method: "X-RAY DIFFRACTION", - keywords: "protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7E6K", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e6k_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e6k", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "GZNWNJDVFSIFLF-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: ["Zhao, Y.", "Rao, Z.H.", "Zhang, Q.", "Yang, H.T."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Viral protease", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zhao, Y.", "Zhang, Q.", "Yang, H.T.", "Rao, Z.H."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e6k_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e6k", - }, - }, - { - title: "SARS-CoV-2 Spike Protein N terminal domain in Complex with N11 Fab", - emdb: null, - pdb: { - dbId: "7E7X", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Spike, NTD, Antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7E7X", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e7x_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e7x", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "N11 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "N11 Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Xiao, J.", "Zhang, Z.", "Shuo, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34021265", - title: - "Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines.", - 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(0000-0001-5918-1078)", - "Yisimayi, A.", - "Bai, Y.", - "Huang, W. (0000-0002-4246-8889)", - "Li, X.", - "Zhang, Z.", - "Yuan, T.", - "An, R.", - "Wang, J.", - "Xiao, T.", - "Du, S.", - "Ma, W.", - "Song, L.", - "Li, Y.", - "Song, W.", - "Wu, J.", - "Liu, S.", - "Zhang, Y.", - "Su, B.", - "Guo, X.", - "Wei, Y. (0000-0002-2363-4941)", - "Gao, C. (0000-0002-7654-9476)", - "Zhang, N.", - "Dou, Y.", - "Xu, X.", - "Shi, R.", - "Lu, B.", - "Jin, R.", - "Ma, Y.", - "Qin, C.", - "Wang, Y. (0000-0001-9769-5141)", - "Feng, Y. (0000-0001-5248-0155)", - "Xiao, J. (0000-0003-1822-1701)", - "Xie, X.S. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s39_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s39", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with EN300-108952", - emdb: null, - pdb: { - dbId: "5S1G", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S1G", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s1g_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s1g", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YZWSTKQAGIQVJK-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s1g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s1g", - }, - }, - { - title: - "SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals Grown with 40 nL Acoustically Ejected Mpro Droplets at 1.48 A Resolution (Cryo-protected)", - emdb: null, - pdb: { - dbId: "7K6D", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Main Protease, 3CLpro/Mpro, Telaprevir, VIRAL PROTEIN, Acoustic Drop Ejection, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7K6D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k6d_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k6d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "FTZGWEAUHOMNIG-FJRGXGLZSA-N"], - dbauthors: [ - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Shi, W.", - "McSweeney, S. (0000-0002-3758-3161)", - "Fuchs, M.R.", - "Soares, A.S.", - "Jakoncic, J.", - "Keereetaweep, J.", - "Shanklin, J.", - "Kreitler, D.F. (0000-0003-4758-7913)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35842458", - title: - "Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.", - journal: "Sci Rep 12: 12197-12197 (2022), 2045-2322", - doi: "https://doi.org/10.1038/s41598-022-15930-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35842458", - pubDate: "2022", - abstract: "", - authors: [ - "Andi, B.", - "Kumaran, D.", - "Kreitler, D.F.", - "Soares, A.S.", - "Keereetaweep, J.", - "Jakoncic, J.", - "Lazo, E.O.", - "Shi, W.", - "Fuchs, M.R.", - "Sweet, R.M.", - "Shanklin, J.", - "Adams, P.D.", - "Schmidt, J.G.", - "Head, M.S.", - "McSweeney, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k6d_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k6d", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 S RBD in complex with BD-508 Fab", - emdb: null, - pdb: { - dbId: "7E86", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Antibody, VIRAL PROTEIN, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7E86", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e86_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e86", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-508 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BD-508 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Xiao, J. (0000-0003-1822-1701)", "Gao, C. (0000-0003-2128-376X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34021265", - title: - "Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines.", - journal: "Cell Res. 31: 732-741 (2021), 1001-0602", - doi: "https://doi.org/10.1038/s41422-021-00514-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34021265", - pubDate: "2021", - abstract: "", - authors: [ - "Cao, Y. (0000-0001-5918-1078)", - "Yisimayi, A.", - "Bai, Y.", - "Huang, W. (0000-0002-4246-8889)", - "Li, X.", - "Zhang, Z.", - "Yuan, T.", - "An, R.", - "Wang, J.", - "Xiao, T.", - "Du, S.", - "Ma, W.", - "Song, L.", - "Li, Y.", - "Song, W.", - "Wu, J.", - "Liu, S.", - "Zhang, Y.", - "Su, B.", - "Guo, X.", - "Wei, Y. (0000-0002-2363-4941)", - "Gao, C. (0000-0002-7654-9476)", - "Zhang, N.", - "Dou, Y.", - "Xu, X.", - "Shi, R.", - "Lu, B.", - "Jin, R.", - "Ma, Y.", - "Qin, C.", - "Wang, Y. (0000-0001-9769-5141)", - "Feng, Y. (0000-0001-5248-0155)", - "Xiao, J. (0000-0003-1822-1701)", - "Xie, X.S. (0000-0001-9281-5239)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e86_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e86", - }, - }, - { - title: "Crystal structure of CoV-2 Nsp3 Macrodomain complex with PARG345", - emdb: null, - pdb: { - dbId: "7LG7", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE, SARS-CoV-2, macrodomain", - refModels: [ - { - emdbId: null, - pdbId: "7LG7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lg7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lg7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JUFGUKJIZDHLKW-UHFFFAOYSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Arvai, A. 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(0000-0002-8086-1753)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33636189", - title: - "Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors.", - journal: "Prog.Biophys.Mol.Biol. 163: 171-186 (2021), 0079-6107", - doi: "https://doi.org/10.1016/j.pbiomolbio.2021.02.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33636189", - pubDate: "2021", - abstract: "", - authors: [ - "Brosey, C.A.", - "Houl, J.H.", - "Katsonis, P.", - "Balapiti-Modarage, L.P.F.", - "Bommagani, S.", - "Arvai, A.", - "Moiani, D.", - "Bacolla, A.", - "Link, T.", - "Warden, L.S.", - "Lichtarge, O.", - "Jones, D.E.", - "Ahmed, Z.", - "Tainer, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lg7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lg7", - }, - }, - { - title: "SARS-CoV-2 Main protease immature form - F2X Entry Library E03 fragment", - emdb: null, - pdb: { - dbId: "7LFE", - method: "X-RAY DIFFRACTION", - keywords: "3cl, protease, sars, sars-cov-2, covid, main protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7LFE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lfe_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lfe", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "OYDNXLZZNODBTK-NXEZZACHSA-N", - ], - dbauthors: [ - "Noske, G.D.", - "Oliva, G.", - "Godoy, A.S.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Lima, G.M.A.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34174328", - title: - "A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.", - journal: "J.Mol.Biol. 433: 167118-167118 (2021), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2021.167118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34174328", - pubDate: "2021", - abstract: "", - authors: [ - "Noske, G.D.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Lima, G.M.A.", - "Rosa, H.V.D.", - "Pereira, H.D.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "Freire, M.C.L.C.", - "Fearon, D.", - "Douangamath, A.", - "von Delft, F.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lfe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lfe", - }, - }, - { - title: "SARS-CoV2 RBD bound to Fab06", - emdb: null, - pdb: { - dbId: "7WPH", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-Cov2 RBD, antibody, PROTEIN BINDING, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7WPH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wph_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wph", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "FAB06 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab06 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Lin, J.Q. (0000-0003-4336-9003)", - "Lescar, J. (0000-0002-9623-8130)", - "El Sahili, A. (0000-0003-3973-686X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36138032", - title: - "Engineering SARS-CoV-2 specific cocktail antibodies into a bispecific format improves neutralizing potency and breadth.", - journal: "Nat Commun 13: 5552-5552 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-33284-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36138032", - pubDate: "2022", - abstract: "", - authors: [ - "Ku, Z. (0000-0001-8347-0013)", - "Xie, X. (0000-0003-0918-016X)", - "Lin, J. (0000-0003-4336-9003)", - "Gao, P.", - "Wu, B. (0000-0002-0883-8006)", - "El Sahili, A. (0000-0003-3973-686X)", - "Su, H.", - "Liu, Y.", - "Ye, X. (0000-0002-2300-4739)", - "Tan, E.Y.", - "Li, X.", - "Fan, X.", - "Goh, B.C.", - "Xiong, W.", - "Boyd, H.", - "Muruato, A.E.", - "Deng, H.", - "Xia, H. (0000-0002-2520-7038)", - "Zou, J.", - "Kalveram, B.K.", - "Menachery, V.D. (0000-0001-8803-7606)", - "Zhang, N. (0000-0002-4348-2180)", - "Lescar, J. (0000-0002-9623-8130)", - "Shi, P.Y. (0000-0001-5553-1616)", - "An, Z. (0000-0001-9309-2335)", - "Ku, Z.", - "Xie, X.", - "Lin, J.", - "El Sahili, A.", - "Ye, X.", - "Xia, H.", - "Jing, Z.", - "Menachery, V.D.", - "Zhang, N.", - "Lescar, J.", - "Shi, P.Y.", - "An, Z.", - ], - }, - { - pmID: "35132410", - title: - "Engineering SARS-CoV-2 cocktail antibodies into a bispecific format improves neutralizing potency and breadth.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.02.01.478504", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35132410", - pubDate: "2022", - abstract: "", - authors: [ - "Ku, Z. (0000-0001-8347-0013)", - "Xie, X. (0000-0003-0918-016X)", - "Lin, J. (0000-0003-4336-9003)", - "Gao, P.", - "Wu, B. (0000-0002-0883-8006)", - "El Sahili, A. (0000-0003-3973-686X)", - "Su, H.", - "Liu, Y.", - "Ye, X. (0000-0002-2300-4739)", - "Tan, E.Y.", - "Li, X.", - "Fan, X.", - "Goh, B.C.", - "Xiong, W.", - "Boyd, H.", - "Muruato, A.E.", - "Deng, H.", - "Xia, H. (0000-0002-2520-7038)", - "Zou, J.", - "Kalveram, B.K.", - "Menachery, V.D. (0000-0001-8803-7606)", - "Zhang, N. (0000-0002-4348-2180)", - "Lescar, J. (0000-0002-9623-8130)", - "Shi, P.Y. (0000-0001-5553-1616)", - "An, Z. (0000-0001-9309-2335)", - "Ku, Z.", - "Xie, X.", - "Lin, J.", - "El Sahili, A.", - "Ye, X.", - "Xia, H.", - "Jing, Z.", - "Menachery, V.D.", - "Zhang, N.", - "Lescar, J.", - "Shi, P.Y.", - "An, Z.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wph_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wph", - }, - }, - { - title: "S2P6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide", - emdb: null, - pdb: { - dbId: "7RNJ", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, neutralizing monoclonal antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex, ANTIVIRAL PROTEIN, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7RNJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rnj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rnj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S2P6 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S2P6 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike glycoprotein stem helix peptide", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Snell, G.", - "Veesler, D.", - "Pinto, D.", - "Corti, D.", - "Beltramello, M.", - "Cameroni, E.", - "Czudnochowski, N.", - "Nix, J.C.", - "Croll, T.I.", - "Sauer, M.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34344823", - title: - "Broad betacoronavirus neutralization by a stem helix-specific human antibody.", - journal: "Science 373: 1109-1116 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abj3321", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34344823", - pubDate: "2021", - abstract: "", - authors: [ - "Pinto, D.", - "Sauer, M.M. (0000-0003-0908-0775)", - "Czudnochowski, N. (0000-0002-3146-4110)", - "Low, J.S. (0000-0002-1775-0778)", - "Tortorici, M.A. (0000-0002-2260-2577)", - "Housley, M.P.", - "Noack, J. (0000-0002-9113-8181)", - "Walls, A.C. (0000-0002-9636-8330)", - "Bowen, J.E. (0000-0003-3590-9727)", - "Guarino, B. (0000-0003-3759-3252)", - "Rosen, L.E. (0000-0002-8030-0219)", - "di Iulio, J. (0000-0001-9343-127X)", - "Jerak, J. (0000-0001-5358-5055)", - "Kaiser, H. (0000-0002-3991-7401)", - "Islam, S.", - "Jaconi, S.", - "Sprugasci, N. (0000-0003-3258-5552)", - "Culap, K. (0000-0002-0956-0018)", - "Abdelnabi, R. (0000-0001-9771-7312)", - "Foo, C. (0000-0002-6380-4917)", - "Coelmont, L. (0000-0002-7888-4534)", - "Bartha, I. (0000-0003-3360-1999)", - "Bianchi, S. (0000-0002-5100-8905)", - "Silacci-Fregni, C.", - "Bassi, J. (0000-0002-4723-6892)", - "Marzi, R. (0000-0001-6025-6735)", - "Vetti, E.", - "Cassotta, A. (0000-0001-8674-4294)", - "Ceschi, A. (0000-0002-4308-0405)", - "Ferrari, P. (0000-0002-9619-3104)", - "Cippa, P.E.", - "Giannini, O. (0000-0003-2306-0498)", - "Ceruti, S. (0000-0003-4146-3434)", - "Garzoni, C. (0000-0002-0832-2376)", - "Riva, A. (0000-0003-3171-3049)", - "Benigni, F. (0000-0002-1974-5606)", - "Cameroni, E.", - "Piccoli, L.", - "Pizzuto, M.S.", - "Smithey, M.", - "Hong, D.", - "Telenti, A.", - "Lempp, F.A.", - "Neyts, J.", - "Havenar-Daughton, C.", - "Lanzavecchia, A.", - "Sallusto, F.", - "Snell, G.", - "Virgin, H.W.", - "Beltramello, M.", - "Corti, D.", - "Veesler, D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rnj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rnj", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF THE SARS-COV-2 (2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 4", - emdb: null, - pdb: { - dbId: "7L10", - method: "X-RAY DIFFRACTION", - keywords: "NOVEL CORONAVIRUS, ANTIVIRAL, DRUG DESIGN, VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7L10", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l10_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l10", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KXGLBZMRWKVPSY-UHFFFAOYSA-N"], - dbauthors: [ - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Stone, E.A. (0000-0002-2253-3452)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33786375", - title: - "Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations.", - journal: "Acs Cent.Sci. 7: 467-475 (2021), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.1c00039", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33786375", - pubDate: "2021", - abstract: "", - authors: [ - "Zhang, C.H.", - "Stone, E.A.", - "Deshmukh, M.", - "Ippolito, J.A.", - "Ghahremanpour, M.M.", - "Tirado-Rives, J.", - "Spasov, K.A.", - "Zhang, S.", - "Takeo, Y.", - "Kudalkar, S.N.", - "Liang, Z.", - "Isaacs, F.", - "Lindenbach, B.", - "Miller, S.J.", - "Anderson, K.S.", - "Jorgensen, W.L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l10_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l10", - }, - }, - { - title: - "Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7KAG", - method: "X-RAY DIFFRACTION", - keywords: - "VIRAL PROTEIN, SARS-COV-2, NON-STRUCTURAL PROTEIN, NSP3, UBIQUITIN-LIKE DOMAIN, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, NIAID", - refModels: [ - { - emdbId: null, - pdbId: "7KAG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kag_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kag", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Kim, Y.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Satchell, K.J.F.", - "Chang, C.", - "Stogios, P.J.", - "Skarina, T.", - "Di Leo, R.", - "Savchenko, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of the ubiquitin-like domain 1 (Ubl1) of Nsp3 from SARS-CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Stogios, P.J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kag_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kag", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166Q Mutant", - emdb: null, - pdb: { - dbId: "8D4N", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, Mutation, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8D4N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8d4n_final.pdb", - externalLink: "https://pdb-redo.eu/db/8d4n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36119652", - title: - "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.28.497978", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36119652", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, Y.", - "Lewandowski, E.M.", - "Tan, H.", - "Zhang, X.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Butler, S.G.", - "Gongora, M.V.", - "Choy, J.", - "Deng, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8d4n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8d4n", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir", - emdb: null, - pdb: { - dbId: "8DCZ", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, Mutation, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DCZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dcz_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dcz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36119652", - title: - "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.28.497978", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36119652", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, Y.", - "Lewandowski, E.M.", - "Tan, H.", - "Zhang, X.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Butler, S.G.", - "Gongora, M.V.", - "Choy, J.", - "Deng, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dcz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dcz", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z1039058598", - emdb: null, - pdb: { - dbId: "5SQZ", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SQZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sqz_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sqz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DZWJUUHHWFVLBE-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sra_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sra", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINCoD000001aHBe", - emdb: null, - pdb: { - dbId: "5SSE", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SSE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sse_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sse", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XCWBRJUZKURZCA-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sse_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sse", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2", - emdb: null, - pdb: { - dbId: "6M0J", - method: "X-RAY DIFFRACTION", - keywords: "spike, receptor binding, VIRAL PROTEIN-HYDROLASE complex", - refModels: [ - { - emdbId: null, - pdbId: "6M0J", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6m0j_final.pdb", - externalLink: "https://pdb-redo.eu/db/6m0j", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: ["Wang, X.", "Ge, J.", "Yu, J.", "Shan, S.", "Lan, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32225176", - title: - "Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.", - journal: "Nature 581: 215-220 (2020), 1476-4687", - doi: "https://doi.org/10.1038/s41586-020-2180-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32225176", - pubDate: "2020", - abstract: "", - authors: [ - "Lan, J.", - "Ge, J.", - "Yu, J.", - "Shan, S.", - "Zhou, H.", - "Fan, S.", - "Zhang, Q.", - "Shi, X.", - "Wang, Q.", - "Zhang, L.", - "Wang, X.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6m0j_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6m0j", - }, - }, - { - title: "SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01", - emdb: null, - pdb: { - dbId: "7RTD", - method: "X-RAY DIFFRACTION", - keywords: - "human leukocyte antigen, major histocompatibility complex, HLA-A2, HLA-A*02:01, YLQPRTFLL, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7RTD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rtd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rtd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q53Z42", - organism: "9606", - name: "HLA class I antigen", - details: "", - altNames: - "HLA class I histocompatibility antigen,HLA class I histocompatibility antigen A alpha chain,A alpha chain,MHC class I antigen,MHC class I protein,MHC class I protein (HLA-A)", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Szeto, C. 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sr7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sr7", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5459166300", - emdb: null, - pdb: { - dbId: "5SSR", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SSR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5ssr_final.pdb", - externalLink: "https://pdb-redo.eu/db/5ssr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XGVGMKBKRWQGTN-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5ssr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5ssr", - }, - }, - { - title: "Crystal structure of the 2019-nCoV main protease", - emdb: null, - pdb: { - dbId: "7BRO", - method: "X-RAY DIFFRACTION", - keywords: "2019-nCoV main protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7BRO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bro_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bro", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Fu, L.F."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32887884", - title: - "Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease.", - journal: "Nat Commun 11: 4417-4417 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18233-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32887884", - pubDate: "2020", - abstract: "", - authors: [ - "Fu, L. 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(0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35779291", - title: - "A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114570-114570 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114570", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35779291", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, Y.", - "Yang, K.S.", - "Geng, Z.Z.", - "Alugubelli, Y.R.", - "Shaabani, N.", - "Vatansever, E.C.", - "Ma, X.R.", - "Cho, C.C.", - "Khatua, K.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rvn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rvn", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with REAL250003296134 - (R) isomer", - emdb: null, - pdb: { - dbId: "5SPK", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SPK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5spk_final.pdb", - externalLink: "https://pdb-redo.eu/db/5spk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JURSYTNKCJMCTM-MRVPVSSYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sqx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sqx", - }, - }, - { - title: "H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex", - emdb: null, - pdb: { - dbId: "6Z2M", - method: "X-RAY DIFFRACTION", - keywords: "Antibody, nanobody complex, rbd, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6Z2M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6z2m_final.pdb", - externalLink: "https://pdb-redo.eu/db/6z2m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CR3022 antibody", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "nanobody D4", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Ren, J. (0000-0003-4015-1404)", - "Stuart, D.I. (0000-0002-3426-4210)", - "Naismith, J.H. (0000-0001-6744-5061)", - "Zhao, Y. (0000-0001-8916-8552)", - "Zhou, D. (0000-0002-7188-5243)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structural characterisation of a nanobody derived from a naive library that neutralises SARS-CoV-2", - journal: "To Be Published (2020)", - doi: "", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: ["Naismith, J.H. (0000-0001-6744-5061)"], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6z2m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6z2m", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI25", - emdb: null, - pdb: { - dbId: "7RVY", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, main protease, reversible covalent inhibitors, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RVY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rvy_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rvy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NMIBOPATDHUKKK-BFDHNVDPSA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35779291", - title: - "A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114570-114570 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114570", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35779291", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, Y.", - "Yang, K.S.", - "Geng, Z.Z.", - "Alugubelli, Y.R.", - "Shaabani, N.", - "Vatansever, E.C.", - "Ma, X.R.", - "Cho, C.C.", - "Khatua, K.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rvy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rvy", - }, - }, - { - title: "SARS-CoV-2 YLQ peptide-specific TCR pYLQ7 binds to YLQ-HLA-A2", - emdb: null, - pdb: { - dbId: "7N1F", - method: "X-RAY DIFFRACTION", - keywords: "TCR-pMHC, SARS-CoV-2, SPIKE, YLQ, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7N1F", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n1f_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n1f", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "pYLQ7 T cell receptor alpha chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "pYLQ7 T cell receptor beta chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "A0A5B8RNS7", - organism: "9606", - name: "MHC class I antigen, A-2 alpha chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wu, D. 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(0000-0003-4459-9142)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rnh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rnh", - }, - }, - { - title: - "Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2", - emdb: null, - pdb: { - dbId: "6XDH", - method: "X-RAY DIFFRACTION", - keywords: - "SSGCID, endoribonuclease, nsp15, COVID-19, SARS-CoV-2, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, VIRAL PROTEIN, Hydrolase-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "6XDH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xdh_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xdh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "KRKNYBCHXYNGOX-UHFFFAOYSA-N", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Seattle Structural Genomics Center for Infectious Disease (SSGCID)", - "Seattle Structural Genomics Center for Infectious Disease", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2", - journal: "to be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Dranow, D.M.", - "Abendroth, J.", - "Lorimer, D.D.", - "Horanyi, P.S.", - "Edwards, T.E.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xdh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xdh", - }, - }, - { - title: "SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment", - emdb: null, - pdb: { - dbId: "7LDX", - method: "X-RAY DIFFRACTION", - keywords: "3cl, protease, sars, sars-cov-2, covid, main protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7LDX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ldx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ldx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "HCBGIBWAPOFRKI-PBWFPOADSA-N", - ], - dbauthors: [ - "Noske, G.D.", - "Oliva, G.", - "Godoy, A.S.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Lima, G.M.A.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34174328", - title: - "A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.", - journal: "J.Mol.Biol. 433: 167118-167118 (2021), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2021.167118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34174328", - pubDate: "2021", - abstract: "", - authors: [ - "Noske, G.D.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Lima, G.M.A.", - "Rosa, H.V.D.", - "Pereira, H.D.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "Freire, M.C.L.C.", - "Fearon, D.", - "Douangamath, A.", - "von Delft, F.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ldx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ldx", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 14", - emdb: null, - pdb: { - dbId: "7L12", - method: "X-RAY DIFFRACTION", - keywords: "NOVEL CORONAVIRUS, ANTIVIRAL, DRUG DESIGN, VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7L12", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l12_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l12", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IVPUTCRGJCQUQU-UHFFFAOYSA-N"], - dbauthors: [ - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - "Zhang, C.H. (0000-0002-4579-9202)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33786375", - title: - "Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations.", - journal: "Acs Cent.Sci. 7: 467-475 (2021), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.1c00039", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33786375", - pubDate: "2021", - abstract: "", - authors: [ - "Zhang, C.H.", - "Stone, E.A.", - "Deshmukh, M.", - "Ippolito, J.A.", - "Ghahremanpour, M.M.", - "Tirado-Rives, J.", - "Spasov, K.A.", - "Zhang, S.", - "Takeo, Y.", - "Kudalkar, S.N.", - "Liang, Z.", - "Isaacs, F.", - "Lindenbach, B.", - "Miller, S.J.", - "Anderson, K.S.", - "Jorgensen, W.L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l12_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l12", - }, - }, - { - title: "SARS-CoV-2 Main protease immature form - F2X Entry Library G05 fragment", - emdb: null, - pdb: { - dbId: "7LFP", - method: "X-RAY DIFFRACTION", - keywords: "3cl, protease, sars, sars-cov-2, covid, main protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7LFP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lfp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lfp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "CIBUQXSYGPGEGX-UHFFFAOYSA-N", - ], - dbauthors: [ - "Noske, G.D.", - "Oliva, G.", - "Godoy, A.S.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Lima, G.M.A.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34174328", - title: - "A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.", - journal: "J.Mol.Biol. 433: 167118-167118 (2021), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2021.167118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34174328", - pubDate: "2021", - abstract: "", - authors: [ - "Noske, G.D.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Lima, G.M.A.", - "Rosa, H.V.D.", - "Pereira, H.D.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "Freire, M.C.L.C.", - "Fearon, D.", - "Douangamath, A.", - "von Delft, F.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lfp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lfp", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with POB0140", - emdb: null, - pdb: { - dbId: "5S3Z", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3z_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RNGNQMRREZVUSH-RYUDHWBXSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3z", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-270", - emdb: null, - pdb: { - dbId: "6XKP", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Antibody, Spike, Coronavirus, COVID-19, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "6XKP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xkp_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xkp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV07-270 Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV07-270 Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Liu, H. (0000-0002-2412-7853)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. (0000-0001-9754-4503)", - "Wu, N.C. (0000-0002-9078-6697)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33058755", - title: - "A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.", - journal: "Cell 183 (2020), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2020.09.049", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33058755", - pubDate: "2020", - abstract: "", - authors: [ - "Kreye, J.", - "Reincke, S.M.", - "Kornau, H.C.", - "Sanchez-Sendin, E.", - "Corman, V.M.", - "Liu, H.", - "Yuan, M.", - "Wu, N.C.", - "Zhu, X.", - "Lee, C.D.", - "Trimpert, J.", - "Holtje, M.", - "Dietert, K.", - "Stoffler, L.", - "von Wardenburg, N.", - "van Hoof, S.", - "Homeyer, M.A.", - "Hoffmann, J.", - "Abdelgawad, A.", - "Gruber, A.D.", - "Bertzbach, L.D.", - "Vladimirova, D.", - "Li, L.Y.", - "Barthel, P.C.", - "Skriner, K.", - "Hocke, A.C.", - "Hippenstiel, S.", - "Witzenrath, M.", - "Suttorp, N.", - "Kurth, F.", - "Franke, C.", - "Endres, M.", - "Schmitz, D.", - "Jeworowski, L.M.", - "Richter, A.", - "Schmidt, M.L.", - "Schwarz, T.", - "Muller, M.A.", - "Drosten, C.", - "Wendisch, D.", - "Sander, L.E.", - "Osterrieder, N.", - "Wilson, I.A.", - "Pruss, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xkp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xkp", - }, - }, - { - title: - "Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C102", - emdb: null, - pdb: { - dbId: "7K8M", - method: "X-RAY DIFFRACTION", - keywords: - "Human Neutralizing Antibody, SARS-CoV-2, Receptor Binding Domain, COVID-19, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7K8M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k8m_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k8m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "C102 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "C102 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Bjorkman, P.J.", "Barnes, C.O.", "Jette, C.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33045718", - title: - "SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.", - journal: "Nature 588: 682-687 (2020), 1476-4687", - doi: "https://doi.org/10.1038/s41586-020-2852-1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33045718", - pubDate: "2020", - abstract: "", - authors: [ - "Barnes, C.O.", - "Jette, C.A.", - "Abernathy, M.E.", - "Dam, K.A.", - "Esswein, S.R.", - "Gristick, H.B.", - "Malyutin, A.G.", - "Sharaf, N.G.", - "Huey-Tubman, K.E.", - "Lee, Y.E.", - "Robbiani, D.F.", - "Nussenzweig, M.C.", - "West Jr., A.P.", - "Bjorkman, P.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k8m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k8m", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with AB-601_30915014", - emdb: null, - pdb: { - dbId: "5S1E", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S1E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s1e_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s1e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WXPLRSVMGRAIGW-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s1e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s1e", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z45656995", - emdb: null, - pdb: { - dbId: "5S3M", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3m_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DVCWUTSWCVQZSC-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3m", - }, - }, - { - title: - "1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 3d (deuterated analog of inhibitor 3c)", - emdb: null, - pdb: { - dbId: "7LKW", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LKW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lkw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lkw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ZIWRGXZFSGDQST-REFFYEJJSA-N", - "ZIWRGXZFSGDQST-UIEASHSYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Rathnayake, A.D.", - "Baird, M.A.", - "Shadipeni, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34213885", - title: - "Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease.", - journal: "J.Med.Chem. 64: 10047-10058 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00319", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34213885", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Kim, Y.", - "Bickmeier, N.", - "Rathnayake, A.D.", - "Nguyen, H.N.", - "Zheng, J.", - "Kashipathy, M.M.", - "Baird, M.A.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lkw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lkw", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z57299529", - emdb: null, - pdb: { - dbId: "5S2I", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S2I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s2i_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s2i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OWETVOGOOABRTJ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rug_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rug", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000006490906", - emdb: null, - pdb: { - dbId: "5RTC", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RTC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rtc_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rtc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XRGHQBXKSHAQRB-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rtc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rtc", - }, - }, - { - title: - "Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication", - emdb: null, - pdb: { - dbId: "6WTJ", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, 3CLpro, coronavirus, main protease, kinetics, SARS, VIRAL PROTEIN, Hydrolase-Hydrolase Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "6WTJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wtj_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wtj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: [ - "Khan, M.B. (0000-0002-4164-9573)", - "Lemieux, M.J. (0000-0003-4745-9153)", - "Arutyunova, E.", - "Young, H.S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli O103:H2 str. 12009", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32855413", - title: - "Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication.", - journal: "Nat Commun 11: 4282-4282 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18096-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32855413", - pubDate: "2020", - abstract: "", - authors: [ - "Vuong, W. (0000-0002-3439-8788)", - "Khan, M.B. (0000-0002-4164-9573)", - "Fischer, C. (0000-0002-2289-010X)", - "Arutyunova, E.", - "Lamer, T. (0000-0002-1511-4540)", - "Shields, J. (0000-0003-4701-4576)", - "Saffran, H.A.", - "McKay, R.T. (0000-0002-0255-159X)", - "van Belkum, M.J. (0000-0002-9296-6069)", - "Joyce, M.A. (0000-0002-9173-7299)", - "Young, H.S.", - "Tyrrell, D.L. (0000-0002-0983-7267)", - "Vederas, J.C. (0000-0002-2996-0326)", - "Lemieux, M.J. (0000-0003-4745-9153)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wtj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wtj", - }, - }, - { - title: - "Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at 293 K (C2 crystal form)", - emdb: null, - pdb: { - dbId: "7TX5", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, room temperature diffraction, protein dynamics, water networks, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TX5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tx5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tx5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-KEOHHSTQSA-N"], - dbauthors: [ - "Kovalevsky, A. (0000-0003-4459-9142)", - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at 293 K (C2 crystal form)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tx5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tx5", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to RS102895", - emdb: null, - pdb: { - dbId: "7ABU", - method: "X-RAY DIFFRACTION", - keywords: "inhibitor, complex, screen, sars-cov-2, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ABU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7abu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7abu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "HIDWEYPGMLIQSN-UHFFFAOYSA-N", - "RAXXELZNTBOGNW-UHFFFAOYSA-O", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Reinke, P.Y.A.", - "Lieske, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7abu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7abu", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 RBD in complex with the ultrapotent antibody CV2.1169 and CR3022", - emdb: null, - pdb: { - dbId: "7QEZ", - method: "X-RAY DIFFRACTION", - keywords: "neutralization, antibody, coronavirus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7QEZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qez_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qez", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CR3022 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CR3022 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV2.1169 IgA heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV2.1169 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: ["Fernandez, I.", "Rey, F.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Drosophila melanogaster", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35704748", - title: - "Potent human broadly SARS-CoV-2-neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2.", - journal: "J.Exp.Med. 219 (2022), 1540-9538", - doi: "https://doi.org/10.1084/jem.20220638", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35704748", - pubDate: "2022", - abstract: "", - authors: [ - "Planchais, C. 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(0000-0001-8536-8995)", - "Simon-Loriere, E. (0000-0001-8420-7743)", - "Bourhy, H. (0000-0002-2608-5589)", - "Montagutelli, X. (0000-0002-9372-5398)", - "Rey, F.A. (0000-0002-9953-7988)", - "Schwartz, O. (0000-0002-0729-1475)", - "Mouquet, H. (0000-0002-4230-610X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qez_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qez", - }, - }, - { - title: "SARS-CoV-2 3CL protease crystallized under reducing conditions", - emdb: null, - pdb: { - dbId: "7JR3", - method: "X-RAY DIFFRACTION", - keywords: "hydrolase, cysteine endopeptidases", - refModels: [ - { - emdbId: null, - pdbId: "7JR3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jr3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jr3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "de Oliveira, R.R.", - "Trivella, D.B.B.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 3CL protease crystallized under reducing conditions.", - journal: "To be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "de Oliveira, R.R.", - "Nascimento, A.F.Z.", - "Zeri, A.C.M.", - "Trivella, D.B.B.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jr3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jr3", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 main protease in complex with INZ-1", - emdb: null, - pdb: { - dbId: "7CX9", - method: "X-RAY DIFFRACTION", - keywords: - "coronavirus, protease, inhibitor, complex, VIRAL PROTEIN., VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CX9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cx9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cx9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QWWAONJINWEHJL-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zeng, R.", - "Lei, J.", - "Wang, Y.F.", - "Liu, X.L.", - "Qiao, J.X.", - "Nan, J.S.", - "Li, Y.S.", - "Yang, S.Y.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of the SARS-CoV-2 main protease in complex with INZ-1", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Qiao, J.X.", - "Zeng, R.", - "Liu, X.L.", - "Nan, J.S.", - "Wang, Y.F.", - "Li, Y.S.", - "Lei, J.", - "Yang, S.Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cx9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cx9", - }, - }, - { - title: "SARS CoV-2 PLpro in complex with inhibitor 3k", - emdb: null, - pdb: { - dbId: "7TZJ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, papain-like protease, 3k, COVID19, inhibitor, complex, HYDROLASE/Inhibitor, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7TZJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tzj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tzj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "XJTWGMHOQKGBDO-GOSISDBHSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Klemm, T. (0000-0002-2847-3550)", - "Calleja, D.J. (0000-0002-8306-0900)", - "Lechtenberg, B.C. (0000-0002-5674-6894)", - "Komander, D. (0000-0002-8092-4320)", - "Kuchel, N.W.", - "Lessene, G. (0000-0002-1193-8147)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35494659", - title: - "Insights Into Drug Repurposing, as Well as Specificity and Compound Properties of Piperidine-Based SARS-CoV-2 PLpro Inhibitors.", - journal: "Front Chem 10: 861209-861209 (2022), 2296-2646", - doi: "https://doi.org/10.3389/fchem.2022.861209", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35494659", - pubDate: "2022", - abstract: "", - authors: [ - "Calleja, D.J.", - "Kuchel, N.", - "Lu, B.G.C.", - "Birkinshaw, R.W.", - "Klemm, T.", - "Doerflinger, M.", - "Cooney, J.P.", - "Mackiewicz, L.", - "Au, A.E.", - "Yap, Y.Q.", - "Blackmore, T.R.", - "Katneni, K.", - "Crighton, E.", - "Newman, J.", - "Jarman, K.E.", - "Call, M.J.", - "Lechtenberg, B.C.", - "Czabotar, P.E.", - "Pellegrini, M.", - "Charman, S.A.", - "Lowes, K.N.", - "Mitchell, J.P.", - "Nachbur, U.", - "Lessene, G.", - "Komander, D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tzj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tzj", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal RNA binding domain at 2.0A resolution", - emdb: null, - pdb: { - dbId: "7F2B", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7F2B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f2b_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f2b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NBIIXXVUZAFLBC-UHFFFAOYSA-K", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: ["Liu, C.", "Chen, Y.W."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34665939", - title: - "Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies.", - journal: "Febs J. 289: 3813-3825 (2022), 1742-464X", - doi: "https://doi.org/10.1111/febs.16239", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34665939", - pubDate: "2022", - abstract: "", - authors: [ - "Jia, Z.", - "Liu, C.", - "Chen, Y.", - "Jiang, H.", - "Wang, Z.", - "Yao, J.", - "Yang, J.", - "Zhu, J.", - "Zhang, B.", - "Yuchi, Z. (0000-0003-2595-9106)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7f2b_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7f2b", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-49 and FI-3A Fabs", - emdb: null, - pdb: { - dbId: "7Q0G", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 alpha variant, beta variant, gamma variant, delta variant, B.1.1.7, B.1.351, P.1, B.1.617.2, antibody, RBD, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7Q0G", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7q0g_final.pdb", - externalLink: "https://pdb-redo.eu/db/7q0g", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "FI-3A Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "FI-3A Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-49 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-49 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "NPYPAHLBTDXSSS-UHFFFAOYSA-N", - "FEWJPZIEWOKRBE-LWMBPPNESA-N", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34921776", - title: - "The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.", - journal: "Cell Host Microbe 30 (2022), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2021.11.013", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34921776", - pubDate: "2022", - abstract: "", - authors: [ - "Liu, C.", - "Zhou, D.", - "Nutalai, R.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Dejnirattisai, W.", - "Supasa, P.", - "Mentzer, A.J.", - "Wang, B.", - "Case, J.B.", - "Zhao, Y.", - "Skelly, D.T.", - "Chen, R.E.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Malik, T.", - "Temperton, N.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Clare, D.K.", - "Howe, A.", - "Goulder, P.J.R.", - "Fry, E.E.", - "Diamond, M.S.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Afonine, P.V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7q0g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7q0g", - }, - }, - { - title: - "Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P21 crystal form)", - emdb: null, - pdb: { - dbId: "7TX4", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, room temperature diffraction, protein dynamics, water networks, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TX4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tx4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tx4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Kovalevsky, A. (0000-0003-4459-9142)", - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P21 crystal form)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tx4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tx4", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI1", - emdb: null, - pdb: { - dbId: "7JPZ", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, main protease, reversible covalent inhibitors, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JPZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jpz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jpz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SDSQZWABGUFEMG-ACRUOGEOSA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33283984", - title: - "A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*.", - journal: "Chemmedchem 16: 942-948 (2021), 1860-7187", - doi: "https://doi.org/10.1002/cmdc.202000924", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33283984", - pubDate: "2021", - abstract: "", - authors: [ - "Yang, K.S.", - "Ma, X.R.", - "Ma, Y.", - "Alugubelli, Y.R.", - "Scott, D.A.", - "Vatansever, E.C.", - "Drelich, A.K.", - "Sankaran, B.", - "Geng, Z.Z.", - "Blankenship, L.R.", - "Ward, H.E.", - "Sheng, Y.J.", - "Hsu, J.C.", - "Kratch, K.C.", - "Zhao, B.", - "Hayatshahi, H.S.", - "Liu, J.", - "Li, P.", - "Fierke, C.A.", - "Tseng, C.K.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jpz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jpz", - }, - }, - { - title: - "Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication", - emdb: null, - pdb: { - dbId: "6WTK", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, 3CLpro, coronavirus, main protease, kinetics, SARS, VIRAL PROTEIN, Hydrolase-Hydrolase Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "6WTK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wtk_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wtk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JUCVXDDMQHPCKT-BZSNNMDCSA-N"], - dbauthors: [ - "Khan, M.B. (0000-0002-4164-9573)", - "Lemieux, M.J. (0000-0003-4745-9153)", - "Arutyunova, E.", - "Young, H.S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli O103:H2 str. 12009", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32855413", - title: - "Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication.", - journal: "Nat Commun 11: 4282-4282 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18096-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32855413", - pubDate: "2020", - abstract: "", - authors: [ - "Vuong, W. (0000-0002-3439-8788)", - "Khan, M.B. (0000-0002-4164-9573)", - "Fischer, C. (0000-0002-2289-010X)", - "Arutyunova, E.", - "Lamer, T. (0000-0002-1511-4540)", - "Shields, J. (0000-0003-4701-4576)", - "Saffran, H.A.", - "McKay, R.T. (0000-0002-0255-159X)", - "van Belkum, M.J. (0000-0002-9296-6069)", - "Joyce, M.A. (0000-0002-9173-7299)", - "Young, H.S.", - "Tyrrell, D.L. (0000-0002-0983-7267)", - "Vederas, J.C. (0000-0002-2996-0326)", - "Lemieux, M.J. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5ruq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5ruq", - }, - }, - { - title: - "Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 at 1.65A resolution (spacegroup C2).", - emdb: null, - pdb: { - dbId: "7ALH", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ALH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7alh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7alh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Costanzi, E.", - "Demitri, N.", - "Storici, P.", - "Giabbai, B.", - "Heroux, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34769210", - title: - "Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L.", - journal: "Int J Mol Sci 22 (2021), 1422-0067", - doi: "https://doi.org/10.3390/ijms222111779", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34769210", - pubDate: "2021", - abstract: "", - authors: [ - "Costanzi, E.", - "Kuzikov, M. (0000-0001-8771-1865)", - "Esposito, F. (0000-0001-9725-7977)", - "Albani, S. (0000-0002-3560-4539)", - "Demitri, N.", - "Giabbai, B.", - "Camasta, M.", - "Tramontano, E. (0000-0002-4849-0980)", - "Rossetti, G. (0000-0002-2032-4630)", - "Zaliani, A. (0000-0002-1740-8390)", - "Storici, P. (0000-0002-2590-3332)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7alh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7alh", - }, - }, - { - title: "SARS-CoV-2 main protease (Mpro) apo structure (space group P212121)", - emdb: null, - pdb: { - dbId: "7CAM", - method: "X-RAY DIFFRACTION", - keywords: "main protease, 3CL protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CAM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cam_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cam", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Chen, Y.", - "Wang, Y.C.", - "Yang, C.S.", - "Hou, M.H.", - "Tsai, C.L.", - "Chou, Y.Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32905393", - title: - "Structural basis of SARS-CoV-2 main protease inhibition by a broad-spectrum anti-coronaviral drug.", - journal: "Am J Cancer Res 10: 2535-2545 (2020), 2156-6976", - doi: "", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32905393", - pubDate: "2020", - abstract: "", - authors: [ - "Wang, Y.C.", - "Yang, W.H.", - "Yang, C.S.", - "Hou, M.H.", - "Tsai, C.L.", - "Chou, Y.Z.", - "Hung, M.C.", - "Chen, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cam_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cam", - }, - }, - { - title: - "1.7A resolution structure of SARS-CoV-2 main protease (Mpro) in complex with broad-spectrum coronavirus protease inhibitor GC376", - emdb: null, - pdb: { - dbId: "7CB7", - method: "X-RAY DIFFRACTION", - keywords: - "main protease, 3C-like proteinase, protein-inhibitor complex, GC376, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CB7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cb7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cb7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "BSPZFJDYQHDZNR-BOSXTWCSSA-N", - "BSPZFJDYQHDZNR-OGNFBWPZSA-N", - ], - dbauthors: [ - "Chen, Y.", - "Wang, Y.C.", - "Yang, C.S.", - "Hou, M.H.", - "Tsai, C.L.", - "Chou, Y.Z.", - "Hung, M.C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32905393", - title: - "Structural basis of SARS-CoV-2 main protease inhibition by a broad-spectrum anti-coronaviral drug.", - journal: "Am J Cancer Res 10: 2535-2545 (2020), 2156-6976", - doi: "", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32905393", - pubDate: "2020", - abstract: "", - authors: [ - "Wang, Y.C.", - "Yang, W.H.", - "Yang, C.S.", - "Hou, M.H.", - "Tsai, C.L.", - "Chou, Y.Z.", - "Hung, M.C.", - "Chen, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cb7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cb7", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab (crystal form 1)", - emdb: null, - pdb: { - dbId: "6YM0", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, receptor binding domain (RBD), CR3022, Vagabond, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6YM0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6ym0_final.pdb", - externalLink: "https://pdb-redo.eu/db/6ym0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhao, Y.", - "Zhou, D.", - "Ren, J.", - "Stuart, D.I.", - "Ginn, H.M.", - "Huo, J.", - "Fry, E.E.", - "Owens, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.", - journal: "Cell Host Microbe 28: 445-454.e6 (2020), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2020.06.010", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Huo, J.", - "Zhao, Y.", - "Ren, J.", - "Zhou, D.", - "Duyvesteyn, H.M.E.", - "Ginn, H.M.", - "Carrique, L.", - "Malinauskas, T.", - "Ruza, R.R.", - "Shah, P.N.M.", - "Tan, T.K.", - "Rijal, P.", - "Coombes, N.", - "Bewley, K.R.", - "Tree, J.A.", - "Radecke, J.", - "Paterson, N.G.", - "Supasa, P.", - "Mongkolsapaya, J.", - "Screaton, G.R.", - "Carroll, M.", - "Townsend, A.", - "Fry, E.E.", - "Owens, R.J.", - "Stuart, D.I.", - "Duyvesteyn, H.M.E. (0000-0002-4641-5442)", - "Carrique, L. (0000-0001-5332-8593)", - "Ren, J. (0000-0003-4015-1404)", - "Stuart, D.I. (0000-0002-3426-4210)", - "Fry, E.E. (0000-0001-9754-5303)", - "Zhao, Y. (0000-0001-8916-8552)", - "Malinauskas, T. (0000-0002-4847-5529)", - "Zhou, D. (0000-0002-7188-5243)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6ym0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6ym0", - }, - }, - { - title: - "Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide", - emdb: null, - pdb: { - dbId: "7JJC", - method: "X-RAY DIFFRACTION", - keywords: - "Neuropilin-1, receptor binding, Coronavirus, SARS-CoV-2, spike protein, SIGNALING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7JJC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jjc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jjc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "O14786", - organism: "9606", - name: "Neuropilin-1", - details: "", - altNames: "Vascular endothelial cell growth factor 165 receptor", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MTHSVFCYNBDYFN-UHFFFAOYSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Chen, K.-E. (0000-0003-1106-1629)", - "Collins, B.M. (0000-0002-6070-3774)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33082294", - title: "Neuropilin-1 is a host factor for SARS-CoV-2 infection.", - journal: "Science 370: 861-865 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abd3072", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33082294", - pubDate: "2020", - abstract: "", - authors: [ - "Daly, J.L.", - "Simonetti, B.", - "Klein, K.", - "Chen, K.E.", - "Williamson, M.K.", - "Anton-Plagaro, C.", - "Shoemark, D.K.", - "Simon-Gracia, L.", - "Bauer, M.", - "Hollandi, R.", - "Greber, U.F.", - "Horvath, P.", - "Sessions, R.B.", - "Helenius, A.", - "Hiscox, J.A.", - "Teesalu, T.", - "Matthews, D.A.", - "Davidson, A.D.", - "Collins, B.M.", - "Cullen, P.J.", - "Yamauchi, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jjc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jjc", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv", - emdb: null, - pdb: { - dbId: "7DET", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, RBD, antibody, VIRAL PROTEIN, ANTIVIRAL PROTEIN, VIRAL PROTEIN-ANTIVIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7DET", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7det_final.pdb", - externalLink: "https://pdb-redo.eu/db/7det", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "antibody scFv", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Zhang, G.", - "Rao, Z.", - "Guo, Y. (0000-0002-8109-7515)", - "Wang, Y.", - "Li, X. (0000-0003-0896-8713)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33961621", - title: - "Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes.", - journal: "Plos Biol. 19: e3001209-e3001209 (2021), 1545-7885", - doi: "https://doi.org/10.1371/journal.pbio.3001209", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33961621", - pubDate: "2021", - abstract: "", - authors: [ - "Fu, D.", - "Zhang, G.", - "Wang, Y.", - "Zhang, Z.", - "Hu, H.", - "Shen, S.", - "Wu, J. (0000-0002-4457-5485)", - "Li, B.", - "Li, X.", - "Fang, Y.", - "Liu, J.", - "Wang, Q.", - "Zhou, Y. 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(0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rld_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rld", - }, - }, - { - title: "Complex Structure of SARS-CoV-2 3CL Protease with TG-0203770", - emdb: null, - pdb: { - dbId: "7C8R", - method: "X-RAY DIFFRACTION", - keywords: "Inhibitor, Complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7C8R", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c8r_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c8r", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GENYQFMDDNZIRG-UCWBBBRQSA-N"], - dbauthors: [ - "Lee, C.C. (0000-0002-8259-4388)", - "Wang, A.H.J. (0000-0002-0016-5337)", - "Kuo, C.J. (0000-0002-4988-5124)", - "Liang, P.H. 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(0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. 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(0000-0001-5904-1905)", - "Gully, B.S. (0000-0002-8197-0871)", - "Rossjohn, J. (0000-0002-2020-7522)", - "Riboldi-Tunnicliffe, A. (0000-0003-2244-2486)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32592996", - title: - "Crystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9.", - journal: "Iscience 23: 101258-101258 (2020), 2589-0042", - doi: "https://doi.org/10.1016/j.isci.2020.101258", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32592996", - pubDate: "2020", - abstract: "", - authors: [ - "Littler, D.R.", - "Gully, B.S.", - "Colson, R.N.", - "Rossjohn, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w9q_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w9q", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to LSN2463359.", - emdb: null, - pdb: { - dbId: "7AWU", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-!9, PEPTIDE BINDING PROTEIN", - 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(0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. 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(0000-0001-9891-916X)", - "Pancera, M. (0000-0001-9217-6270)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35411021", - title: - "Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit.", - journal: "Commun Biol 5: 342-342 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03262-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35411021", - pubDate: "2022", - abstract: "", - authors: [ - "Hurlburt, N.K.", - "Homad, L.J.", - "Sinha, I.", - "Jennewein, M.F.", - "MacCamy, A.J.", - "Wan, Y.H.", - "Boonyaratanakornkit, J.", - "Sholukh, A.M.", - "Jackson, A.M.", - "Zhou, P.", - "Burton, D.R.", - "Andrabi, R.", - "Ozorowski, G.", - "Ward, A.B.", - "Stamatatos, L.", - "Pancera, M.", - "McGuire, A.T.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7raq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7raq", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-250", - emdb: null, - pdb: { - dbId: "6XKQ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Antibody, Spike, Coronavirus, COVID-19, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "6XKQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xkq_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xkq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV07-250 Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV07-250 Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Liu, H. (0000-0002-2412-7853)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. (0000-0001-9754-4503)", - "Wu, N.C. (0000-0002-9078-6697)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33058755", - title: - "A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.", - journal: "Cell 183 (2020), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2020.09.049", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33058755", - pubDate: "2020", - abstract: "", - authors: [ - "Kreye, J.", - "Reincke, S.M.", - "Kornau, H.C.", - "Sanchez-Sendin, E.", - "Corman, V.M.", - "Liu, H.", - "Yuan, M.", - "Wu, N.C.", - "Zhu, X.", - "Lee, C.D.", - "Trimpert, J.", - "Holtje, M.", - "Dietert, K.", - "Stoffler, L.", - "von Wardenburg, N.", - "van Hoof, S.", - "Homeyer, M.A.", - "Hoffmann, J.", - "Abdelgawad, A.", - "Gruber, A.D.", - "Bertzbach, L.D.", - "Vladimirova, D.", - "Li, L.Y.", - "Barthel, P.C.", - "Skriner, K.", - "Hocke, A.C.", - "Hippenstiel, S.", - "Witzenrath, M.", - "Suttorp, N.", - "Kurth, F.", - "Franke, C.", - "Endres, M.", - "Schmitz, D.", - "Jeworowski, L.M.", - "Richter, A.", - "Schmidt, M.L.", - "Schwarz, T.", - "Muller, M.A.", - "Drosten, C.", - "Wendisch, D.", - "Sander, L.E.", - "Osterrieder, N.", - "Wilson, I.A.", - "Pruss, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xkq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xkq", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-52", - emdb: null, - pdb: { - dbId: "7RME", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RME", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rme_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rme", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CVDMNVBBLCPUMH-UHFFFAOYSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34705466", - title: - "Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.", - journal: "J.Med.Chem. 64: 17366-17383 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01475", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34705466", - pubDate: "2021", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Li, H. (0000-0002-6964-9962)", - "Galanie, S.", - "Phillips, G.", - "Labbe, A.", - "Weiss, K.L. (0000-0002-6486-8007)", - "Zhang, Q.", - "Arnould, M.A.", - "Clyde, A.", - "Ma, H.", - "Ramanathan, A. (0000-0002-1622-5488)", - "Jonsson, C.B. (0000-0002-2640-7672)", - "Head, M.S.", - "Coates, L. (0000-0003-2342-049X)", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rme_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rme", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1272494722", - emdb: null, - pdb: { - dbId: "5SKW", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SKW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5skw_final.pdb", - externalLink: "https://pdb-redo.eu/db/5skw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QUKZXHGECCPEIZ-JGVFFNPUSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5skw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5skw", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 21", - emdb: null, - pdb: { - dbId: "7L13", - method: "X-RAY DIFFRACTION", - keywords: "NOVEL CORONAVIRUS, ANTIVIRAL, DRUG DESIGN, VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7L13", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l13_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l13", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NFXZAFCZOMISJH-UHFFFAOYSA-N"], - dbauthors: [ - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - "Zhang, C.H. (0000-0002-4579-9202)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33786375", - title: - "Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations.", - journal: "Acs Cent.Sci. 7: 467-475 (2021), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.1c00039", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33786375", - pubDate: "2021", - abstract: "", - authors: [ - "Zhang, C.H.", - "Stone, E.A.", - "Deshmukh, M.", - "Ippolito, J.A.", - "Ghahremanpour, M.M.", - "Tirado-Rives, J.", - "Spasov, K.A.", - "Zhang, S.", - "Takeo, Y.", - "Kudalkar, S.N.", - "Liang, Z.", - "Isaacs, F.", - "Lindenbach, B.", - "Miller, S.J.", - "Anderson, K.S.", - "Jorgensen, W.L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l13_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l13", - }, - }, - { - title: - "Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.", - emdb: null, - pdb: { - dbId: "6X1B", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus 2, endoribonuclease, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6X1B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6x1b_final.pdb", - externalLink: "https://pdb-redo.eu/db/6x1b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "DNA (5'-R(*GP*U)-3')", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NBIIXXVUZAFLBC-UHFFFAOYSA-K", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Welk, L.", - "Michalska, K.", - "Chang, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dodecameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33564093", - title: - "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.", - journal: "Commun Biol 4: 193-193 (2021), 2399-3642", - doi: "https://doi.org/10.1038/s42003-021-01735-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33564093", - pubDate: "2021", - abstract: "", - authors: [ - "Kim, Y.", - "Wower, J. (0000-0001-8096-7745)", - "Maltseva, N. (0000-0002-2871-465X)", - "Chang, C.", - "Jedrzejczak, R.", - "Wilamowski, M.", - "Kang, S.", - "Nicolaescu, V.", - "Randall, G.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Wower, J.", - "Maltseva, N.", - "Nicolaescu,, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - { - pmID: "", - title: - "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.06.26.173872", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Kim, Y.", - "Wower, J. (0000-0001-8096-7745)", - "Maltseva, N. (0000-0002-2871-465X)", - "Chang, C.", - "Jedrzejczak, R.", - "Wilamowski, M.", - "Kang, S.", - "Nicolaescu, V.", - "Randall, G.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Wower, J.", - "Maltseva, N.", - "Nicolaescu,, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6x1b_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6x1b", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, at room temperature", - emdb: null, - pdb: { - dbId: "6XG3", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6XG3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xg3_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xg3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Tesar, C.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33531496", - title: - "Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.", - journal: "Nat Commun 12: 743-743 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-21060-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33531496", - pubDate: "2021", - abstract: "", - authors: [ - "Osipiuk, J.", - "Azizi, S.A. (0000-0002-9226-9917)", - "Dvorkin, S.", - "Endres, M.", - "Jedrzejczak, R.", - "Jones, K.A. (0000-0003-0711-5516)", - "Kang, S.", - "Kathayat, R.S. (0000-0002-9159-2413)", - "Kim, Y.", - "Lisnyak, V.G. (0000-0002-4406-8440)", - "Maki, S.L. (0000-0001-6917-3602)", - "Nicolaescu, V.", - "Taylor, C.A.", - "Tesar, C.", - "Zhang, Y.A.", - "Zhou, Z. (0000-0002-2792-8429)", - "Randall, G.", - "Michalska, K.", - "Snyder, S.A. (0000-0003-3594-8769)", - "Dickinson, B.C. (0000-0002-9616-1911)", - "Joachimiak, A. 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(0000-0002-4883-1933)", - "Zocher, G. (0000-0001-8711-2088)", - "Stehle, T. (0000-0002-4571-8548)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33904225", - title: - "NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies.", - journal: "Embo Rep. 22: e52325-e52325 (2021), 1469-3178", - doi: "https://doi.org/10.15252/embr.202052325", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33904225", - pubDate: "2021", - abstract: "", - authors: [ - "Wagner, T.R. (0000-0002-1050-5948)", - "Ostertag, E.", - "Kaiser, P.D.", - "Gramlich, M.", - "Ruetalo, N.", - "Junker, D.", - "Haering, J.", - "Traenkle, B.", - "Becker, M.", - "Dulovic, A.", - "Schweizer, H. (0000-0001-9407-944X)", - "Nueske, S.", - "Scholz, A.", - "Zeck, A.", - "Schenke-Layland, K.", - "Nelde, A.", - "Strengert, M.", - "Walz, J.S.", - "Zocher, G.", - "Stehle, T.", - "Schindler, M.", - "Schneiderhan-Marra, N.", - "Rothbauer, U. 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(0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36119652", - title: - "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.28.497978", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36119652", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, Y.", - "Lewandowski, E.M.", - "Tan, H.", - "Zhang, X.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Butler, S.G.", - "Gongora, M.V.", - "Choy, J.", - "Deng, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8d4m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8d4m", - }, - }, - { - title: - "The crystal structure of SARS-CoV-2 Main Protease with the formation of Cys145-1H-indole-5-carboxylate", - emdb: null, - pdb: { - dbId: "7KYU", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-COV-2, Main protease, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7KYU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kyu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kyu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YPFWNRLSYPAVJB-UHFFFAOYSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Joachimiak, A. 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sp8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sp8", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with REAL300019621104", - emdb: null, - pdb: { - dbId: "5SPY", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SPY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5spy_final.pdb", - externalLink: "https://pdb-redo.eu/db/5spy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QXNLGIPKEFPOOU-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. 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(0000-0001-5904-1905)", - "Gully, B.S. (0000-0002-8197-0871)", - "Rossjohn, J. 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(0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nio_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nio", - }, - }, - { - title: "The N-terminal crystal structure of SARS-CoV-2 NSP2", - emdb: null, - pdb: { - dbId: "7EXM", - method: "X-RAY DIFFRACTION", - keywords: "zinc finger, nucleic acid binding protein, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7EXM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7exm_final.pdb", - externalLink: "https://pdb-redo.eu/db/7exm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 2", - details: "", - altNames: "nsp2,p65 homolog", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Ma, J.", "Chen, Z. (0000-0003-1319-9664)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34398430", - title: - "Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2.", - journal: "Virol Sin 36: 1104-1112 (2021), 1995-820X", - doi: "https://doi.org/10.1007/s12250-021-00431-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34398430", - pubDate: "2021", - abstract: "", - authors: ["Ma, J.", "Chen, Y.", "Wu, W.", "Chen, Z."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7exm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7exm", - }, - }, - { - title: "Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL", - emdb: null, - pdb: { - dbId: "7LG0", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, CD8+, epitope, HLA, human major histocompatibility complex, SPRWYFYYL, HLA-B7, HLA-B*07:02, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7LG0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lg0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lg0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01889", - organism: "9606", - name: "HLA class I histocompatibility antigen, B-7 alpha chain", - details: "", - altNames: "MHC class I antigen B*7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IIRDTKBZINWQAW-UHFFFAOYSA-N"], - dbauthors: [ - "Patskovsky, Y.", - "Krogsgaard, M.", - "Patskovska, L. (0000-0002-8910-0504)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Patskovska, L.", "Patskovsky, Y.", "Krogsgaard, M."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lg0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lg0", - }, - }, - { - title: "SARS-CoV-2 receptor binding domain in complex with WNb-2", - emdb: null, - pdb: { - dbId: "7LDJ", - method: "X-RAY DIFFRACTION", - keywords: "Nanobody, Complex, SARS-CoV-2, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7LDJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ldj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ldj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "Nanobody 2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: [ - "WQZGKKKJIJFFOK-QTVWNMPRSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Pymm, P. (0000-0003-2722-4621)", - "Tham, W.H. (0000-0001-7950-8699)", - "Tan, L.L. (0000-0003-0606-4446)", - "Dietrich, M.H. (0000-0002-2780-4389)", - "Adair, A. (0000-0002-2952-7987)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2 receptor binding domain in complex with WNb-2", - journal: "Proc.Natl.Acad.Sci.USA (2021), 1091-6490", - doi: "https://doi.org/10.1073/pnas.210191811", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Pymm, P. (0000-0003-2722-4621)", - "Adair, A. (0000-0002-2952-7987)", - "Chan, L.J.", - "Cooney, J.P.", - "Mordant, F.L.", - "Allison, C.C.", - "Lopez, E.", - "Haycroft, E.", - "O'Neill, M.T.", - "Tan, L.L. (0000-0003-0606-4446)", - "Dietrich, M.H. (0000-0002-2780-4389)", - "Drew, D.", - "Doerflinger, M.", - "Dengler, M.", - "Scott, N.E.", - "Wheatley, A.K.", - "Gherardin, N.A.", - "Venugopal, H.", - "Cromer, D.", - "Davenport, M.P.", - "Pickering, R.", - "Godfrey, D.I.", - "Purcell, D.J.", - "Kent, S.J.", - "Chung, A.W.", - "Subbarao, K.", - "Pellegrini, M.", - "Glukhova, A.", - "Tham, W.H. (0000-0001-7950-8699)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ldj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ldj", - }, - }, - { - title: "Structure of SARS-CoV-2 nonstuctural protein 1", - emdb: null, - pdb: { - dbId: "7K7P", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, coronavirus, NSP1, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7K7P", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k7p_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k7p", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Host translation inhibitor nsp1", - details: "", - altNames: "Leader protein,Non-structural protein 1,nsp1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Green, T.J.", "Petit, C.M.", "Clark, L.K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33234675", - title: "Structure of Nonstructural Protein 1 from SARS-CoV-2.", - journal: "J.Virol. 95 (2021), 1098-5514", - doi: "https://doi.org/10.1128/JVI.02019-20", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33234675", - pubDate: "2021", - abstract: "", - authors: [ - "Clark, L.K.", - "Green, T.J. (0000-0003-1158-4710)", - "Petit, C.M. (0000-0003-4933-6245)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k7p_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k7p", - }, - }, - { - title: - "Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody B6", - emdb: null, - pdb: { - dbId: "7R98", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, nanobody, nucleocapsid, VIRUS, VIRAL PROTEIN-IMMUNE SYSTEM complex, RNA BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7R98", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7r98_final.pdb", - externalLink: "https://pdb-redo.eu/db/7r98", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody B6", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Ye, Q.", "Corbett, K.D. (0000-0001-5854-2388)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34381460", - title: - "Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies.", - journal: "Front Immunol 12: 719037-719037 (2021), 1664-3224", - doi: "https://doi.org/10.3389/fimmu.2021.719037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381460", - pubDate: "2021", - abstract: "", - authors: ["Ye, Q.", "Lu, S.", "Corbett, K.D."], - }, - { - pmID: "34100017", - title: - "Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.06.01.446591", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34100017", - pubDate: "2021", - abstract: "", - authors: ["Ye, Q.", "Lu, S.", "Corbett, K.D."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7r98_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7r98", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z2856434892", - emdb: null, - pdb: { - dbId: "5S3H", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3H", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3h_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3h", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CGFLTCVMZJDNKM-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3h_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3h", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 1", - emdb: null, - pdb: { - dbId: "7B2U", - method: "X-RAY DIFFRACTION", - keywords: "Inhibitor, complex, protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7B2U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7b2u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7b2u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MTRGOOHUDUKDJK-ZDUSSCGKSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Talibov, V.O. (0000-0002-1135-2744)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimer (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35142215", - title: - "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", - journal: "J.Am.Chem.Soc. 144: 2905-2920 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08402", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35142215", - pubDate: "2022", - abstract: "", - authors: [ - "Luttens, A. (0000-0003-2915-7901)", - "Gullberg, H.", - "Abdurakhmanov, E.", - "Vo, D.D.", - "Akaberi, D. (0000-0002-9595-9796)", - "Talibov, V.O.", - "Nekhotiaeva, N.", - "Vangeel, L.", - "De Jonghe, S. (0000-0002-3872-6558)", - "Jochmans, D.", - "Krambrich, J.", - "Tas, A.", - "Lundgren, B.", - "Gravenfors, Y. (0000-0001-6025-4908)", - "Craig, A.J.", - "Atilaw, Y.", - "Sandstrom, A.", - "Moodie, L.W.K. (0000-0002-9500-4535)", - "Lundkvist, A.", - "van Hemert, M.J.", - "Neyts, J.", - "Lennerstrand, J.", - "Kihlberg, J. (0000-0002-4205-6040)", - "Sandberg, K.", - "Danielson, U.H. (0000-0003-2728-0340)", - "Carlsson, J. 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(0000-0001-5380-2339)", - "Pazgier, M. (0000-0003-0594-5057)", - "Tolbert, W. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s1w_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s1w", - }, - }, - { - title: - "1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 2a", - emdb: null, - pdb: { - dbId: "7LKR", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LKR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lkr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lkr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PGYROSRJIVXTOE-HATFLPCOSA-N", - "PGYROSRJIVXTOE-HCKQHCFMSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Rathnayake, A.D.", - "Baird, M.A.", - "Shadipeni, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34213885", - title: - "Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease.", - journal: "J.Med.Chem. 64: 10047-10058 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00319", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34213885", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Kim, Y.", - "Bickmeier, N.", - "Rathnayake, A.D.", - "Nguyen, H.N.", - "Zheng, J.", - "Kashipathy, M.M.", - "Baird, M.A.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lkr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lkr", - }, - }, - { - title: - "Structure of SARS-CoV-2 Mpro mutant (K90R) in complex with Nirmatrelvir (PF-07321332)", - emdb: null, - pdb: { - dbId: "7U29", - method: "X-RAY DIFFRACTION", - keywords: - "Protease, SARS-CoV-2, covalent complex, inhibitor, HYDROLASE-INHIBITOR complex, Omicron, nirmatrelvir, PF-07321332, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7U29", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u29_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u29", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: [ - "Stewart, A.E.", - "Greasley, S.E. (0000-0002-7978-6477)", - "Ferre, R.A. (0000-0001-7462-1879)", - "Liu, W. (0000-0002-8541-4928)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35461811", - title: - "Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants.", - journal: "J.Biol.Chem. 298: 101972-101972 (2022), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2022.101972", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35461811", - pubDate: "2022", - abstract: "", - authors: [ - "Greasley, S.E.", - "Noell, S.", - "Plotnikova, O.", - "Ferre, R.", - "Liu, W.", - "Bolanos, B.", - "Fennell, K.", - "Nicki, J.", - "Craig, T.", - "Zhu, Y.", - "Stewart, A.E.", - "Steppan, C.M.", - ], - }, - { - pmID: "", - title: - "Structural basis for Nirmatrelvir in vitro efficacy against the Omicron variant of SARS-CoV-2", - journal: "Biorxiv (2022)", - doi: "https://doi.org/10.1101/2022.01.17.476556", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Greasley, S.E.", - "Noell, S.", - "Plotnikova, O.", - "Ferre, R.", - "Liu, W.", - "Bolanos, B.", - "Fennell, K.", - "Nicki, J.", - "Craig, T.", - "Zhu, Y.", - "Stewart, A.E.", - "Steppan, C.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7u29_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7u29", - }, - }, - { - title: "SARS-CoV-2 RBD in complex with Fab 15033", - emdb: null, - pdb: { - dbId: "7KLG", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, spike glycoprotein, Fab, VIRAL PROTEIN-Immune System complex", - refModels: [ - { - emdbId: null, - pdbId: "7KLG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7klg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7klg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Fab 15033 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Fab 15033 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Li, Z.", "Rini, J.M."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34329642", - title: - "Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.", - journal: "J.Mol.Biol. 433: 167177-167177 (2021), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2021.167177", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34329642", - pubDate: "2021", - abstract: "", - authors: [ - "Miersch, S.", - "Li, Z.", - "Saberianfar, R.", - "Ustav, M.", - "Brett Case, J.", - "Blazer, L.", - "Chen, C.", - "Ye, W.", - "Pavlenco, A.", - "Gorelik, M.", - "Garcia Perez, J.", - "Subramania, S.", - "Singh, S.", - "Ploder, L.", - "Ganaie, S.", - "Chen, R.E.", - "Leung, D.W.", - "Pandolfi, P.P.", - "Novelli, G.", - "Matusali, G.", - "Colavita, F.", - "Capobianchi, M.R.", - "Jain, S.", - "Gupta, J.B.", - "Amarasinghe, G.K.", - "Diamond, M.S.", - "Rini, J.", - "Sidhu, S.S.", - "Case, J.B.", - "Perez, J.G.", - "Novelli, G. (0000-0002-7781-602X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7klg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7klg", - }, - }, - { - title: - "Crystal structure of SARS CoV2 main protease in complex with inhibitor Boceprevir", - emdb: null, - pdb: { - dbId: "6ZRU", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Boceprevir, inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6ZRU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6zru_final.pdb", - externalLink: "https://pdb-redo.eu/db/6zru", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Main Protease", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "FEBWCINGHXXUCV-GFLQDLJJSA-N"], - dbauthors: [ - "Oerlemans, R. (0000-0001-7114-3736)", - "Domling, A. (0000-0002-9923-8873)", - "Groves, M.R. (0000-0001-9859-5177)", - "Wang, W. (0000-0002-6272-3381)", - "Lunev, S. (0000-0001-9867-6866)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34041486", - title: - "Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics.", - journal: "Rsc Med Chem 12: 370-379 (2020), 2632-8682", - doi: "https://doi.org/10.1039/d0md00367k", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34041486", - pubDate: "2020", - abstract: "", - authors: [ - "Oerlemans, R.", - "Ruiz-Moreno, A.J. (0000-0002-2798-5386)", - "Cong, Y.", - "Dinesh Kumar, N.", - "Velasco-Velazquez, M.A.", - "Neochoritis, C.G. (0000-0001-5098-5504)", - "Smith, J.", - "Reggiori, F.", - "Groves, M.R.", - "Domling, A. (0000-0002-9923-8873)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zru_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zru", - }, - }, - { - title: "X-ray crystal structure of the SARS-CoV-2 main protease in space group C2", - emdb: null, - pdb: { - dbId: "7LKE", - method: "X-RAY DIFFRACTION", - keywords: "Protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7LKE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lke_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lke", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Narwal, M. (0000-0002-9718-5827)", - "Murakami, K.S. (0000-0003-2244-0501)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35217718", - title: - "Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay.", - journal: "Commun Biol 5: 169-169 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03090-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35217718", - pubDate: "2022", - abstract: "", - authors: [ - "Narayanan, A.", - "Narwal, M.", - "Majowicz, S.A. (0000-0002-6331-7780)", - "Varricchio, C.", - "Toner, S.A.", - "Ballatore, C.", - "Brancale, A. (0000-0002-9728-3419)", - "Murakami, K.S. (0000-0003-2244-0501)", - "Jose, J. (0000-0003-1261-6921)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lke_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lke", - }, - }, - { - title: - "Crystal structure of MG-132 covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.", - emdb: null, - pdb: { - dbId: "7BE7", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN, MG-132", - refModels: [ - { - emdbId: null, - pdbId: "7BE7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7be7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7be7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "WUJQMWDTZKIKQZ-VABKMULXSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P.", "Giabbai, B."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34769210", - title: - "Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L.", - journal: "Int J Mol Sci 22 (2021), 1422-0067", - doi: "https://doi.org/10.3390/ijms222111779", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34769210", - pubDate: "2021", - abstract: "", - authors: [ - "Costanzi, E.", - "Kuzikov, M. (0000-0001-8771-1865)", - "Esposito, F. (0000-0001-9725-7977)", - "Albani, S. (0000-0002-3560-4539)", - "Demitri, N.", - "Giabbai, B.", - "Camasta, M.", - "Tramontano, E. (0000-0002-4849-0980)", - "Rossetti, G. (0000-0002-2032-4630)", - "Zaliani, A. (0000-0002-1740-8390)", - "Storici, P. 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(0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34161756", - title: - "Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.", - journal: "Structure 29 (2021), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2021.06.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34161756", - pubDate: "2021", - abstract: "", - authors: [ - "Deshmukh, M.G.", - "Ippolito, J.A.", - "Zhang, C.H.", - "Stone, E.A.", - "Reilly, R.A.", - "Miller, S.J.", - "Jorgensen, W.L.", - "Anderson, K.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m8y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m8y", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 main protease in complex with Tafenoquine", - emdb: null, - pdb: { - dbId: "7DDC", - method: "X-RAY DIFFRACTION", - keywords: "main protease, 3C-like proteinase, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7DDC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ddc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ddc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LBHLFPGPEGDCJG-HNNXBMFYSA-N"], - dbauthors: ["Chen, Y.", "Wang, Y.C.", "Yang, C.S.", "Hung, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35101449", - title: - "Tafenoquine and its derivatives as inhibitors for the severe acute respiratory syndrome coronavirus 2.", - journal: "J.Biol.Chem. 298: 101658-101658 (2022), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2022.101658", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35101449", - pubDate: "2022", - abstract: "", - authors: [ - "Chen, Y.", - "Yang, W.H.", - "Chen, H.F.", - "Huang, L.M.", - "Gao, J.Y.", - "Lin, C.W.", - "Wang, Y.C.", - "Yang, C.S.", - "Liu, Y.L.", - "Hou, M.H.", - "Tsai, C.L.", - "Chou, Y.Z.", - "Huang, B.Y.", - "Hung, C.F.", - "Hung, Y.L.", - "Wang, W.J.", - "Su, W.C.", - "Kumar, V.", - "Wu, Y.C.", - "Chao, S.W.", - "Chang, C.S.", - "Chen, J.S.", - "Chiang, Y.P.", - "Cho, D.Y.", - "Jeng, L.B.", - "Tsai, C.H.", - "Hung, M.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ddc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ddc", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 16", - emdb: null, - pdb: { - dbId: "7M8N", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7M8N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m8n_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m8n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CXKRCAINPQDWER-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, C.H.", - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34161756", - title: - "Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.", - journal: "Structure 29 (2021), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2021.06.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34161756", - pubDate: "2021", - abstract: "", - authors: [ - "Deshmukh, M.G.", - "Ippolito, J.A.", - "Zhang, C.H.", - "Stone, E.A.", - "Reilly, R.A.", - "Miller, S.J.", - "Jorgensen, W.L.", - "Anderson, K.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m8n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m8n", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal RNA binding domain", - emdb: null, - 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genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder608 inhibitor", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Lisnyak, V.", - "Maki, S.", - "Taylor, C.", - "Zhang, Y.", - "Zhou, Z.", - "Azizi, S.A.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - "Dickinson, B.C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sgu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sgu", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 10c", - emdb: null, - pdb: { - dbId: "7T49", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7T49", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t49_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t49", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DXHKTWBJEAVWSD-QUJKESNLSA-N", "DXHKTWBJEAVWSD-DBSRCYSRSA-N"], - dbauthors: [ - "Liu, L.", - "Kim, Y.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35638577", - title: - "Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.", - journal: "J.Med.Chem. 65: 7818-7832 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00224", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35638577", - pubDate: "2022", - abstract: "", - authors: [ - "Dampalla, C.S. (0000-0002-8199-2376)", - "Rathnayake, A.D. (0000-0003-2588-7624)", - "Galasiti Kankanamalage, A.C.", - "Kim, Y.", - "Perera, K.D. (0000-0002-3778-4975)", - "Nguyen, H.N.", - "Miller, M.J.", - "Madden, T.K.", - "Picard, H.R.", - "Thurman, H.A.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P. (0000-0003-0833-3259)", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Battaile, K.P.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t49_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t49", - }, - }, - { - title: - "Crystal Structure of ADP ribose phosphatase of NSP3 from SARS-CoV-2 in complex with MES", - emdb: null, - pdb: { - dbId: "6WCF", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Coronavirus, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6WCF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wcf_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wcf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SXGZJKUKBWWHRA-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Mesecar, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32939273", - title: - "Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes.", - journal: "Iucrj 7: 814-824 (2020), 2052-2525", - doi: "https://doi.org/10.1107/S2052252520009653", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32939273", - pubDate: "2020", - abstract: "", - authors: [ - "Michalska, K.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Stols, L.", - "Endres, M.", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wcf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wcf", - }, - }, - { - title: "SARS-CoV-2 receptor binding domain bound to Fab PDI 210", - emdb: null, - pdb: { - dbId: "7MZL", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, spike, RBD, human antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7MZL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mzl_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mzl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "PDI 210 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "PDI 210 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Pymm, P. (0000-0003-2722-4621)", - "Tham, W.H. (0000-0001-7950-8699)", - "Chan, L.J. (0000-0002-9439-3487)", - "Tan, L.L. (0000-0003-0606-4446)", - "Dietrich, M.H. (0000-0002-2780-4389)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34610292", - title: - "Landscape of human antibody recognition of the SARS-CoV-2 receptor binding domain.", - journal: "Cell Rep 37: 109822-109822 (2021), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2021.109822", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34610292", - pubDate: "2021", - abstract: "", - authors: [ - "Wheatley, A.K.", - "Pymm, P.", - "Esterbauer, R.", - "Dietrich, M.H.", - "Lee, W.S.", - "Drew, D.", - "Kelly, H.G.", - "Chan, L.J.", - "Mordant, F.L.", - "Black, K.A.", - "Adair, A.", - "Tan, H.X.", - "Juno, J.A.", - "Wragg, K.M.", - "Amarasena, T.", - "Lopez, E.", - "Selva, K.J.", - "Haycroft, E.R.", - "Cooney, J.P.", - "Venugopal, H.", - "Tan, L.L.", - "O Neill, M.T.", - "Allison, C.C.", - "Cromer, D.", - "Davenport, M.P.", - "Bowen, R.A.", - "Chung, A.W.", - "Pellegrini, M.", - "Liddament, M.T.", - "Glukhova, A.", - "Subbarao, K.", - "Kent, S.J.", - "Tham, W.H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mzl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mzl", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000039575", - emdb: null, - pdb: { - dbId: "5RV8", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RV8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rv8_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rv8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IJXDURUAYOKSIS-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rt0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rt0", - }, - }, - { - title: "SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3af", - emdb: null, - pdb: { - dbId: "7X6J", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7X6J", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x6j_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x6j", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LOAUVZALPPNFOQ-UHFFFAOYSA-N"], - dbauthors: ["Xu, Y.", "Su, H.", "Li, M.J.", "Xie, H.", "Nie, T.", "Li, Z.W."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35709506", - title: - "Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination.", - journal: "J.Med.Chem. 65: 9376-9395 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00636", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35709506", - pubDate: "2022", - abstract: "", - authors: [ - "Pillaiyar, T.", - "Flury, P.", - "Kruger, N.", - "Su, H.", - "Schakel, L.", - "Barbosa Da Silva, E.", - "Eppler, O.", - "Kronenberger, T.", - "Nie, T.", - "Luedtke, S.", - "Rocha, C.", - "Sylvester, K.", - "Petry, M.R.I.", - "McKerrow, J.H.", - "Poso, A.", - "Pohlmann, S.", - "Gutschow, M.", - "O'Donoghue, A.J.", - "Xu, Y.", - "Muller, C.E.", - "Laufer, S.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x6j_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x6j", - }, - }, - { - title: "Crystal structure of the 76E1 Fab in complex with a SARS-CoV-2 spike peptide", - emdb: null, - pdb: { - dbId: "7X9E", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Antibody, Fab, Spike, Fusion peptide, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7X9E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x9e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x9e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "76E1 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "76E1 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Chen, X.", "Sun, B.", "Sun, X.", "Zhang, T.", "Ding, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35773398", - title: - "Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2.", - journal: "Nat Microbiol 7: 1063-1074 (2022), 2058-5276", - doi: "https://doi.org/10.1038/s41564-022-01155-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35773398", - pubDate: "2022", - abstract: "", - authors: [ - "Sun, X.", - "Yi, C.", - "Zhu, Y.", - "Ding, L.", - "Xia, S.", - "Chen, X. (0000-0003-3432-7469)", - "Liu, M.", - "Gu, C.", - "Lu, X.", - "Fu, Y. (0000-0002-4133-6067)", - "Chen, S.", - "Zhang, T.", - "Zhang, Y. (0000-0002-2417-6516)", - "Yang, Z.", - "Ma, L.", - "Gu, W.", - "Hu, G.", - "Du, S.", - "Yan, R.", - "Fu, W.", - "Yuan, S.", - "Qiu, C.", - "Zhao, C. (0000-0002-0718-7707)", - "Zhang, X. (0000-0002-3193-1401)", - "He, Y.", - "Qu, A.", - "Zhou, X.", - "Li, X.", - "Wong, G.", - "Deng, Q. (0000-0002-3381-3417)", - "Zhou, Q. (0000-0002-6237-8813)", - "Lu, H.", - "Ling, Z. (0000-0001-8873-6773)", - "Ding, J. (0000-0001-7029-7346)", - "Lu, L. (0000-0002-2255-0391)", - "Xu, J.", - "Xie, Y. (0000-0002-2416-7708)", - "Sun, B. (0000-0003-2545-5282)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x9e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x9e", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43 crystal form)", - emdb: null, - pdb: { - dbId: "7TX0", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, room temperature diffraction, protein dynamics, water networks, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TX0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tx0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tx0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-ZQSHOCFMSA-N"], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43 crystal form)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tx0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tx0", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with ADP-ribose", - emdb: null, - pdb: { - dbId: "6YWL", - method: "X-RAY DIFFRACTION", - keywords: - 'NSP3, macrodomain, ADP-ribose-1"-phosphatase, ADRP, Covid-19, SARS-COV-2, ADP-ribose, Structural Genomics, Structural Genomics Consortium, SGC, VIRAL PROTEIN', - refModels: [ - { - emdbId: null, - pdbId: "6YWL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6ywl_final.pdb", - externalLink: "https://pdb-redo.eu/db/6ywl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "NSP3 macrodomain", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SRNWOUGRCWSEMX-KEOHHSTQSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Ni, X.", - "Wang, M.", - "Schroeder, M.", - "Olieric, V.", - "Sharpe, E.M.", - "Wojdyla, J.A.", - "Knapp, S.", - "Chaikuad, A.", - "Structural Genomics Consortium (SGC)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33850605", - title: - "Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain.", - journal: "Acs Med.Chem.Lett. 12: 603-609 (2021), 1948-5875", - doi: "https://doi.org/10.1021/acsmedchemlett.0c00684", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33850605", - pubDate: "2021", - abstract: "", - authors: [ - "Ni, X.", - "Schroder, M.", - "Olieric, V.", - "Sharpe, M.E.", - "Hernandez-Olmos, V.", - "Proschak, E.", - "Merk, D.", - "Knapp, S.", - "Chaikuad, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6ywl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6ywl", - }, - }, - { - title: - "The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 10mer ssRNA", - emdb: null, - pdb: { - dbId: "7ACT", - method: "SOLUTION NMR", - keywords: "protein-RNA complex, docking, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "ssRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Veverka, V. (0000-0003-3782-5279)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33264373", - title: - "Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein.", - journal: "Plos Pathog. 16: e1009100-e1009100 (2020), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1009100", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33264373", - pubDate: "2020", - abstract: "", - authors: [ - "Dinesh, D.C. (0000-0001-9125-4775)", - "Chalupska, D. (0000-0002-9666-4228)", - "Silhan, J.", - "Koutna, E.", - "Nencka, R. (0000-0001-6167-0380)", - "Veverka, V. (0000-0003-3782-5279)", - "Boura, E. (0000-0002-9652-4065)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7act_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7act", - }, - }, - { - title: "Structure of SARS-CoV-2 macro domain in complex with ADP-ribose", - emdb: null, - pdb: { - dbId: "7CZ4", - method: "X-RAY DIFFRACTION", - keywords: "COVID-19, SARS-CoV-2, NSP3, macro domain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CZ4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cz4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cz4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-KEOHHSTQSA-N"], - dbauthors: ["Lin, M.H.", "Hsu, C.H. (0000-0002-0008-7383)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32946224", - title: - "Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain.", - journal: "Acs Infect Dis. 6: 2970-2978 (2020), 2373-8227", - doi: "https://doi.org/10.1021/acsinfecdis.0c00441", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32946224", - pubDate: "2020", - abstract: "", - authors: [ - "Lin, M.H.", - "Chang, S.C.", - "Chiu, Y.C.", - "Jiang, B.C.", - "Wu, T.H.", - "Hsu, C.H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cz4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cz4", - }, - }, - { - title: "SARS-CoV-2 macrodomain Nsp3b bound to the remdesivir nucleoside GS-441524", - emdb: null, - pdb: { - dbId: "7QG7", - method: "X-RAY DIFFRACTION", - keywords: - "NSP3, Macrodomain, SARS-COV-2, Remdesivir, GS-441524, COVID-19, Viral Protein, Drug Discovery", - refModels: [ - { - emdbId: null, - pdbId: "7QG7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qg7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qg7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BRDWIEOJOWJCLU-LTGWCKQJSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Wollenhaupt, J. 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(0000-0001-5693-7909)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35839840", - title: - "Binding Adaptation of GS-441524 Diversifies Macro Domains and Downregulates SARS-CoV-2 de-MARylation Capacity.", - journal: "J.Mol.Biol. 434: 167720-167720 (2022), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2022.167720", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35839840", - pubDate: "2022", - abstract: "", - authors: [ - "Tsika, A.C.", - "Gallo, A.", - "Fourkiotis, N.K.", - "Argyriou, A.I.", - "Sreeramulu, S.", - "Lohr, F.", - "Rogov, V.V.", - "Richter, C.", - "Linhard, V.", - "Gande, S.L.", - "Altincekic, N.", - "Krishnathas, R.", - "Elamri, I.", - "Schwalbe, H.", - "Wollenhaupt, J.", - "Weiss, M.S.", - "Spyroulias, G.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qg7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qg7", - }, - }, - { - title: "A SARS-CoV-2 neutralizing antibody", - emdb: null, - pdb: { - dbId: "7F0X", - method: "X-RAY DIFFRACTION", - keywords: "neutralizing antibody, VIRAL PROTEIN-ANTIVIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7F0X", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f0x_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f0x", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Antibody", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhang, G.", - "Guo, Y. 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(0000-0002-7174-3851)", - "Yao, S.", - "Zhao, W. (0000-0003-2517-4747)", - "Zhang, Y. (0000-0003-0767-1221)", - "Liu, J. (0000-0002-8167-9750)", - "Shao, Q.", - "Wang, Q. (0000-0003-1028-1267)", - "Li, M.", - "Xie, H.", - "Shang, W.", - "Ke, C.", - "Feng, L.", - "Jiang, X.", - "Shen, J. (0000-0001-9679-9934)", - "Xiao, G.", - "Jiang, H. (0000-0003-0656-6315)", - "Zhang, L. (0000-0002-2593-2571)", - "Ye, Y. (0000-0003-1316-5915)", - "Xu, Y. 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(0000-0002-0008-7383)", "Tan, K.P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of post fusion core of SARS-CoV-2 S2 subunit", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Tan, K.P.", - "Lin, M.H.", - "Kuo, P.C.", - "Hsu, C.H. (0000-0002-0008-7383)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cot_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cot", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CC40.8", - emdb: null, - pdb: { - dbId: "7SJS", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Antibody, Spike, S2, stem helix, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7SJS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sjs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sjs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "CC40.8 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC40.8 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "stem helix peptide of Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: ["Wilson, I.A. 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(0000-0002-9891-6476)", - "Peng, L. (0000-0002-3600-2134)", - "Ricketts, J. (0000-0002-9057-5937)", - "Parren, M.", - "Garcia, E.", - "Rawlings, S.A. (0000-0003-3637-1447)", - "Smith, D.M. (0000-0003-3603-1733)", - "Nemazee, D. (0000-0002-4769-6311)", - "Teijaro, J.R. (0000-0001-8280-8887)", - "Rogers, T.F. (0000-0001-9756-327X)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Burton, D.R. (0000-0001-6711-9864)", - "Andrabi, R. (0000-0001-8837-7520)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sjs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sjs", - }, - }, - { - title: - "Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape", - emdb: null, - pdb: { - dbId: "7M7W", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, neutralizing monoclonal antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7M7W", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m7w_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m7w", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S2X259 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S2X259 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S2H97 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S2H97 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Snell, G.", - "Pinto, D.", - "Corti, D.", - "Beltramello, M.", - "Cameroni, E.", - "Czudnochowski, N.", - "Nix, J.C.", - "Croll, T.I.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34261126", - title: - "SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape.", - journal: "Nature 597: 97-102 (2021), 1476-4687", - doi: "https://doi.org/10.1038/s41586-021-03807-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34261126", - pubDate: "2021", - abstract: "", - authors: [ - "Starr, T.N.", - "Czudnochowski, N.", - "Liu, Z.", - "Zatta, F.", - "Park, Y.J.", - "Addetia, A.", - "Pinto, D.", - "Beltramello, M.", - "Hernandez, P.", - "Greaney, A.J.", - "Marzi, R.", - "Glass, W.G.", - "Zhang, I.", - "Dingens, A.S.", - "Bowen, J.E.", - "Tortorici, M.A.", - "Walls, A.C.", - "Wojcechowskyj, J.A.", - "De Marco, A.", - "Rosen, L.E.", - "Zhou, J.", - "Montiel-Ruiz, M.", - "Kaiser, H.", - "Dillen, J.R.", - "Tucker, H.", - "Bassi, J.", - "Silacci-Fregni, C.", - "Housley, M.P.", - "di Iulio, J.", - "Lombardo, G.", - "Agostini, M.", - "Sprugasci, N.", - "Culap, K.", - "Jaconi, S.", - "Meury, M.", - "Dellota Jr., E.", - "Abdelnabi, R.", - "Foo, S.C.", - "Cameroni, E.", - "Stumpf, S.", - "Croll, T.I.", - "Nix, J.C.", - "Havenar-Daughton, C.", - "Piccoli, L.", - "Benigni, F.", - "Neyts, J.", - "Telenti, A.", - "Lempp, F.A.", - "Pizzuto, M.S.", - "Chodera, J.D.", - "Hebner, C.M.", - "Virgin, H.W.", - "Whelan, S.P.J.", - "Veesler, D.", - "Corti, D.", - "Bloom, J.D.", - "Snell, G.", - "Starr, T.N. 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(0000-0003-1267-3408)", - ], - }, - { - pmID: "33851154", - title: - "Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.04.06.438709", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33851154", - pubDate: "2021", - abstract: "", - authors: [ - "Starr, T.N.", - "Czudnochowski, N.", - "Liu, Z.", - "Zatta, F.", - "Park, Y.J.", - "Addetia, A.", - "Pinto, D.", - "Beltramello, M.", - "Hernandez, P.", - "Greaney, A.J.", - "Marzi, R.", - "Glass, W.G.", - "Zhang, I.", - "Dingens, A.S.", - "Bowen, J.E.", - "Tortorici, M.A.", - "Walls, A.C.", - "Wojcechowskyj, J.A.", - "De Marco, A.", - "Rosen, L.E.", - "Zhou, J.", - "Montiel-Ruiz, M.", - "Kaiser, H.", - "Dillen, J.R.", - "Tucker, H.", - "Bassi, J.", - "Silacci-Fregni, C.", - "Housley, M.P.", - "di Iulio, J.", - "Lombardo, G.", - "Agostini, M.", - "Sprugasci, N.", - "Culap, K.", - "Jaconi, S.", - "Meury, M.", - "Dellota Jr., E.", - "Abdelnabi, R.", - "Foo, S.C.", - "Cameroni, E.", - "Stumpf, S.", - "Croll, T.I.", - "Nix, J.C.", - "Havenar-Daughton, C.", - "Piccoli, L.", - "Benigni, F.", - "Neyts, J.", - "Telenti, A.", - "Lempp, F.A.", - "Pizzuto, M.S.", - "Chodera, J.D.", - "Hebner, C.M.", - "Virgin, H.W.", - "Whelan, S.P.J.", - "Veesler, D.", - "Corti, D.", - "Bloom, J.D.", - "Snell, G.", - "Starr, T.N. (0000-0001-6713-6904)", - "Czudnochowski, N. (0000-0002-0771-0721)", - "Zatta, F. (0000-0003-4945-8058)", - "Liu, Z. (0000-0001-8198-0976)", - "Addetia, A. (0000-0001-6703-3841)", - "Pinto, D. (0000-0001-5737-8467)", - "Beltramello, M. (0000-0001-5550-5629)", - "Greaney, A.J. (0000-0001-7202-3349)", - "Glass, W.G. (0000-0002-4099-9280)", - "Zhang, I. (0000-0003-0628-6276)", - "Dingens, A.S. (0000-0001-9603-9409)", - "Bowen, J.E. (0000-0003-3590-9727)", - "De Marco, A. (0000-0001-9641-4838)", - "Rosen, L.E. (0000-0002-8030-0219)", - "Zhou, J. (0000-0002-4231-3422)", - "Kaiser, H. (0000-0002-3991-7401)", - "di Iulio, J. (0000-0001-9343-127X)", - "Dellota, E. (0000-0002-2006-3880)", - "Cameroni, E. (0000-0002-9102-8943)", - "Croll, T.I. (0000-0002-3514-8377)", - "Nix, J.C. (0000-0002-4041-4975)", - "Havenar-Daughton, C. (0000-0002-2880-3927)", - "Telenti, A. (0000-0001-6290-7677)", - "Pizzuto, M.S. (0000-0001-5776-654X)", - "Chodera, J.D. (0000-0003-0542-119X)", - "Whelan, S.P.J. (0000-0003-1564-8590)", - "Virgin, H.W. (0000-0001-8580-7628)", - "Veesler, D. (0000-0002-6019-8675)", - "Corti, D. (0000-0002-5797-1364)", - "Bloom, J.D. (0000-0003-1267-3408)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m7w_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m7w", - }, - }, - { - title: "The crystal structure of papain-like protease of SARS CoV-2", - emdb: null, - pdb: { - dbId: "6W9C", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2 in papain-like protease, IDP51000, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6W9C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6w9c_final.pdb", - externalLink: "https://pdb-redo.eu/db/6w9c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Kim, Y.", - "Tesar, C.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Stols, L.", - "Babnigg, G.", - "Michalska, K.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of papain-like protease of SARS CoV-2", - journal: "to be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Jedrzejczak, R.", - "Tesar, C.", - "Endres, M.", - "Stols, L.", - "Babnigg, G.", - "Kim, Y.", - "Michalska, K.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w9c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w9c", - }, - }, - { - title: "Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 5/6", - emdb: null, - pdb: { - dbId: "7T8M", - method: "X-RAY DIFFRACTION", - keywords: - "Coronavirus, COVID-19, COVID, PROTEASE, DRUG RESISTANCE, COMPLEX, HYDROLASE, DURG DISCOVERY, MAIN PROTEASE, MPRO, SUBSTRATE COMPLEX, NSP 5/6, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7T8M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t8m_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t8m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "562", - name: "Nonstructural protein 5/6", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Shaqra, A.M. (0000-0001-6994-2416)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35729165", - title: - "Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.", - journal: "Nat Commun 13: 3556-3556 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-31210-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35729165", - pubDate: "2022", - abstract: "", - authors: [ - "Shaqra, A.M.", - "Zvornicanin, S.N.", - "Huang, Q.Y.J. (0000-0001-5107-2336)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Knapp, M.", - "Tandeske, L.", - "Bakan, D.T.", - "Flynn, J. (0000-0002-5490-393X)", - "Bolon, D.N.A.", - "Moquin, S.", - "Dovala, D.", - "Kurt Yilmaz, N. (0000-0002-5036-676X)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t8m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t8m", - }, - }, - { - title: - "Structure of sybody MR17 in complex with the SARS-CoV-2 S receptor-binding domain (RBD)", - emdb: null, - pdb: { - dbId: "7C8W", - method: "X-RAY DIFFRACTION", - keywords: - "coronavirus, Covid-19, nanobody, neutralizing antibody, receptor binding protein, SARS-CoV-2, S protein, synthetic antibody, VHH., PROTEIN BINDING", - refModels: [ - { - emdbId: null, - pdbId: "7C8W", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c8w_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c8w", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "32630", - name: "Synthetic nanobody MR17", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: true, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Li, D. 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(0000-0002-9718-5827)", - "Murakami, K.S. (0000-0003-2244-0501)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35217718", - title: - "Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay.", - journal: "Commun Biol 5: 169-169 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03090-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35217718", - pubDate: "2022", - abstract: "", - authors: [ - "Narayanan, A.", - "Narwal, M.", - "Majowicz, S.A. (0000-0002-6331-7780)", - "Varricchio, C.", - "Toner, S.A.", - "Ballatore, C.", - "Brancale, A. (0000-0002-9728-3419)", - "Murakami, K.S. (0000-0003-2244-0501)", - "Jose, J. (0000-0003-1261-6921)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lkd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lkd", - }, - }, - { - title: - "Crystal structure of SARS CoV2 main protease in complex with inhibitor Telaprevir", - emdb: null, - pdb: { - dbId: "6ZRT", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Telaprevir, inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6ZRT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6zrt_final.pdb", - externalLink: "https://pdb-redo.eu/db/6zrt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Main Protease", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "FTZGWEAUHOMNIG-FJRGXGLZSA-N"], - dbauthors: [ - "Oerlemans, R. (0000-0001-7114-3736)", - "Domling, A. (0000-0002-9923-8873)", - "Groves, M.R. (0000-0001-9859-5177)", - "Wang, W. (0000-0002-6272-3381)", - "Lunev, S. (0000-0001-9867-6866)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34041486", - title: - "Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics.", - journal: "Rsc Med Chem 12: 370-379 (2020), 2632-8682", - doi: "https://doi.org/10.1039/d0md00367k", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34041486", - pubDate: "2020", - abstract: "", - authors: [ - "Oerlemans, R.", - "Ruiz-Moreno, A.J. (0000-0002-2798-5386)", - "Cong, Y.", - "Dinesh Kumar, N.", - "Velasco-Velazquez, M.A.", - "Neochoritis, C.G. (0000-0001-5098-5504)", - "Smith, J.", - "Reggiori, F.", - "Groves, M.R.", - "Domling, A. (0000-0002-9923-8873)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zrt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zrt", - }, - }, - { - title: "immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 6D6", - emdb: null, - pdb: { - dbId: "7EAN", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Receptor binding domain, neutralizing antibody, immune complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7EAN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ean_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ean", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Heavy chain of SARS-CoV-2 cross-neutralizing mAb 6D6", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Light chain of SARS-CoV-2 cross-neutralizing mAb 6D6", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Li, T.T. (0000-0002-9917-7804)", - "Gu, Y. (0000-0002-2870-2800)", - "Li, S.W. (0000-0002-3374-1038)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Cross-neutralizing antibodies bind a SARS-CoV-2 cryptic site and resist circulating variants.", - journal: "Nat Commun 12 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25997-3", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Li, T. (0000-0002-9917-7804)", - "Xue, W.", - "Zheng, Q. (0000-0002-7516-9965)", - "Song, S. (0000-0002-0289-2941)", - "Yang, C.", - "Xiong, H.", - "Zhang, S.", - "Hong, M.", - "Zhang, Y.", - "Yu, H.", - "Sun, H.", - "Huang, Y.", - "Deng, T.", - "Chi, X.", - "Li, J.", - "Wang, S.", - "Zhou, L.", - "Chen, T.", - "Wang, Y.", - "Cheng, T. (0000-0002-1638-6214)", - "Zhang, T. (0000-0002-2477-329X)", - "Yuan, Q. (0000-0001-5487-561X)", - "Zhao, Q.", - "Zhang, J.", - "McLellan, J.S. (0000-0003-3991-542X)", - "Zhou, Z.H. (0000-0002-8373-4717)", - "Zhang, Z. (0000-0002-3544-1389)", - "Li, S. (0000-0002-3374-1038)", - "Gu, Y. (0000-0002-2870-2800)", - "Xia, N. (0000-0003-0179-5266)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ean_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ean", - }, - }, - { - title: - "Structure of SARS-CoV-2 Mpro Lambda (G15S) in complex with Nirmatrelvir (PF-07321332)", - emdb: null, - pdb: { - dbId: "7U28", - method: "X-RAY DIFFRACTION", - keywords: - "Protease, SARS-CoV-2, covalent complex, inhibitor, HYDROLASE-INHIBITOR complex, Omicron, PF-07321332, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7U28", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u28_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u28", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: [ - "Stewart, A.E.", - "Greasley, S.E. (0000-0002-7978-6477)", - "Ferre, R.A. (0000-0001-7462-1879)", - "Liu, W. (0000-0002-8541-4928)", - "Plotnikova, O. (0000-0002-2513-7287)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35461811", - title: - "Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants.", - journal: "J.Biol.Chem. 298: 101972-101972 (2022), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2022.101972", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35461811", - pubDate: "2022", - abstract: "", - authors: [ - "Greasley, S.E.", - "Noell, S.", - "Plotnikova, O.", - "Ferre, R.", - "Liu, W.", - "Bolanos, B.", - "Fennell, K.", - "Nicki, J.", - "Craig, T.", - "Zhu, Y.", - "Stewart, A.E.", - "Steppan, C.M.", - ], - }, - { - pmID: "", - title: - "Structural basis for Nirmatrelvir in vitro efficacy against the Omicron variant of SARS-CoV-2", - journal: "Biorxiv (2022)", - doi: "https://doi.org/10.1101/2022.01.17.476556", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Greasley, S.E.", - "Noell, S.", - "Plotnikova, O.", - "Ferre, R.", - "Liu, W.", - "Bolanos, B.", - "Fennell, K.", - "Nicki, J.", - "Craig, T.", - "Zhu, Y.", - "Stewart, A.E.", - "Steppan, C.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7u28_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7u28", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z56827661", - emdb: null, - pdb: { - dbId: "5S2M", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S2M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s2m_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s2m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YKAKNMHEIJUKEX-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s2m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s2m", - }, - }, - { - title: - "SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab", - emdb: null, - pdb: { - dbId: "7R6W", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, neutralizing monoclonal antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7R6W", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7r6w_final.pdb", - externalLink: "https://pdb-redo.eu/db/7r6w", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Light Chain of Fab domain of monoclonal antibody S309", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy Chain of Fab domain of monoclonal antibody S309", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light Chain of Fab domain of monoclonal antibody S2X35", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy Chain of Fab domain of monoclonal antibody S2X35", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "BDERNNFJNOPAEC-UHFFFAOYSA-N", - ], - dbauthors: [ - "Snell, G.", - "Pinto, D.", - "Corti, D.", - "Beltramello, M.", - "Cameroni, E.", - "Czudnochowski, N.", - "Nix, J.C.", - "Croll, T.I.", - "Hernandez, P.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34261126", - title: - "SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape.", - journal: "Nature 597: 97-102 (2021), 1476-4687", - doi: "https://doi.org/10.1038/s41586-021-03807-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34261126", - pubDate: "2021", - abstract: "", - authors: [ - "Starr, T.N.", - "Czudnochowski, N.", - "Liu, Z.", - "Zatta, F.", - "Park, Y.J.", - "Addetia, A.", - "Pinto, D.", - "Beltramello, M.", - "Hernandez, P.", - "Greaney, A.J.", - "Marzi, R.", - "Glass, W.G.", - "Zhang, I.", - "Dingens, A.S.", - "Bowen, J.E.", - "Tortorici, M.A.", - "Walls, A.C.", - "Wojcechowskyj, J.A.", - "De Marco, A.", - "Rosen, L.E.", - "Zhou, J.", - "Montiel-Ruiz, M.", - "Kaiser, H.", - "Dillen, J.R.", - "Tucker, H.", - "Bassi, J.", - "Silacci-Fregni, C.", - "Housley, M.P.", - "di Iulio, J.", - "Lombardo, G.", - "Agostini, M.", - "Sprugasci, N.", - "Culap, K.", - "Jaconi, S.", - "Meury, M.", - "Dellota Jr., E.", - "Abdelnabi, R.", - "Foo, S.C.", - "Cameroni, E.", - "Stumpf, S.", - "Croll, T.I.", - "Nix, J.C.", - "Havenar-Daughton, C.", - "Piccoli, L.", - "Benigni, F.", - "Neyts, J.", - "Telenti, A.", - "Lempp, F.A.", - "Pizzuto, M.S.", - "Chodera, J.D.", - "Hebner, C.M.", - "Virgin, H.W.", - "Whelan, S.P.J.", - "Veesler, D.", - "Corti, D.", - "Bloom, J.D.", - "Snell, G.", - "Starr, T.N. 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(0000-0003-1267-3408)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7r6w_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7r6w", - }, - }, - { - title: - "1.70 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 2f", - emdb: null, - pdb: { - dbId: "7LKS", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LKS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lks_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lks", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "CDEICDIJDMTLMS-JBKSVKCVSA-N", - "CDEICDIJDMTLMS-NFFJHMNLSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Rathnayake, A.D.", - "Baird, M.A.", - "Shadipeni, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34213885", - title: - "Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease.", - journal: "J.Med.Chem. 64: 10047-10058 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00319", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34213885", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Kim, Y.", - "Bickmeier, N.", - "Rathnayake, A.D.", - "Nguyen, H.N.", - "Zheng, J.", - "Kashipathy, M.M.", - "Baird, M.A.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lks_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lks", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with the Fab fragments of neutralizing antibodies 298 and 52", - emdb: null, - pdb: { - dbId: "7K9Z", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Receptor Binding Domain, Neutralizing antibodies, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7K9Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k9z_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k9z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "52 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "52 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "298 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "298 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Kucharska, I. (0000-0001-6150-3419)", - "Julien, J.P. (0000-0001-7602-3995)", - "Newton, J.C. (0000-0001-9987-0580)", - "Rujas, E. (0000-0002-4465-5071)", - "Cui, H. (0000-0001-9917-047X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34135340", - title: - "Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers.", - journal: "Nat Commun 12: 3661-3661 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23825-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34135340", - pubDate: "2021", - abstract: "", - authors: [ - "Rujas, E.", - "Kucharska, I.", - "Tan, Y.Z. (0000-0001-6656-6320)", - "Benlekbir, S.", - "Cui, H.", - "Zhao, T.", - "Wasney, G.A.", - "Budylowski, P.", - "Guvenc, F.", - "Newton, J.C.", - "Sicard, T.", - "Semesi, A.", - "Muthuraman, K.", - "Nouanesengsy, A.", - "Aschner, C.B. (0000-0001-8940-5423)", - "Prieto, K.", - "Bueler, S.A.", - "Youssef, S.", - "Liao-Chan, S.", - "Glanville, J.", - "Christie-Holmes, N.", - "Mubareka, S.", - "Gray-Owen, S.D. (0000-0002-1477-3616)", - "Rubinstein, J.L. (0000-0003-0566-2209)", - "Treanor, B. (0000-0002-8626-5944)", - "Julien, J.P. (0000-0001-7602-3995)", - "Tan, Y.Z.", - "Wasney, G.", - "Gray-Owen, S.D.", - "Rubinstein, J.L.", - "Treanor, B.", - "Julien, J.P.", - ], - }, - { - pmID: "", - title: - "Multivalency transforms SARS-CoV-2 antibodies into broad and ultrapotent neutralizers", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.10.15.341636", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Rujas, E.", - "Kucharska, I.", - "Tan, Y.Z. (0000-0001-6656-6320)", - "Benlekbir, S.", - "Cui, H.", - "Zhao, T.", - "Wasney, G.A.", - "Budylowski, P.", - "Guvenc, F.", - "Newton, J.C.", - "Sicard, T.", - "Semesi, A.", - "Muthuraman, K.", - "Nouanesengsy, A.", - "Aschner, C.B. (0000-0001-8940-5423)", - "Prieto, K.", - "Bueler, S.A.", - "Youssef, S.", - "Liao-Chan, S.", - "Glanville, J.", - "Christie-Holmes, N.", - "Mubareka, S.", - "Gray-Owen, S.D. (0000-0002-1477-3616)", - "Rubinstein, J.L. (0000-0003-0566-2209)", - "Treanor, B. (0000-0002-8626-5944)", - "Julien, J.P. (0000-0001-7602-3995)", - "Tan, Y.Z.", - "Wasney, G.", - "Gray-Owen, S.D.", - "Rubinstein, J.L.", - "Treanor, B.", - "Julien, J.P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k9z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k9z", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494 inhibitor", - emdb: null, - pdb: { - dbId: "7KOJ", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7KOJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7koj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7koj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "UPLVMSAQDITPGI-QGZVFWFLSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder494", - journal: "to be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Lisnyak, V.", - "Maki, S.", - "Taylor, C.", - "Zhang, Y.", - "Zhou, Z.", - "Azizi, S.A.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - "Dickinson, B.C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7koj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7koj", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z50145861", - emdb: null, - pdb: { - dbId: "5S3I", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3i_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QELUYTUMUWHWMC-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3i", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-68", - emdb: null, - pdb: { - dbId: "7RLS", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RLS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rls_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rls", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BYGXXTSBJDGVES-UHFFFAOYSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34705466", - title: - "Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.", - journal: "J.Med.Chem. 64: 17366-17383 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01475", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34705466", - pubDate: "2021", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Li, H. (0000-0002-6964-9962)", - "Galanie, S.", - "Phillips, G.", - "Labbe, A.", - "Weiss, K.L. (0000-0002-6486-8007)", - "Zhang, Q.", - "Arnould, M.A.", - "Clyde, A.", - "Ma, H.", - "Ramanathan, A. (0000-0002-1622-5488)", - "Jonsson, C.B. (0000-0002-2640-7672)", - "Head, M.S.", - "Coates, L. (0000-0003-2342-049X)", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A. 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(0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Lee, J.M.", - "Nalivaika, E.A.", - "Yilmaz, N.K. (0000-0002-5036-676X)", - "Thompson, P.R. (0000-0002-1621-3372)", - "Reyes, A.C. (0000-0001-9955-393X)", - "Ali, A. (0000-0003-3491-791X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33503819", - title: - "Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188.", - journal: "Viruses 13 (2021), 1999-4915", - doi: "https://doi.org/10.3390/v13020174", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33503819", - pubDate: "2021", - abstract: "", - authors: [ - "Lockbaum, G.J.", - "Reyes, A.C. (0000-0001-9955-393X)", - "Lee, J.M.", - "Tilvawala, R.", - "Nalivaika, E.A.", - "Ali, A.", - "Kurt Yilmaz, N.", - "Thompson, P.R.", - "Schiffer, C.A. 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5spx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5spx", - }, - }, - { - title: - "Crystal structure of MG-132 covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2 in spacegroup P1.", - emdb: null, - pdb: { - dbId: "7NG3", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN, MG-132", - refModels: [ - { - emdbId: null, - pdbId: "7NG3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ng3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ng3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M", "WUJQMWDTZKIKQZ-VABKMULXSA-N"], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P.", "Giabbai, B."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34769210", - title: - "Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L.", - journal: "Int J Mol Sci 22 (2021), 1422-0067", - doi: "https://doi.org/10.3390/ijms222111779", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34769210", - pubDate: "2021", - abstract: "", - authors: [ - "Costanzi, E.", - "Kuzikov, M. (0000-0001-8771-1865)", - "Esposito, F. (0000-0001-9725-7977)", - "Albani, S. (0000-0002-3560-4539)", - "Demitri, N.", - "Giabbai, B.", - "Camasta, M.", - "Tramontano, E. (0000-0002-4849-0980)", - "Rossetti, G. (0000-0002-2032-4630)", - "Zaliani, A. (0000-0002-1740-8390)", - "Storici, P. (0000-0002-2590-3332)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ng3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ng3", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z3508769536 - (S) isomer", - emdb: null, - pdb: { - dbId: "5SP9", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SP9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sp9_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sp9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AOHBVEDXTIZALI-HNNXBMFYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sp9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sp9", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINCk500000doQ8X", - emdb: null, - pdb: { - dbId: "5SSC", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SSC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5ssc_final.pdb", - externalLink: "https://pdb-redo.eu/db/5ssc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YHUMVPIVKSGDRU-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5ssc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5ssc", - }, - }, - { - title: "SARS-CoV-2 RLQ peptide binds to HLA-A2", - emdb: null, - pdb: { - dbId: "7N1B", - method: "X-RAY DIFFRACTION", - keywords: "pMHC, SARS-CoV-2, SPIKE, RLQ, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7N1B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n1b_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n1b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "A0A5B8RNS7", - organism: "9606", - name: "MHC class I antigen, A-2 alpha chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2", - details: - "Lysine at N-terminal is used for biochemical assays; two serines were added at N-terminal to increase the peptide solubility in PBS", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wu, D. (0000-0003-2086-0190)", "Mariuzza, R.A. (0000-0003-0748-5875)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35013235", - title: - "Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and private T-cell receptors.", - journal: "Nat Commun 13: 19-19 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-27669-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35013235", - pubDate: "2022", - abstract: "", - authors: [ - "Wu, D. (0000-0003-2086-0190)", - "Kolesnikov, A.", - "Yin, R. (0000-0001-5330-8306)", - "Guest, J.D. (0000-0003-1521-5242)", - "Gowthaman, R. (0000-0002-0008-6401)", - "Shmelev, A. (0000-0002-4842-9338)", - "Serdyuk, Y. (0000-0003-1573-7614)", - "Dianov, D.V.", - "Efimov, G.A. (0000-0001-7129-6062)", - "Pierce, B.G. (0000-0003-4821-0368)", - "Mariuzza, R.A. (0000-0003-0748-5875)", - "Wu, D.", - "Yin, R.", - "Guest, J.D.", - "Gowthaman, R.", - "Shmelev, A.", - "Serdyuk, Y.", - "Efimov, G.A.", - "Pierce, B.G.", - "Mariuzza, R.A.", - ], - }, - { - pmID: "", - title: - "Structural basis for recognition of two HLA-A2-restricted SARS-CoV-2 spike epitopes by public and private T cell receptors", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.07.28.454232", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Wu, D. (0000-0003-2086-0190)", - "Kolesnikov, A.", - "Yin, R. (0000-0001-5330-8306)", - "Guest, J.D. (0000-0003-1521-5242)", - "Gowthaman, R. (0000-0002-0008-6401)", - "Shmelev, A. (0000-0002-4842-9338)", - "Serdyuk, Y. (0000-0003-1573-7614)", - "Dianov, D.V.", - "Efimov, G.A. (0000-0001-7129-6062)", - "Pierce, B.G. (0000-0003-4821-0368)", - "Mariuzza, R.A. (0000-0003-0748-5875)", - "Wu, D.", - "Yin, R.", - "Guest, J.D.", - "Gowthaman, R.", - "Shmelev, A.", - "Serdyuk, Y.", - "Efimov, G.A.", - "Pierce, B.G.", - "Mariuzza, R.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n1b_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n1b", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with noncovalent inhibitor Jun8-76-3A", - emdb: null, - pdb: { - dbId: "7KX5", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, 76-3A, noncovalent, inhibitor, non-covalent, main protease, 3cl, SARS, SARS-CoV-2, COVID, COVID-19, 3c-like, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7KX5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kx5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kx5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RYGJIKURQDMMQZ-YUDQIZAISA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34860011", - title: - "Discovery of Di- and Trihaloacetamides as Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity.", - journal: "J.Am.Chem.Soc. 143: 20697-20709 (2021), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08060", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34860011", - pubDate: "2021", - abstract: "", - authors: [ - "Ma, C.", - "Xia, Z.", - "Sacco, M.D.", - "Hu, Y.", - "Townsend, J.A.", - "Meng, X.", - "Choza, J.", - "Tan, H.", - "Jang, J.", - "Gongora, M.V.", - "Zhang, X.", - "Zhang, F.", - "Xiang, Y.", - "Marty, M.T. (0000-0001-8115-1772)", - "Chen, Y.", - "Wang, J. (0000-0002-4845-4621)", - "Kitamura, N.", - "Ba, M.", - "Szeto, T.", - "Kukuljac, A.", - "Marty, M.T.", - "Schultz, D.", - "Cherry, S.", - "Wang, J.", - ], - }, - { - pmID: "33891389", - title: - "Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors.", - journal: "J.Med.Chem. 65: 2848-2865 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00509", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33891389", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, C.", - "Xia, Z.", - "Sacco, M.D.", - "Hu, Y.", - "Townsend, J.A.", - "Meng, X.", - "Choza, J.", - "Tan, H.", - "Jang, J.", - "Gongora, M.V.", - "Zhang, X.", - "Zhang, F.", - "Xiang, Y.", - "Marty, M.T. (0000-0001-8115-1772)", - "Chen, Y.", - "Wang, J. (0000-0002-4845-4621)", - "Kitamura, N.", - "Ba, M.", - "Szeto, T.", - "Kukuljac, A.", - "Marty, M.T.", - "Schultz, D.", - "Cherry, S.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kx5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kx5", - }, - }, - { - title: "Structure of SARS-CoV-2 Papain-like protease PLpro", - emdb: null, - pdb: { - dbId: "7NFV", - method: "X-RAY DIFFRACTION", - keywords: - "Papain-like protease SARS-CoV-2 Hydrolase Zinc binding protein, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7NFV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nfv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nfv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Wang, M.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Hinrichs, W.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Brognaro, H.", - "Brings, L.", - "Lorenzen, K.", - "Betzel, C.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Ginn, H.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Ullah, N.", - "Andaleeb, H.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Saouane, S.", - "Ehrt, C.", - "Rarey, M.", - "Gunther, S.", - "Lieske, J.", - "Ewert, W.", - "Srinivasan, V. (0000-0002-8895-5885)", - "Sprenger, J.", - "Perk, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35953531", - title: - "Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.", - journal: "Commun Biol 5: 805-805 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03737-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35953531", - pubDate: "2022", - abstract: "", - authors: [ - "Srinivasan, V. (0000-0002-8895-5885)", - "Brognaro, H.", - "Prabhu, P.R.", - "de Souza, E.E.", - "Gunther, S. (0000-0002-7329-6653)", - "Reinke, P.Y.A.", - "Lane, T.J. (0000-0003-2627-4432)", - "Ginn, H.", - "Han, H.", - "Ewert, W. (0000-0001-8626-4864)", - "Sprenger, J.", - "Koua, F.H.M. (0000-0001-8371-9587)", - "Falke, S.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N. 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(0000-0002-1135-2744)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35142215", - title: - "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", - journal: "J.Am.Chem.Soc. 144: 2905-2920 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08402", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35142215", - pubDate: "2022", - abstract: "", - authors: [ - "Luttens, A. (0000-0003-2915-7901)", - "Gullberg, H.", - "Abdurakhmanov, E.", - "Vo, D.D.", - "Akaberi, D. (0000-0002-9595-9796)", - "Talibov, V.O.", - "Nekhotiaeva, N.", - "Vangeel, L.", - "De Jonghe, S. (0000-0002-3872-6558)", - "Jochmans, D.", - "Krambrich, J.", - "Tas, A.", - "Lundgren, B.", - "Gravenfors, Y. (0000-0001-6025-4908)", - "Craig, A.J.", - "Atilaw, Y.", - "Sandstrom, A.", - "Moodie, L.W.K. 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(0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33786375", - title: - "Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations.", - journal: "Acs Cent.Sci. 7: 467-475 (2021), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.1c00039", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33786375", - pubDate: "2021", - abstract: "", - authors: [ - "Zhang, C.H.", - "Stone, E.A.", - "Deshmukh, M.", - "Ippolito, J.A.", - "Ghahremanpour, M.M.", - "Tirado-Rives, J.", - "Spasov, K.A.", - "Zhang, S.", - "Takeo, Y.", - "Kudalkar, S.N.", - "Liang, Z.", - "Isaacs, F.", - "Lindenbach, B.", - "Miller, S.J.", - "Anderson, K.S.", - "Jorgensen, W.L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l14_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l14", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z645232558", - emdb: null, - pdb: { - dbId: "5S2O", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S2O", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s2o_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s2o", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZUNGTEUNVMHDIX-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-4883-1933)", - "Zocher, G. (0000-0001-8711-2088)", - "Stehle, T. (0000-0002-4571-8548)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33904225", - title: - "NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies.", - journal: "Embo Rep. 22: e52325-e52325 (2021), 1469-3178", - doi: "https://doi.org/10.15252/embr.202052325", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33904225", - pubDate: "2021", - abstract: "", - authors: [ - "Wagner, T.R. (0000-0002-1050-5948)", - "Ostertag, E.", - "Kaiser, P.D.", - "Gramlich, M.", - "Ruetalo, N.", - "Junker, D.", - "Haering, J.", - "Traenkle, B.", - "Becker, M.", - "Dulovic, A.", - "Schweizer, H. (0000-0001-9407-944X)", - "Nueske, S.", - "Scholz, A.", - "Zeck, A.", - "Schenke-Layland, K.", - "Nelde, A.", - "Strengert, M.", - "Walz, J.S.", - "Zocher, G.", - "Stehle, T.", - "Schindler, M.", - "Schneiderhan-Marra, N.", - "Rothbauer, U. (0000-0001-5923-8986)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7b27_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7b27", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z219104216", - emdb: null, - pdb: { - dbId: "5S3K", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3K", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3k_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3k", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MVJDUNKELBBNKM-UHFFFAOYSA-N", "MNIGYIKCFSPQRJ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. 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(0000-0002-1241-2577)", - "Anson, B.A. (0000-0003-2670-974X)", - "Ghosh, A.K. 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}, - }, - { - title: - "Crystal structure of myricetin covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7B3E", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN, myricetin", - refModels: [ - { - emdbId: null, - pdbId: "7B3E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7b3e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7b3e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Main Protease", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "YMWUJEATGCHHMB-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P.", "Giabbai, B."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s29_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s29", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z1139246057", - emdb: null, - pdb: { - dbId: "5S2X", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S2X", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s2x_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s2x", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QLSDWIHANVSIEK-SECBINFHSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s2x_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s2x", - }, - }, - { - title: - "Covalent complex of SARS-CoV-2 main protease with N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide", - emdb: null, - pdb: { - dbId: "6XHM", - method: "X-RAY DIFFRACTION", - keywords: "coronavirus protease inhibitor complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6XHM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xhm_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xhm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FDQSUXUTXIGUIA-PRIDNEQBSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: ["Ferre, R.A.", "Stewart, A.E.", "Gajiwala, K.S.", "Ryan, K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33054210", - title: - "Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19.", - journal: "J.Med.Chem. 63: 12725-12747 (2020), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.0c01063", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33054210", - pubDate: "2020", - abstract: "", - authors: [ - "Hoffman, R.L.", - "Kania, R.S.", - "Brothers, M.A.", - "Davies, J.F.", - "Ferre, R.A.", - "Gajiwala, K.S.", - "He, M.", - "Hogan, R.J.", - "Kozminski, K.", - "Li, L.Y.", - "Lockner, J.W.", - "Lou, J.", - "Marra, M.T.", - "Mitchell Jr., L.J.", - "Murray, B.W.", - "Nieman, J.A.", - "Noell, S.", - "Planken, S.P.", - "Rowe, T.", - "Ryan, K.", - "Smith 3rd, G.J.", - "Solowiej, J.E.", - "Steppan, C.M.", - "Taggart, B.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xhm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xhm", - }, - }, - { - title: - "Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2", - emdb: null, - pdb: { - dbId: "6LZG", - method: "X-RAY DIFFRACTION", - keywords: "Novel Coronavirus, Spike protein, receptor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6LZG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6lzg_final.pdb", - externalLink: "https://pdb-redo.eu/db/6lzg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Qi, J.X. (0000-0002-9358-4732)", - "Song, H. (0000-0002-2811-0370)", - "Wang, Q.H. (0000-0003-0032-4956)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Insect cell expression vector pTIE1", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32275855", - title: - "Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.", - journal: "Cell 181: 894-904.e9 (2020), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2020.03.045", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32275855", - pubDate: "2020", - abstract: "", - authors: [ - "Wang, Q.", - "Zhang, Y.", - "Wu, L.", - "Niu, S.", - "Song, C.", - "Zhang, Z.", - "Lu, G.", - "Qiao, C.", - "Hu, Y.", - "Yuen, K.Y.", - "Zhou, H.", - "Yan, J.", - "Qi, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6lzg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6lzg", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z56923284", - emdb: null, - pdb: { - dbId: "5RLC", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RLC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rlc_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rlc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "YBUXKQSCKVQATK-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rlc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rlc", - }, - }, - { - title: "The crystal structure of COVID-19 main protease in complex with GC376", - emdb: null, - pdb: { - dbId: "7C8U", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7C8U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c8u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c8u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: [ - "Wang, H.", - "Zhang, S.", - "Wang, Y.", - "Zhang, L.", - "Wang, F.", - "Zhou, R.", - "Zhang, Z.", - "Wu, W.", - "Liu, M.", - "Luan, X.", - "Yin, W.", - "Jiang, Y.", - "Cheng, W.", - "Jin, Y.", - "Xu, H.E.", - "Tian, R.", - "Gao, M.", - "Shang, W.", - "Jiang, H.W.", - "Feng, S.", - "Tian, Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of COVID-19 main protease in complex with GC376", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Zhang, S.Y. (0000-0002-1532-0029)", - "Luan, X.D. (0000-0002-1279-5432)", - "Wang, F. (0000-0002-4384-5834)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7c8u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7c8u", - }, - }, - { - title: - "Structure of SARS-CoV2 3CL protease covalently bound to peptidomimetic inhibitor", - emdb: null, - pdb: { - dbId: "7MBI", - method: "X-RAY DIFFRACTION", - keywords: "viral protein, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7MBI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mbi_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mbi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["HDPZWFCIPQRUTJ-VDGAXYAQSA-N", "YUGIEZXMHZFOFD-UHFFFAOYSA-N"], - dbauthors: [ - "Lu, J. (0000-0002-4090-5176)", - "Khan, M.B. (0000-0002-4164-9573)", - "Young, H.S. (0000-0002-5990-8422)", - "Lemieux, M.J. (0000-0003-4745-9153)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli O103:H2", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34242027", - title: - "Peptidomimetic alpha-Acyloxymethylketone Warheads with Six-Membered Lactam P1 Glutamine Mimic: SARS-CoV-2 3CL Protease Inhibition, Coronavirus Antiviral Activity, and in Vitro Biological Stability.", - journal: "J.Med.Chem. 65: 2905-2925 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00616", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34242027", - pubDate: "2022", - abstract: "", - authors: [ - "Bai, B.", - "Belovodskiy, A.", - "Hena, M.", - "Kandadai, A.S.", - "Joyce, M.A.", - "Saffran, H.A.", - "Shields, J.A.", - "Khan, M.B.", - "Arutyunova, E.", - "Lu, J.", - "Bajwa, S.K.", - "Hockman, D.", - "Fischer, C.", - "Lamer, T.", - "Vuong, W.", - "van Belkum, M.J.", - "Gu, Z.", - "Lin, F.", - "Du, Y.", - "Xu, J.", - "Rahim, M.", - "Young, H.S.", - "Vederas, J.C.", - "Tyrrell, D.L.", - "Lemieux, M.J.", - "Nieman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mbi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mbi", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z285675722", - emdb: null, - pdb: { - dbId: "5RMG", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RMG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rmg_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rmg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "ZLIBICFPKPWGIZ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rmg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rmg", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z53116498", - emdb: null, - pdb: { - dbId: "5RLT", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RLT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rlt_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rlt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "HZTUIHZIQKFSIL-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rlt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rlt", - }, - }, - { - title: - "PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease covalent inhibitors -- Crystal Structure of SARS-CoV-2 main protease in complex with LON-WEI-adc59df6-30 (Mpro-x3359)", - emdb: null, - pdb: { - dbId: "5RL5", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5RL5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rl5_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rl5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "YWMXVWPDEYVMJP-HXUWFJFHSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "London, N.", - "Zaidman, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease covalent inhibitors", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Zaidman, D.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Gorrie-Stone, T.J.", - "Skyner, R.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rl5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rl5", - }, - }, - { - title: "The crystal structure of SARS-CoV-2 3CL protease in complex with compound 3", - emdb: null, - pdb: { - dbId: "7VU6", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITO COMPLEX, Viral protein-inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7VU6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vu6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vu6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QMPBBNUOBOFBFS-UHFFFAOYSA-N"], - dbauthors: [ - "Yamamoto, S. (0000-0002-1731-7931)", - "Yamane, J.", - "Tachibana, Y. (0000-0001-6845-4453)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35352927", - title: - "Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19.", - journal: "J.Med.Chem. 65: 6499-6512 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00117", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35352927", - pubDate: "2022", - abstract: "", - authors: [ - "Unoh, Y.", - "Uehara, S. (0000-0001-5214-8531)", - "Nakahara, K.", - "Nobori, H.", - "Yamatsu, Y.", - "Yamamoto, S. (0000-0002-1731-7931)", - "Maruyama, Y.", - "Taoda, Y. (0000-0001-8469-3788)", - "Kasamatsu, K.", - "Suto, T.", - "Kouki, K.", - "Nakahashi, A.", - "Kawashima, S.", - "Sanaki, T.", - "Toba, S.", - "Uemura, K.", - "Mizutare, T.", - "Ando, S. (0000-0002-9148-6530)", - "Sasaki, M.", - "Orba, Y.", - "Sawa, H.", - "Sato, A.", - "Sato, T.", - "Kato, T.", - "Tachibana, Y. (0000-0001-6845-4453)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vu6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vu6", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 main protease in complex with Z-VAD(OMe)-FMK", - emdb: null, - pdb: { - dbId: "7C8B", - method: "X-RAY DIFFRACTION", - keywords: - "Coronavirus, Protease, Inhibitor, Complex, Viral Protein, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7C8B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c8b_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c8b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - 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}, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Tegafur", - emdb: null, - pdb: { - dbId: "7AWR", - method: "X-RAY DIFFRACTION", - keywords: "inhibitor, complex, screen, sars-cov-2, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AWR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7awr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7awr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WFWLQNSHRPWKFK-ZCFIWIBFSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7awr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7awr", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z426041412", - emdb: null, - pdb: { - dbId: "5RM1", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RM1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rm1_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rm1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "IZJVPNBRAKIMBK-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. 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(0000-0001-5524-3542)", - "Zhu, Y.", - "Wang, C.", - "Xu, W.", - "Li, Y.", - "Wang, L.", - "Jiao, F.", - "Zhou, J.", - "Hua, C.", - "Wang, Q.", - "Cai, X.", - "Wu, Y.", - "Gao, J.", - "Liu, H.", - "Sun, G.", - "Munch, J. (0000-0001-7316-7141)", - "Kirchhoff, F. (0000-0002-7052-2360)", - "Yuan, Z.", - "Xie, Y. (0000-0002-2416-7708)", - "Sun, F.", - "Jiang, S. (0000-0001-8283-7135)", - "Lu, L. (0000-0002-2255-0391)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7c53_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7c53", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 29", - emdb: null, - pdb: { - dbId: "7M8Z", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7M8Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m8z_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m8z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JKRQOBZCXCNDAL-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, C.H.", - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34161756", - title: - "Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.", - journal: "Structure 29 (2021), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2021.06.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34161756", - pubDate: "2021", - abstract: "", - authors: [ - "Deshmukh, M.G.", - "Ippolito, J.A.", - "Zhang, C.H.", - "Stone, E.A.", - "Reilly, R.A.", - "Miller, S.J.", - "Jorgensen, W.L.", - "Anderson, K.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m8z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m8z", - }, - }, - { - title: "SARS-CoV-2 S stem helix peptide bound to Fab22", - emdb: null, - pdb: { - dbId: "7S3N", - method: "X-RAY DIFFRACTION", - keywords: "Spike, Fusion, Antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7S3N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s3n_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s3n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "Fab22 Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "Fab22 Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["McLellan, J.S.", "Goldsmith, J.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34710354", - title: - "Stabilized coronavirus spike stem elicits a broadly protective antibody.", - journal: "Cell Rep 37: 109929-109929 (2021), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2021.109929", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34710354", - pubDate: "2021", - abstract: "", - authors: [ - "Hsieh, C.L.", - "Werner, A.P.", - "Leist, S.R.", - "Stevens, L.J.", - "Falconer, E.", - "Goldsmith, J.A.", - "Chou, C.W.", - "Abiona, O.M.", - "West, A.", - "Westendorf, K.", - "Muthuraman, K.", - "Fritch, E.J.", - "Dinnon 3rd, K.H.", - "Schafer, A.", - "Denison, M.R.", - "Chappell, J.D.", - "Baric, R.S.", - "Graham, B.S.", - "Corbett, K.S.", - "McLellan, J.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s3n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s3n", - }, - }, - { - title: - "Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder630 inhibitor", - emdb: null, - pdb: { - dbId: "7SGV", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, coronavirus, SARS, COV-2, papain-like protease, IDP51000, IDP52003, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7SGV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sgv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sgv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OZOFJVFWGZHBHV-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder630 inhibitor", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Lisnyak, V.", - "Maki, S.", - "Taylor, C.", - "Zhang, Y.", - "Zhou, Z.", - "Azizi, S.A.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - "Dickinson, B.C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sgv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sgv", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 11", - emdb: null, - pdb: { - dbId: "7M8M", - method: "X-RAY DIFFRACTION", - keywords: "NOVEL CORONAVIRUS, ANTIVIRAL, DRUG DESIGN, VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7M8M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m8m_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m8m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GJCBTWHGKCNYAB-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, C.H.", - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34161756", - title: - "Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.", - journal: "Structure 29 (2021), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2021.06.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34161756", - pubDate: "2021", - abstract: "", - authors: [ - "Deshmukh, M.G.", - "Ippolito, J.A.", - "Zhang, C.H.", - "Stone, E.A.", - "Reilly, R.A.", - "Miller, S.J.", - "Jorgensen, W.L.", - "Anderson, K.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m8m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m8m", - }, - }, - { - title: - "Structure of the SARS-CoV-2 RBD in complex with neutralizing antibody N-612-056", - emdb: null, - pdb: { - dbId: "7S0B", - method: "X-RAY DIFFRACTION", - keywords: - "Antibody, SARS-CoV-2, COVID-19, mRNA Display, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7S0B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s0b_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s0b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "N-612-056 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "N-612-056 Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Bjorkman, P.J.", "Barnes, C.O.", "Tanaka, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35114110", - title: - "Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display.", - journal: "Cell Rep 38: 110348-110348 (2022), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2022.110348", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35114110", - pubDate: "2022", - abstract: "", - authors: [ - "Tanaka, S.", - "Olson, C.A.", - "Barnes, C.O.", - "Higashide, W.", - "Gonzalez, M.", - "Taft, J.", - "Richardson, A.", - "Martin-Fernandez, M.", - "Bogunovic, D.", - "Gnanapragasam, P.N.P.", - "Bjorkman, P.J.", - "Spilman, P.", - "Niazi, K.", - "Rabizadeh, S.", - "Soon-Shiong, P.", - "Anders Olson, C.", - "Soon-Shiong, P. (0000-0002-4682-8298)", - ], - }, - { - pmID: "34545362", - title: - "Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.09.14.460356", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34545362", - pubDate: "2021", - abstract: "", - authors: [ - "Tanaka, S.", - "Olson, C.A.", - "Barnes, C.O.", - "Higashide, W.", - "Gonzalez, M.", - "Taft, J.", - "Richardson, A.", - "Martin-Fernandez, M.", - "Bogunovic, D.", - "Gnanapragasam, P.N.P.", - "Bjorkman, P.J.", - "Spilman, P.", - "Niazi, K.", - "Rabizadeh, S.", - "Soon-Shiong, P.", - "Anders Olson, C.", - "Soon-Shiong, P. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. 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(0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 4 (P43 crystal form)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7twj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7twj", - }, - }, - { - title: - "SARS-CoV-2 3CL protease with alternative conformation of the active site promoted by methylene-bridged cysteine and lysine residues", - emdb: null, - pdb: { - dbId: "7JR4", - method: "X-RAY DIFFRACTION", - keywords: "hydrolase, cysteine endopeptidases", - refModels: [ - { - emdbId: null, - pdbId: "7JR4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jr4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jr4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "de Oliveira, R.R.", - "Trivella, D.B.B.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 3CL protease with alternative conformation of the active site promoted by methylene-bridged cysteine and lysine residues", - journal: "To be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Nascimento, A.F.Z.", - "de Oliveira, R.R.", - "Zeri, A.C.M.", - "Trivella, D.B.B.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jr4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jr4", - }, - }, - { - title: "SARS-CoV-2 nucleocapsid protein C-terminal domain (dodecamer)", - emdb: null, - pdb: { - dbId: "7F2E", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 nucleocapsid protein, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7F2E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f2e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f2e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NBIIXXVUZAFLBC-UHFFFAOYSA-K"], - dbauthors: ["Jiang, H.", "Liu, C. (0000-0002-0136-934X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34665939", - title: - "Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies.", - journal: "Febs J. 289: 3813-3825 (2022), 1742-464X", - doi: "https://doi.org/10.1111/febs.16239", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34665939", - pubDate: "2022", - abstract: "", - authors: [ - "Jia, Z.", - "Liu, C.", - "Chen, Y.", - "Jiang, H.", - "Wang, Z.", - "Yao, J.", - "Yang, J.", - "Zhu, J.", - "Zhang, B.", - "Yuchi, Z. (0000-0003-2595-9106)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7f2e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7f2e", - }, - }, - { - title: - "Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P43 crystal form)", - emdb: null, - pdb: { - dbId: "7TX3", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, room temperature diffraction, protein dynamics, water networks, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TX3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tx3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tx3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MNIGYIKCFSPQRJ-UHFFFAOYSA-N"], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Meilleur, F. (0000-0001-9313-8989)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P43 crystal form)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tx3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tx3", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.6264", - emdb: null, - pdb: { - dbId: "7QF1", - method: "X-RAY DIFFRACTION", - keywords: "neutralization, antibody, coronavirus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7QF1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qf1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qf1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV2.6264 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV2.6264 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Fernandez, I.", "Pederzoli, R.", "Rey, F.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Drosophila melanogaster", - assembly: "hexameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35704748", - title: - "Potent human broadly SARS-CoV-2-neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2.", - journal: "J.Exp.Med. 219 (2022), 1540-9538", - doi: "https://doi.org/10.1084/jem.20220638", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35704748", - pubDate: "2022", - abstract: "", - authors: [ - "Planchais, C. 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(0000-0001-8536-8995)", - "Simon-Loriere, E. (0000-0001-8420-7743)", - "Bourhy, H. (0000-0002-2608-5589)", - "Montagutelli, X. (0000-0002-9372-5398)", - "Rey, F.A. (0000-0002-9953-7988)", - "Schwartz, O. (0000-0002-0729-1475)", - "Mouquet, H. (0000-0002-4230-610X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qf1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qf1", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.2325", - emdb: null, - pdb: { - dbId: "7QF0", - method: "X-RAY DIFFRACTION", - keywords: "neutralization, antibody, coronavirus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7QF0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qf0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qf0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV2.2325 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV2.2325 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: ["Fernandez, I.", "Pederzoli, R.", "Rey, F.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35704748", - title: - "Potent human broadly SARS-CoV-2-neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2.", - journal: "J.Exp.Med. 219 (2022), 1540-9538", - doi: "https://doi.org/10.1084/jem.20220638", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35704748", - pubDate: "2022", - abstract: "", - authors: [ - "Planchais, C. (0000-0002-5142-7253)", - "Fernandez, I. (0000-0003-2632-8111)", - "Bruel, T. (0000-0002-3952-4261)", - "de Melo, G.D. (0000-0003-0747-7760)", - "Prot, M. (0000-0003-2337-2491)", - "Beretta, M. (0000-0001-6202-1948)", - "Guardado-Calvo, P. (0000-0001-7292-5270)", - "Dufloo, J. (0000-0002-4963-1378)", - "Molinos-Albert, L.M. (0000-0001-5447-6803)", - "Backovic, M. (0000-0001-8814-4428)", - "Chiaravalli, J. (0000-0001-9135-4565)", - "Giraud, E. (0000-0002-0028-1944)", - "Vesin, B. (0000-0001-9458-9861)", - "Conquet, L. (0000-0003-1911-4887)", - "Grzelak, L. (0000-0002-1298-7565)", - "Planas, D. (0000-0002-2509-9954)", - "Staropoli, I. (0000-0001-8637-4545)", - "Guivel-Benhassine, F. (0000-0003-3410-5671)", - "Hieu, T. (0000-0003-2831-571X)", - "Boulle, M. (0000-0002-6486-8533)", - "Cervantes-Gonzalez, M. (0000-0003-2813-2219)", - "Ungeheuer, M.N. (0000-0002-1639-9613)", - "Charneau, P. (0000-0003-1184-5773)", - "van der Werf, S.", - "Agou, F. (0000-0001-6280-239X)", - "Dimitrov, J.D. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rt2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rt2", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to PD 168568.", - emdb: null, - pdb: { - dbId: "7AMJ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, MPro, COVID-19, PEPTIDE BINDING PROTEIN, virus protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7AMJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7amj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7amj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "WQEPZBNLBWDIRZ-NRFANRHFSA-N", - ], - dbauthors: [ - "Oberthuer, D. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - { - pmID: "", - title: - "Inhibition of SARS-CoV-2 main protease by allosteric drug-binding", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.11.12.378422", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7amj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7amj", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000159004", - emdb: null, - pdb: { - dbId: "5RTS", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RTS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rts_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rts", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VKFXHYRIHRTEIV-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-3705-2993)", - "Huo, J.", - "Clark, J.", - "Clare, D.", - "Harrison, P.", - "Tree, J.", - "Buttigieg, K.", - "Salguero, F.", - "Watson, R.", - "Carnell, O.", - "Ngabo, D.", - "Elmore, M.", - "Ward, P.", - "Dumoux, M.", - "Hiscox, J.", - "Owen, A.", - "James, W.", - "Carroll, M.", - "Stewart, J.", - "Naismith, J.", - "Owens, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7oaq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7oaq", - }, - }, - { - title: "Crystal structure of Omicron BA.3 RBD complexed with hACE2", - emdb: null, - pdb: { - dbId: "7XB1", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Omicron, RBD, hACE2, complex structure, VIRAL PROTEIN, HYDROLASE-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7XB1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xb1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xb1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Meng, Y.", "Li, W.", "Liao, H."], - details: [ - { - sample: { - name: "", - exprSystem: "Mammalian expression vector EGFP-MCS-pcDNA3.1", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35809570", - title: - "Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1.", - journal: "Cell 185: 2952-2960.e10 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.06.023", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35809570", - pubDate: "2022", - abstract: "", - authors: [ - "Li, L.", - "Liao, H.", - "Meng, Y.", - "Li, W.", - "Han, P.", - "Liu, K.", - "Wang, Q.", - "Li, D.", - "Zhang, Y.", - "Wang, L.", - "Fan, Z.", - "Zhao, X.", - "Sun, Y.", - "Huang, N.", - "Qi, J.", - "Gao, G.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7xb1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7xb1", - }, - }, - { - title: - "Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication", - emdb: null, - pdb: { - dbId: "6WTM", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, 3CLpro, coronavirus, main protease, kinetics, SARS, VIRAL PROTEIN, Hydrolase-Hydrolase Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "6WTM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wtm_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wtm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Khan, M.B. (0000-0002-4164-9573)", - "Lemieux, M.J. (0000-0003-4745-9153)", - "Arutyunova, E.", - "Young, H.S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32855413", - title: - "Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication.", - journal: "Nat Commun 11: 4282-4282 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18096-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32855413", - pubDate: "2020", - abstract: "", - authors: [ - "Vuong, W. (0000-0002-3439-8788)", - "Khan, M.B. (0000-0002-4164-9573)", - "Fischer, C. (0000-0002-2289-010X)", - "Arutyunova, E.", - "Lamer, T. (0000-0002-1511-4540)", - "Shields, J. (0000-0003-4701-4576)", - "Saffran, H.A.", - "McKay, R.T. (0000-0002-0255-159X)", - "van Belkum, M.J. (0000-0002-9296-6069)", - "Joyce, M.A. (0000-0002-9173-7299)", - "Young, H.S.", - "Tyrrell, D.L. (0000-0002-0983-7267)", - "Vederas, J.C. (0000-0002-2996-0326)", - "Lemieux, M.J. 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(0000-0003-2535-6209)", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Tan, K. (0000-0002-4003-7903)", - "Maltseva, N.I.", - "Endres, M.J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in complex with masitinib", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Tan, K. (0000-0002-4003-7903)", - "Maltseva, N.I.", - "Endres, M.J.", - "Joachimiak, A. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rtd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rtd", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022", - emdb: null, - pdb: { - dbId: "6W41", - method: "X-RAY DIFFRACTION", - keywords: - "Antibody, Virus, Complex, SARS-CoV-2, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "6W41", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6w41_final.pdb", - externalLink: "https://pdb-redo.eu/db/6w41", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "CR3022 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CR3022 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: [ - "Wilson, I.A. (0000-0002-6469-2419)", - "Yuan, M. (0000-0001-9754-4503)", - "Wu, N.C. (0000-0002-9078-6697)", - "Zhu, X.Y. (0000-0002-6021-3740)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32245784", - title: - "A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV.", - journal: "Science 368: 630-633 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abb7269", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32245784", - pubDate: "2020", - abstract: "", - authors: [ - "Yuan, M.", - "Wu, N.C.", - "Zhu, X.", - "Lee, C.D.", - "So, R.T.Y.", - "Lv, H.", - "Mok, C.K.P.", - "Wilson, I.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w41_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w41", - }, - }, - { - title: "Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 inhibitor", - emdb: null, - pdb: { - dbId: "7SGW", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, coronavirus, SARS, COV-2, papain-like protease, IDP51000, IDP52003, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7SGW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sgw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sgw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OZOFJVFWGZHBHV-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 inhibitor", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Lisnyak, V.", - "Maki, S.", - "Taylor, C.", - "Zhang, Y.", - "Zhou, Z.", - "Azizi, S.A.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - "Dickinson, B.C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sgw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sgw", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420", - emdb: null, - pdb: { - dbId: "7JKV", - method: "X-RAY DIFFRACTION", - keywords: - "3C-like proteinase, VIRAL PROTEIN, SARS-CoV-2, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JKV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jkv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jkv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DHQWCSDZTRDSRP-XIBGDNMGSA-N", "JLFNLZLINWHATN-UHFFFAOYSA-N"], - dbauthors: [ - "Bulut, H. (0000-0003-0262-6296)", - "Das, D.", - "Mitsuya, H. (0000-0001-9274-3853)", - "Hattori, S.I.", - "Murayama, K.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33510133", - title: - "A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication.", - journal: "Nat Commun 12: 668-668 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-20900-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33510133", - pubDate: "2021", - abstract: "", - authors: [ - "Hattori, S.I. (0000-0002-5637-3397)", - "Higashi-Kuwata, N. (0000-0002-9404-3532)", - "Hayashi, H.", - "Allu, S.R.", - "Raghavaiah, J.", - "Bulut, H. (0000-0003-0262-6296)", - "Das, D. (0000-0001-9943-5888)", - "Anson, B.J. (0000-0003-2670-974X)", - "Lendy, E.K.", - "Takamatsu, Y. (0000-0001-7967-1576)", - "Takamune, N.", - "Kishimoto, N. (0000-0002-9401-8118)", - "Murayama, K.", - "Hasegawa, K.", - "Li, M.", - "Davis, D.A.", - "Kodama, E.N.", - "Yarchoan, R. (0000-0002-3057-1395)", - "Wlodawer, A. (0000-0002-5510-9703)", - "Misumi, S. (0000-0002-9465-4720)", - "Mesecar, A.D.", - "Ghosh, A.K.", - "Mitsuya, H. (0000-0001-9274-3853)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jkv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jkv", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1492796719", - emdb: null, - pdb: { - dbId: "5RM0", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RM0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rm0_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rm0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "HCEIEGOMGWEGOJ-SNVBAGLBSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rm0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rm0", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to TH-302.", - emdb: null, - pdb: { - dbId: "7AWS", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-19, PEPTIDE BINDING PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7AWS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aws_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aws", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "GTMVCVDSEXJDHD-HXUWFJFHSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Lieske, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0003-2535-6209)", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Tan, K. (0000-0002-4003-7903)", - "Maltseva, N.I.", - "Welk, L.F.", - "Jedrzejczak, R.P.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of 3CL MainPro of SARS-CoV-2 with de-oxidized C145", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Tan, K. (0000-0002-4003-7903)", - "Maltseva, N.I.", - "Welk, L.F.", - "Jedrzejczak, R.P.", - "Joachimiak, A. 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(0000-0003-4459-9142)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rmt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rmt", - }, - }, - { - title: "HLA-B*07:02 in complex with SARS-CoV-2 nucleocapsid peptide N105-113", - emdb: null, - pdb: { - dbId: "7LGD", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, HLA, T cell, cross-reactivity, COVID-19, antigen presentation, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7LGD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lgd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lgd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01889", - organism: "9606", - name: "HLA class I histocompatibility antigen, B alpha chain", - details: "", - altNames: "Human leukocyte antigen B,HLA-B", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "SARS-CoV-2 nucleocapsid peptide N105-113", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Gras, S.", "Chatzileontiadou, D.S.M.", "Szeto, C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33945786", - title: - "CD8 + T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses.", - journal: "Immunity 54 (2021), 1074-7613", - doi: "https://doi.org/10.1016/j.immuni.2021.04.006", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33945786", - pubDate: "2021", - abstract: "", - authors: [ - "Lineburg, K.E.", - "Grant, E.J.", - "Swaminathan, S.", - "Chatzileontiadou, D.S.M.", - "Szeto, C.", - "Sloane, H.", - "Panikkar, A.", - "Raju, J.", - "Crooks, P.", - "Rehan, S.", - "Nguyen, A.T.", - "Lekieffre, L.", - "Neller, M.A.", - "Tong, Z.W.M.", - "Jayasinghe, D.", - "Chew, K.Y.", - "Lobos, C.A.", - "Halim, H.", - "Burrows, J.M.", - "Riboldi-Tunnicliffe, A.", - "Chen, W.", - "D'Orsogna, L.", - "Khanna, R.", - "Short, K.R.", - "Smith, C.", - "Gras, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lgd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lgd", - }, - }, - { - title: "Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope ALWEIQQVV", - emdb: null, - pdb: { - dbId: "7LG2", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, CD8+, epitope, HLA, human major histocompatibility complex, MHC-I, ALWEIQQVV, HLA-A2, HLA-A*02:01 IMMUNE SYSTEM-VIRAL PROTEIN complex, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7LG2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lg2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lg2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 8", - details: "", - altNames: "nsp8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "ZIBGPFATKBEMQZ-UHFFFAOYSA-N"], - dbauthors: ["Patskovsky, Y.", "Krogsgaard, M.", "Patskovska, L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope ALWEIQQVV", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Patskovska, L.", "Patskovsky, Y.", "Krogsgaard, M."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lg2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lg2", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H172Y Mutant in Complex with Inhibitor GC376", - emdb: null, - pdb: { - dbId: "8D4K", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8D4K", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8d4k_final.pdb", - externalLink: "https://pdb-redo.eu/db/8d4k", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36119652", - title: - "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.28.497978", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36119652", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, Y.", - "Lewandowski, E.M.", - "Tan, H.", - "Zhang, X.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Butler, S.G.", - "Gongora, M.V.", - "Choy, J.", - "Deng, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8d4k_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8d4k", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2614735107 - (R) and (S) isomers", - emdb: null, - pdb: { - dbId: "5SRS", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SRS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5srs_final.pdb", - externalLink: "https://pdb-redo.eu/db/5srs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JXLRADUCHRSAKP-NSHDSACASA-N", "JXLRADUCHRSAKP-LLVKDONJSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5srs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5srs", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5010894431- (S,S) isomer", - emdb: null, - pdb: { - dbId: "5SQH", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SQH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sqh_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sqh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DCWUYIIPJAIWML-MAUKXSAKSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sqh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sqh", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with EN300-36602160", - emdb: null, - pdb: { - dbId: "5SR2", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SR2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sr2_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sr2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["HULQKGAWTDMSSA-WMZOPIPTSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. 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(0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35779291", - title: - "A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114570-114570 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114570", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35779291", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, Y.", - "Yang, K.S.", - "Geng, Z.Z.", - "Alugubelli, Y.R.", - "Shaabani, N.", - "Vatansever, E.C.", - "Ma, X.R.", - "Cho, C.C.", - "Khatua, K.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rvs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rvs", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5010903509 - (S,S) isomer", - emdb: null, - pdb: { - dbId: "5SP7", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SP7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sp7_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sp7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BJZXTCJBAZHJRX-RBUKOAKNSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sqe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sqe", - }, - }, - { - title: - "Crystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2", - emdb: null, - pdb: { - dbId: "7N3D", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Coronavirus 2, Nucleocapsid protein, Human antibody Fab, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7N3D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n3d_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n3d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "S24-1564 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "S24-1564 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of Human Fab S24-1564 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n3d_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n3d", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5010894417 - (R,R) and (S,S) isomers", - emdb: null, - pdb: { - dbId: "5SPA", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SPA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5spa_final.pdb", - externalLink: "https://pdb-redo.eu/db/5spa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UYUBQOHPPHHZPI-DZGCQCFKSA-N", "UYUBQOHPPHHZPI-HIFRSBDPSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5spa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5spa", - }, - }, - { - title: - "Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex with Narlaprevir", - emdb: null, - pdb: { - dbId: "6XQT", - method: "X-RAY DIFFRACTION", - keywords: "3c like proteinase, VIRAL PROTEIN, VIRAL PROTEIN-HYDROLASE complex", - refModels: [ - { - emdbId: null, - pdbId: "6XQT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xqt_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xqt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BZXRATSZUNDEEV-FZFXNXQRSA-N"], - dbauthors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33152262", - title: - "Malleability of the SARS-CoV-2 3CL M pro Active-Site Cavity Facilitates Binding of Clinical Antivirals.", - journal: "Structure 28 (2020), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2020.10.007", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33152262", - pubDate: "2020", - abstract: "", - authors: [ - "Kneller, D.W.", - "Galanie, S.", - "Phillips, G.", - "O'Neill, H.M.", - "Coates, L.", - "Kovalevsky, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xqt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xqt", - }, - }, - { - title: "SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound to C144 scFv", - emdb: null, - pdb: { - dbId: "8DCE", - method: "X-RAY DIFFRACTION", - keywords: - "Immunogen, antigen, design, vaccine, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8DCE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dce_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dce", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "C144 scFv", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Tang, W.K. (0000-0003-3209-1675)", - "Tolia, N.H. (0000-0002-2689-1337)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34013270", - title: - "Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response.", - journal: "Biorxiv (2021), 2692-8205", - doi: "https://doi.org/10.1101/2021.05.09.443238", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34013270", - pubDate: "2021", - abstract: "", - authors: [ - "Dickey, T.H. (0000-0001-5773-5372)", - "Tang, W.K.", - "Butler, B.", - "Ouahes, T.", - "Orr-Gonzalez, S.", - "Salinas, N.D. (0000-0003-4105-3718)", - "Lambert, L.E.", - "Tolia, N.H. (0000-0002-2689-1337)", - "Salinas, N.D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dce_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dce", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-69", - emdb: null, - pdb: { - dbId: "7RN4", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RN4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rn4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rn4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BOEMYMIXDCTGER-UHFFFAOYSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34705466", - title: - "Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.", - journal: "J.Med.Chem. 64: 17366-17383 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01475", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34705466", - pubDate: "2021", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Li, H. (0000-0002-6964-9962)", - "Galanie, S.", - "Phillips, G.", - "Labbe, A.", - "Weiss, K.L. (0000-0002-6486-8007)", - "Zhang, Q.", - "Arnould, M.A.", - "Clyde, A.", - "Ma, H.", - "Ramanathan, A. (0000-0002-1622-5488)", - "Jonsson, C.B. (0000-0002-2640-7672)", - "Head, M.S.", - "Coates, L. (0000-0003-2342-049X)", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rn4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rn4", - }, - }, - { - title: "Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope IPRRNVATL", - emdb: null, - pdb: { - dbId: "7LFZ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV2, CD8+, epitope, HLA, human major histocompatibility complex, SPRWYFYYL, HLA-B7, HLA-B*07:02, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7LFZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lfz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lfz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P01889", - organism: "9606", - name: "HLA class I histocompatibility antigen, B-7 alpha chain", - details: "", - altNames: "MHC class I antigen B*7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "ORF1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Patskovsky, Y.", - "Krogsgaard, M.", - "Patskovska, L. (0000-0002-8910-0504)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope IPRRNVATL", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Patskovska, L.", "Patskovsky, Y.", "Krogsgaard, M."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lfz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lfz", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-02", - emdb: null, - pdb: { - dbId: "7EN9", - method: "X-RAY DIFFRACTION", - keywords: "Non-covalent, Inhibitor, 3CLpro, Coronavirus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7EN9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7en9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7en9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CFAZYCDVXXGVDB-NEEKEDPPSA-N"], - dbauthors: [ - "Hou, N. (0000-0003-3489-5271)", - "Peng, C. (0000-0002-4165-5957)", - "Hu, Q. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3g", - }, - }, - { - title: - "Room Temperature Structure of SARS-CoV-2 NSP10/NSP16 Methyltransferase in a Complex with SAM Determined by Fixed-Target Serial Crystallography", - emdb: null, - pdb: { - dbId: "6XKM", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, Serial Crystallography, Methyltransferase, S-Adenosylmethionine, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6XKM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xkm_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xkm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Satchell, K.J.F.", - "Michalska, K.", - "Wilamowski, M.", - "Sherrell, D.A.", - "Lavens, A.", - "Chard, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33972410", - title: - "2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography.", - journal: "Proc.Natl.Acad.Sci.USA 118 (2021), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2100170118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33972410", - pubDate: "2021", - abstract: "", - authors: [ - "Wilamowski, M.", - "Sherrell, D.A. 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(0000-0003-3274-7611)", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xkm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xkm", - }, - }, - { - title: "THE CRYSTAL STRUCTURE OF COVID-19 MAIN PROTEASE apo form at 2.2 angstrom", - emdb: null, - pdb: { - dbId: "7E5X", - method: "X-RAY DIFFRACTION", - keywords: "protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7E5X", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e5x_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e5x", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Liu, X.", "Yang, H.", "Rao, Z.", "Zhao, Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35380892", - title: - "Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2117142119-e2117142119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2117142119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35380892", - pubDate: "2022", - abstract: "", - authors: [ - "Zhao, Y. (0000-0002-2932-2164)", - "Zhu, Y. (0000-0002-7045-4847)", - "Liu, X. (0000-0001-5498-6942)", - "Jin, Z. (0000-0001-6448-820X)", - "Duan, Y.", - "Zhang, Q. (0000-0002-6271-9163)", - "Wu, C. (0000-0001-9178-7467)", - "Feng, L. (0000-0003-1060-6391)", - "Du, X.", - "Zhao, J. (0000-0002-5119-359X)", - "Shao, M. (0000-0002-9762-8608)", - "Zhang, B. (0000-0001-8556-8049)", - "Yang, X. (0000-0003-3443-9815)", - "Wu, L. (0000-0002-2253-0497)", - "Ji, X. (0000-0002-0801-8825)", - "Guddat, L.W. (0000-0002-8204-8408)", - "Yang, K.", - "Rao, Z. (0000-0001-9866-2384)", - "Yang, H. (0000-0002-1875-3268)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e5x_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e5x", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 macrodomain in complex with GMP", - emdb: null, - pdb: { - dbId: "7BF4", - method: "X-RAY DIFFRACTION", - keywords: - "nsp3, macrodomain, SARS-CoV-2, GMP, guanosine monophosphate, covid-19, Structural Genomics, Structural Genomics Consortium, SGC, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7BF4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bf4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bf4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "NSP3 macrodomain", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RQFCJASXJCIDSX-UUOKFMHZSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - 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}, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253 and COVOX-75 Fabs", - emdb: null, - pdb: { - dbId: "7BEN", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, antibody, germline, V-gene, receptor-binding-domain, spike, neutralisation, protection, glycosylation, valency, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7BEN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ben_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ben", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-253 heavy chain", - details: "", - altNames: "", - 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"Siebert, C.A.", - "Clare, D.K.", - "Howe, A.", - "Radecke, J.", - "Song, Y.", - "Townsend, A.R.", - "Huang, K.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Diamond, M.S.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ben_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ben", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z45612755", - emdb: null, - pdb: { - dbId: "5S2C", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S2C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s2c_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s2c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s2t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s2t", - }, - }, - { - title: "The crystal structure of SARS-CoV-2 3CL protease in complex with compound 1", - emdb: null, - pdb: { - dbId: "7VTH", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7VTH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vth_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vth", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JHDIUUFGPILEJO-UHFFFAOYSA-N"], - dbauthors: [ - "Yamamoto, S. (0000-0002-1731-7931)", - "Tachibana, Y. (0000-0001-6845-4453)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35352927", - title: - "Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19.", - journal: "J.Med.Chem. 65: 6499-6512 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00117", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35352927", - pubDate: "2022", - abstract: "", - authors: [ - "Unoh, Y.", - "Uehara, S. (0000-0001-5214-8531)", - "Nakahara, K.", - "Nobori, H.", - "Yamatsu, Y.", - "Yamamoto, S. (0000-0002-1731-7931)", - "Maruyama, Y.", - "Taoda, Y. (0000-0001-8469-3788)", - "Kasamatsu, K.", - "Suto, T.", - "Kouki, K.", - "Nakahashi, A.", - "Kawashima, S.", - "Sanaki, T.", - "Toba, S.", - "Uemura, K.", - "Mizutare, T.", - "Ando, S. (0000-0002-9148-6530)", - "Sasaki, M.", - "Orba, Y.", - "Sawa, H.", - "Sato, A.", - "Sato, T.", - "Kato, T.", - "Tachibana, Y. (0000-0001-6845-4453)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vth_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vth", - }, - }, - { - title: "Antibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide", - emdb: null, - pdb: { - dbId: "7TOW", - method: "X-RAY DIFFRACTION", - keywords: - "Antibody, Fab fragment, IMMUNE SYSTEM, IMMUNE SYSTEM-Viral Protein complex", - refModels: [ - { - emdbId: null, - pdbId: "7TOW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tow_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tow", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "DH1058 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "DH1058 Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2", - details: - "Lysine at N-terminal is used for biochemical assays; two serines were added at N-terminal to increase the peptide solubility in PBS", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BHPQYMZQTOCNFJ-UHFFFAOYSA-N", "NBIIXXVUZAFLBC-UHFFFAOYSA-K"], - dbauthors: [ - "Acharya, P. (0000-0002-0089-277X)", - "Gobeil, S. (0000-0002-0057-2477)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35118469", - title: "Structural diversity of the SARS-CoV-2 Omicron spike.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.01.25.477784", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35118469", - pubDate: "2022", - abstract: "", - authors: [ - "Gobeil, S.M.", - "Henderson, R.", - "Stalls, V.", - "Janowska, K.", - "Huang, X.", - "May, A.", - "Speakman, M.", - "Beaudoin, E.", - "Manne, K.", - "Li, D.", - "Parks, R.", - "Barr, M.", - "Deyton, M.", - "Martin, M.", - "Mansouri, K.", - "Edwards, R.J.", - "Eaton, A.", - "Montefiori, D.C.", - "Sempowski, G.D.", - "Saunders, K.O.", - "Wiehe, K.", - "Williams, W.", - "Korber, B.", - "Haynes, B.F.", - "Acharya, P.", - "Gobeil, S.M. (0000-0002-0057-2477)", - "Henderson, R. (0000-0002-4301-6382)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tow_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tow", - }, - }, - { - title: - "Structure of SARS-CoV-2 Mpro Omicron P132H in complex with Nirmatrelvir (PF-07321332)", - emdb: null, - pdb: { - dbId: "7TLL", - method: "X-RAY DIFFRACTION", - keywords: - "Protease, SARS-CoV-2, covalent complex, inhibitor, HYDROLASE-INHIBITOR complex, mutant, Omicron, P132H, nirmatrelvir, PF-07321332, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TLL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tll_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tll", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: [ - "Stewart, A.E.", - "Greasley, S.E. (0000-0002-7978-6477)", - "Ferre, R.A. (0000-0001-7462-1879)", - "Liu, W. (0000-0002-8541-4928)", - "Plotnikova, O. (0000-0002-2513-7287)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35461811", - title: - "Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants.", - journal: "J.Biol.Chem. 298: 101972-101972 (2022), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2022.101972", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35461811", - pubDate: "2022", - abstract: "", - authors: [ - "Greasley, S.E.", - "Noell, S.", - "Plotnikova, O.", - "Ferre, R.", - "Liu, W.", - "Bolanos, B.", - "Fennell, K.", - "Nicki, J.", - "Craig, T.", - "Zhu, Y.", - "Stewart, A.E.", - "Steppan, C.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tll_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tll", - }, - }, - { - title: "Structure of post fusion core of 2019-nCoV S2 subunit", - emdb: null, - pdb: { - dbId: "6LXT", - method: "X-RAY DIFFRACTION", - keywords: "2019-nCoV, HR1 and HR2 domain, VIRUS, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6LXT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6lxt_final.pdb", - externalLink: "https://pdb-redo.eu/db/6lxt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2, Spike protein S2", - details: - "The fusion protein of SARS-CoV-2 S2 subunit HR1 domain (residues 910-988), linker (SGGRGG), SARS-CoV-2 S2 subunit HR2 domain (residues 1162-1206), and expression tag (GG)", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UWHCKJMYHZGTIT-UHFFFAOYSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: ["Zhu, Y.", "Sun, F."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32231345", - title: - "Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion.", - journal: "Cell Res. 30: 343-355 (2020), 1001-0602", - doi: "https://doi.org/10.1038/s41422-020-0305-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32231345", - pubDate: "2020", - abstract: "", - authors: [ - "Xia, S.", - "Liu, M.", - "Wang, C.", - "Xu, W.", - "Lan, Q. (0000-0001-5524-3542)", - "Feng, S.", - "Qi, F.", - "Bao, L.", - "Du, L.", - "Liu, S.", - "Qin, C.", - "Sun, F. (0000-0002-0351-5144)", - "Shi, Z.", - "Zhu, Y.", - "Jiang, S.", - "Lu, L. (0000-0002-2255-0391)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6lxt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6lxt", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 main protease in complex with Boceprevir (space group P212121)", - emdb: null, - pdb: { - dbId: "7COM", - method: "X-RAY DIFFRACTION", - keywords: - "coronavirus, protease, inhibitor, complex, viral protein., VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7COM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7com_final.pdb", - externalLink: "https://pdb-redo.eu/db/7com", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FEBWCINGHXXUCV-GFLQDLJJSA-N"], - dbauthors: [ - "Zeng, R.", - "Lei, J.", - "Chen, P.", - "Wang, Y.F.", - "Qiao, J.X.", - "Li, Y.S.", - "Yang, S.Y.", - "Yao, R.", - "Zhou, Y.L.", - "Liu, J.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33602867", - title: - "SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model.", - journal: "Science 371: 1374-1378 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf1611", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33602867", - pubDate: "2021", - abstract: "", - authors: [ - "Qiao, J.", - "Li, Y.S.", - "Zeng, R.", - "Liu, F.L.", - "Luo, R.H.", - "Huang, C.", - "Wang, Y.F.", - "Zhang, J.", - "Quan, B.", - "Shen, C.", - "Mao, X.", - "Liu, X.", - "Sun, W.", - "Yang, W.", - "Ni, X.", - "Wang, K.", - "Xu, L.", - "Duan, Z.L.", - "Zou, Q.C.", - "Zhang, H.L.", - "Qu, W.", - "Long, Y.H.", - "Li, M.H.", - "Yang, R.C.", - "You, J.", - "Zhou, Y.", - "Yao, R.", - "Li, W.P.", - "Liu, J.M.", - "Chen, P.", - "Liu, Y.", - "Lin, G.F.", - "Yang, X.", - "Zou, J.", - "Li, L.", - "Hu, Y.", - "Lu, G.W.", - "Li, W.M.", - "Wei, Y.Q.", - "Zheng, Y.T.", - "Lei, J.", - "Yang, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7com_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7com", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1273312153", - emdb: null, - pdb: { - dbId: "5RMK", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RMK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rmk_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rmk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "OKVUYVXDTGOYRU-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. 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(0000-0002-8199-2376)", - "Rathnayake, A.D. (0000-0003-2588-7624)", - "Galasiti Kankanamalage, A.C.", - "Kim, Y.", - "Perera, K.D. (0000-0002-3778-4975)", - "Nguyen, H.N.", - "Miller, M.J.", - "Madden, T.K.", - "Picard, H.R.", - "Thurman, H.A.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P. (0000-0003-0833-3259)", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Battaile, K.P.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t46_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t46", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000020269197", - emdb: null, - pdb: { - dbId: "5RVV", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RVV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rvv_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rvv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PHHZCIOPSFQASN-UHFFFAOYSA-N"], - dbauthors: ["Fraser, J.S.", "Young, I.D.", "Thompson, M.C.", "Correy, G.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-1135-2744)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35142215", - title: - "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", - journal: "J.Am.Chem.Soc. 144: 2905-2920 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08402", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35142215", - pubDate: "2022", - abstract: "", - authors: [ - "Luttens, A. (0000-0003-2915-7901)", - "Gullberg, H.", - "Abdurakhmanov, E.", - "Vo, D.D.", - "Akaberi, D. (0000-0002-9595-9796)", - "Talibov, V.O.", - "Nekhotiaeva, N.", - "Vangeel, L.", - "De Jonghe, S. (0000-0002-3872-6558)", - "Jochmans, D.", - "Krambrich, J.", - "Tas, A.", - "Lundgren, B.", - "Gravenfors, Y. (0000-0001-6025-4908)", - "Craig, A.J.", - "Atilaw, Y.", - "Sandstrom, A.", - "Moodie, L.W.K. (0000-0002-9500-4535)", - "Lundkvist, A.", - "van Hemert, M.J.", - "Neyts, J.", - "Lennerstrand, J.", - "Kihlberg, J. (0000-0002-4205-6040)", - "Sandberg, K.", - "Danielson, U.H. (0000-0003-2728-0340)", - "Carlsson, J. 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(0000-0002-2932-2164)", - "Yang, H.T.", - "Lu, M. (0000-0001-6902-3751)", - "Wang, Z.Y. (0000-0002-2170-7596)", - "Xing, Y.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34075025", - title: - "Identification of proteasome and caspase inhibitors targeting SARS-CoV-2 M pro .", - journal: - "Signal Transduct Target Ther 6: 214-214 (2021), 2059-3635", - doi: "https://doi.org/10.1038/s41392-021-00639-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34075025", - pubDate: "2021", - abstract: "", - authors: [ - "Wang, Z.", - "Zhao, Y.", - "Wang, Q. (0000-0003-1028-1267)", - "Xing, Y.", - "Feng, L.", - "Kong, J.", - "Peng, C. (0000-0002-6814-2676)", - "Zhang, L. (0000-0002-2593-2571)", - "Yang, H.", - "Lu, M. 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7twf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7twf", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000019685960", - emdb: null, - pdb: { - dbId: "5RUZ", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RUZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5ruz_final.pdb", - externalLink: "https://pdb-redo.eu/db/5ruz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FCKYIGWJVZIPLK-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5ruz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5ruz", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000016343276", - emdb: null, - pdb: { - dbId: "5RVA", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RVA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rva_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rva", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FSCXZVPPDJYLDD-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rva_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rva", - }, - }, - { - title: - "Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with potential repurposing drug Tipiracil", - emdb: null, - pdb: { - dbId: "6WXC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus 2, endoribonuclease, refurbishing drug, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WXC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wxc_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wxc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QQHMKNYGKVVGCZ-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Welk, L.", - "Michalska, K.", - "Chang, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33564093", - title: - "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.", - journal: "Commun Biol 4: 193-193 (2021), 2399-3642", - doi: "https://doi.org/10.1038/s42003-021-01735-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33564093", - pubDate: "2021", - abstract: "", - authors: [ - "Kim, Y.", - "Wower, J. (0000-0001-8096-7745)", - "Maltseva, N. (0000-0002-2871-465X)", - "Chang, C.", - "Jedrzejczak, R.", - "Wilamowski, M.", - "Kang, S.", - "Nicolaescu, V.", - "Randall, G.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Wower, J.", - "Maltseva, N.", - "Nicolaescu,, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - { - pmID: "", - title: - "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.06.26.173872", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Kim, Y.", - "Wower, J. (0000-0001-8096-7745)", - "Maltseva, N. (0000-0002-2871-465X)", - "Chang, C.", - "Jedrzejczak, R.", - "Wilamowski, M.", - "Kang, S.", - "Nicolaescu, V.", - "Randall, G.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Wower, J.", - "Maltseva, N.", - "Nicolaescu,, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wxc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wxc", - }, - }, - { - title: "Crystal structure of Mpro with inhibitor r1", - emdb: null, - pdb: { - dbId: "7JP0", - method: "X-RAY DIFFRACTION", - keywords: "MPI, r1, inhibitor, VIRUS, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JP0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jp0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jp0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GLZAWCKOCLSXEU-LRSLUSHPSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Crystal structure of Mpro with inhibitor r1", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Yang, K. (0000-0002-1890-4169)"], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jp0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jp0", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI7", - emdb: null, - pdb: { - dbId: "7JQ4", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, main protease, reversible covalent inhibitors, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JQ4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jq4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jq4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QJOPPFBQFHKESK-FFXRMZKPSA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33283984", - title: - "A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*.", - journal: "Chemmedchem 16: 942-948 (2021), 1860-7187", - doi: "https://doi.org/10.1002/cmdc.202000924", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33283984", - pubDate: "2021", - abstract: "", - authors: [ - "Yang, K.S.", - "Ma, X.R.", - "Ma, Y.", - "Alugubelli, Y.R.", - "Scott, D.A.", - "Vatansever, E.C.", - "Drelich, A.K.", - "Sankaran, B.", - "Geng, Z.Z.", - "Blankenship, L.R.", - "Ward, H.E.", - "Sheng, Y.J.", - "Hsu, J.C.", - "Kratch, K.C.", - "Zhao, B.", - "Hayatshahi, H.S.", - "Liu, J.", - "Li, P.", - "Fierke, C.A.", - "Tseng, C.K.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jq4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jq4", - }, - }, - { - title: - "Crystal structure of the wild type SARS-CoV-2 papain-like protease (PLPro) with inhibitor GRL0617", - emdb: null, - pdb: { - dbId: "7JRN", - method: "X-RAY DIFFRACTION", - keywords: - "COVID, COVID19, COVID-19, SARS, SARS COV2, COV, NCOV 19, CORONAVIRUS, MAIN PROTEASE, 3CL, MPRO, PRO, VIRAL PROTEIN, GC376, calpain inhibitor II, leupeptin, calpain, aldehyde, GC-376, 3cl-like, a-ketoamide, alpheketoamide, alpha, ketoamide, PEPTIDOMIMETIC, PROTEASE, CYSTEINE, HYDROLASE-HYDROLASE INHIBITOR complex, GRL0617, papin-like protease, PLP, PLPro, PL-pro, papain", - refModels: [ - { - emdbId: null, - pdbId: "7JRN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jrn_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jrn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "UVERBUNNCOKGNZ-CQSZACIVSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M.", "Ma, C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34341772", - title: - "Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay.", - journal: "Acs Cent.Sci. 7: 1245-1260 (2021), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.1c00519", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34341772", - pubDate: "2021", - abstract: "", - authors: [ - "Ma, C.", - "Sacco, M.D.", - "Xia, Z.", - "Lambrinidis, G. (0000-0002-2820-9338)", - "Townsend, J.A.", - "Hu, Y.", - "Meng, X.", - "Szeto, T.", - "Ba, M.", - "Zhang, X.", - "Gongora, M.", - "Zhang, F.", - "Marty, M.T.", - "Xiang, Y.", - "Kolocouris, A. (0000-0001-6110-1903)", - "Chen, Y.", - "Wang, J. (0000-0002-4845-4621)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jrn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jrn", - }, - }, - { - title: - "1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0", - emdb: null, - pdb: { - dbId: "7VBE", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Nucleocapsid dimerization domain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VBE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vbe_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vbe", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, J.", "Li, J.", "Zhou, X.L.", "Zhong, F.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zhou, X.L.", "Zhong, F.L.", "Li, J.", "Zhang, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vbe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vbe", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI8", - emdb: null, - pdb: { - dbId: "7JQ5", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, main protease, reversible covalent inhibitors, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JQ5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jq5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jq5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YIWYOEOSWRXENJ-FFXRMZKPSA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33283984", - title: - "A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*.", - journal: "Chemmedchem 16: 942-948 (2021), 1860-7187", - doi: "https://doi.org/10.1002/cmdc.202000924", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33283984", - pubDate: "2021", - abstract: "", - authors: [ - "Yang, K.S.", - "Ma, X.R.", - "Ma, Y.", - "Alugubelli, Y.R.", - "Scott, D.A.", - "Vatansever, E.C.", - "Drelich, A.K.", - "Sankaran, B.", - "Geng, Z.Z.", - "Blankenship, L.R.", - "Ward, H.E.", - "Sheng, Y.J.", - "Hsu, J.C.", - "Kratch, K.C.", - "Zhao, B.", - "Hayatshahi, H.S.", - "Liu, J.", - "Li, P.", - "Fierke, C.A.", - "Tseng, C.K.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jq5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jq5", - }, - }, - { - title: "A SARS-CoV-2 neutralizing antibody", - emdb: null, - pdb: { - dbId: "7F12", - method: "X-RAY DIFFRACTION", - keywords: - "neutralizing antibody, ANTIVIRAL PROTEIN, VIRAL PROTEIN-ANTIVIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7F12", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f12_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f12", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Antibody", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Zhang, G.", - "Guo, Y. (0000-0002-8109-7515)", - "Wang, Y.", - "Li, X. (0000-0003-0896-8713)", - "Yuan, S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "A SARS-CoV-2 neutralizing\nantibody", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Zhang, G.", - "Li, X. (0000-0003-0896-8713)", - "Guo, Y. (0000-0002-8109-7515)", - "Wang, Y.", - "Yuan, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7f12_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7f12", - }, - }, - { - title: - "Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR251", - emdb: null, - pdb: { - dbId: "6WX4", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, CORONAVIRUS, SARS, COV-2, PAPAIN-LIKE PROTEASE, PLpro, deubiquitinating enzyme, ubiquitin, activity-based probe, Hydrolase-Hydrolase Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "6WX4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wx4_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wx4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "VIR251", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: ["Lv, Z.", "Olsen, S.K."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33067239", - title: - "Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design.", - journal: "Sci Adv 6 (2020), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abd4596", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33067239", - pubDate: "2020", - abstract: "", - authors: [ - "Rut, W. (0000-0003-1261-5566)", - "Lv, Z.", - "Zmudzinski, M. (0000-0002-9792-9160)", - "Patchett, S.", - "Nayak, D. (0000-0003-3680-0846)", - "Snipas, S.J. (0000-0002-4239-6862)", - "El Oualid, F. (0000-0002-4447-9960)", - "Huang, T.T.", - "Bekes, M. (0000-0001-8423-9235)", - "Drag, M. (0000-0001-8510-1967)", - "Olsen, S.K.", - "Rut, W.", - "Zmudzinski, M.", - "Nayak, D.", - "Snipas, S.J.", - "El Oualid, F.", - "Bekes, M.", - "Drag, M.", - ], - }, - { - pmID: "32511411", - title: - "Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.04.29.068890", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32511411", - pubDate: "2020", - abstract: "", - authors: [ - "Rut, W. (0000-0003-1261-5566)", - "Lv, Z.", - "Zmudzinski, M. (0000-0002-9792-9160)", - "Patchett, S.", - "Nayak, D. (0000-0003-3680-0846)", - "Snipas, S.J. (0000-0002-4239-6862)", - "El Oualid, F. (0000-0002-4447-9960)", - "Huang, T.T.", - "Bekes, M. (0000-0001-8423-9235)", - "Drag, M. (0000-0001-8510-1967)", - "Olsen, S.K.", - "Rut, W.", - "Zmudzinski, M.", - "Nayak, D.", - "Snipas, S.J.", - "El Oualid, F.", - "Bekes, M.", - "Drag, M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wx4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wx4", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to AZD6482.", - emdb: null, - pdb: { - dbId: "6YVF", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-!9, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6YVF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6yvf_final.pdb", - externalLink: "https://pdb-redo.eu/db/6yvf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "IRTDIKMSKMREGO-OAHLLOKOSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "BHPQYMZQTOCNFJ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Lieske, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rul_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rul", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000158540", - emdb: null, - pdb: { - dbId: "5RV6", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RV6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rv6_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rv6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VDVJGIYXDVPQLP-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rv6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rv6", - }, - }, - { - title: - "Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles", - emdb: null, - pdb: { - dbId: "7MY8", - method: "SOLUTION NMR", - keywords: "Fusion Peptide, LIPID BINDING PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2", - details: - "Lysine at N-terminal is used for biochemical assays; two serines were added at N-terminal to increase the peptide solubility in PBS", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Koppisetti, R.K. (0000-0002-7539-4572)", - "Fulcher, Y.G. (0000-0002-7060-3523)", - "Van Doren, S.R. (0000-0003-2838-4598)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia phage Ecwhy_1", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34375093", - title: - "Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles.", - journal: "J.Am.Chem.Soc. 143: 13205-13211 (2021), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c05435", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34375093", - pubDate: "2021", - abstract: "", - authors: ["Koppisetti, R.K.", "Fulcher, Y.G.", "Van Doren, S.R."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7my8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7my8", - }, - }, - { - title: "Crystal structure of T6 Fab bound to theSARS-CoV-2 RBD of B.1.351", - emdb: null, - pdb: { - dbId: "7FJS", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, receptor binding, complex, antibody, VIRAL PROTEIN, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7FJS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fjs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fjs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "T6 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "T6 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Zhang, S.", "Wang, X.", "Zhang, L.", "Liang, Q."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "hexameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35291264", - title: - "RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants.", - journal: "Iscience 25: 104043-104043 (2022), 2589-0042", - doi: "https://doi.org/10.1016/j.isci.2022.104043", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35291264", - pubDate: "2022", - abstract: "", - authors: [ - "Liang, Q.", - "Wang, Y.", - "Zhang, S.", - "Sun, J.", - "Sun, W.", - "Li, J.", - "Liu, Y.", - "Li, M.", - "Cheng, L.", - "Jiang, Y.", - "Wang, R.", - "Zhang, R.", - "Yang, Z.", - "Ren, Y.", - "Chen, P.", - "Gao, P.", - "Yan, H.", - "Zhang, Z.", - "Zhang, Q.", - "Shi, X.", - "Wang, J.", - "Liu, W.", - "Wang, X.", - "Ying, B.", - "Zhao, J.", - "Qi, H.", - "Zhang, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fjs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fjs", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder457 inhibitor", - emdb: null, - pdb: { - dbId: "7JIR", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7JIR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jir_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jir", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "UVERBUNNCOKGNZ-CQSZACIVSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33531496", - title: - "Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.", - journal: "Nat Commun 12: 743-743 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-21060-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33531496", - pubDate: "2021", - abstract: "", - authors: [ - "Osipiuk, J.", - "Azizi, S.A. (0000-0002-9226-9917)", - "Dvorkin, S.", - "Endres, M.", - "Jedrzejczak, R.", - "Jones, K.A. (0000-0003-0711-5516)", - "Kang, S.", - "Kathayat, R.S. (0000-0002-9159-2413)", - "Kim, Y.", - "Lisnyak, V.G. (0000-0002-4406-8440)", - "Maki, S.L. (0000-0001-6917-3602)", - "Nicolaescu, V.", - "Taylor, C.A.", - "Tesar, C.", - "Zhang, Y.A.", - "Zhou, Z. (0000-0002-2792-8429)", - "Randall, G.", - "Michalska, K.", - "Snyder, S.A. (0000-0003-3594-8769)", - "Dickinson, B.C. (0000-0002-9616-1911)", - "Joachimiak, A. (0000-0003-2535-6209)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jir_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jir", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 main protease complexed with Boceprevir", - emdb: null, - pdb: { - dbId: "7C6S", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7C6S", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c6s_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c6s", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FEBWCINGHXXUCV-GFLQDLJJSA-N"], - dbauthors: ["Feng, Y.", "Fu, L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32887884", - title: - "Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease.", - journal: "Nat Commun 11: 4417-4417 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18233-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32887884", - pubDate: "2020", - abstract: "", - authors: [ - "Fu, L. (0000-0003-0431-5424)", - "Ye, F.", - "Feng, Y.", - "Yu, F.", - "Wang, Q.", - "Wu, Y.", - "Zhao, C.", - "Sun, H.", - "Huang, B.", - "Niu, P.", - "Song, H. (0000-0002-2811-0370)", - "Shi, Y. (0000-0002-3053-2687)", - "Li, X. (0000-0001-8903-9793)", - "Tan, W. (0000-0002-5963-1136)", - "Qi, J.", - "Gao, G.F. (0000-0002-3869-615X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7c6s_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7c6s", - }, - }, - { - title: "SARS-CoV-2 programmed -1 frameshifting element three stem H-type pseudoknot", - emdb: null, - pdb: { - dbId: "7MLX", - method: "X-RAY DIFFRACTION", - keywords: "H-type Pseudoknot, RNA, RNA-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7MLX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mlx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mlx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "BL3-6 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "BL3-6 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "2697049", - name: "RNA (65-MER)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Roman, C. (0000-0001-8538-7475)", "Lewicka, A. (0000-0002-9578-2628)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34328734", - title: - "The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 angstrom Using Chaperone-Assisted RNA Crystallography.", - journal: "Acs Chem.Biol. 16: 1469-1481 (2021), 1554-8937", - doi: "https://doi.org/10.1021/acschembio.1c00324", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34328734", - pubDate: "2021", - abstract: "", - authors: [ - "Roman, C.", - "Lewicka, A.", - "Koirala, D.", - "Li, N.S.", - "Piccirilli, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mlx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mlx", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 11c", - emdb: null, - pdb: { - dbId: "7T4A", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7T4A", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t4a_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t4a", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "CSWBWWIUTWLAOZ-DBSRCYSRSA-N", - "CSWBWWIUTWLAOZ-QUJKESNLSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Liu, L.", - "Kim, Y.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35638577", - title: - "Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.", - journal: "J.Med.Chem. 65: 7818-7832 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00224", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35638577", - pubDate: "2022", - abstract: "", - authors: [ - "Dampalla, C.S. (0000-0002-8199-2376)", - "Rathnayake, A.D. (0000-0003-2588-7624)", - "Galasiti Kankanamalage, A.C.", - "Kim, Y.", - "Perera, K.D. (0000-0002-3778-4975)", - "Nguyen, H.N.", - "Miller, M.J.", - "Madden, T.K.", - "Picard, H.R.", - "Thurman, H.A.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P. (0000-0003-0833-3259)", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Battaile, K.P.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t4a_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t4a", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z45617795", - emdb: null, - pdb: { - dbId: "5R7Y", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5R7Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5r7y_final.pdb", - externalLink: "https://pdb-redo.eu/db/5r7y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "JGDDFCYMSLNOGJ-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Powell, A.J.", - "Wild, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. (0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5r7y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5r7y", - }, - }, - { - title: "Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 15/16", - emdb: null, - pdb: { - dbId: "7TC4", - method: "X-RAY DIFFRACTION", - keywords: - "Coronavirus, COVID-19, COVID, PROTEASE, DRUG RESISTANCE, COMPLEX, HYDROLASE, DURG DISCOVERY, MAIN PROTEASE, MPRO, SUBSTRATE COMPLEX, NSP 15/16, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TC4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tc4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tc4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Nonstructural protein 15/16", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Shaqra, A.M. (0000-0001-6994-2416)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35729165", - title: - "Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.", - journal: "Nat Commun 13: 3556-3556 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-31210-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35729165", - pubDate: "2022", - abstract: "", - authors: [ - "Shaqra, A.M.", - "Zvornicanin, S.N.", - "Huang, Q.Y.J. (0000-0001-5107-2336)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Knapp, M.", - "Tandeske, L.", - "Bakan, D.T.", - "Flynn, J. (0000-0002-5490-393X)", - "Bolon, D.N.A.", - "Moquin, S.", - "Dovala, D.", - "Kurt Yilmaz, N. (0000-0002-5036-676X)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tc4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tc4", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor VBY-825 (Partial Occupancy)", - emdb: null, - pdb: { - dbId: "7MNG", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Main Protease, 3CLpro/Mpro, VBY-825, VIRAL PROTEIN, Inhibitor, HYDROLASE-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MNG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mng_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mng", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DXQKITXDEYCCEL-HAGHYFMRSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Shi, W.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "McSweeney, S. (0000-0002-3758-3161)", - "Kreitler, D.F.", - "Soares, A.S.", - "Jakoncic, J.", - "Keereetaweep, J.", - "Shanklin, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35842458", - title: - "Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.", - journal: "Sci Rep 12: 12197-12197 (2022), 2045-2322", - doi: "https://doi.org/10.1038/s41598-022-15930-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35842458", - pubDate: "2022", - abstract: "", - authors: [ - "Andi, B.", - "Kumaran, D.", - "Kreitler, D.F.", - "Soares, A.S.", - "Keereetaweep, J.", - "Jakoncic, J.", - "Lazo, E.O.", - "Shi, W.", - "Fuchs, M.R.", - "Sweet, R.M.", - "Shanklin, J.", - "Adams, P.D.", - "Schmidt, J.G.", - "Head, M.S.", - "McSweeney, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mng_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mng", - }, - }, - { - title: "PanDDA analysis group deposition of ground-state model of SARS-CoV-2 helicase", - emdb: null, - pdb: { - dbId: "5ROB", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5ROB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rob_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rob", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "NBIIXXVUZAFLBC-UHFFFAOYSA-K"], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition of ground-state model", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Newman, J.A.", - "Yosaatmadja, Y.", - "Douangamath, A.", - "Aimon, A.", - "Powell, A.J.", - "Dias, A.", - "Fearon, D.", - "Dunnett, L.", - "Brandao-Neto, J.", - "Krojer, T.", - "Skyner, R.", - "Gorrie-Stone, T.", - "Thompson, W.", - "von Delft, F.", - "Arrowsmith, C.H.", - "Edwards, A.", - "Bountra, C.", - "Gileadi, O.", - "Imprachim, N.", - "von-Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rob_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rob", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z53825177", - emdb: null, - pdb: { - dbId: "5RL8", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RL8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rl8_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rl8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MRTGYFRQZQCITC-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rl8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rl8", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 PLpro with GRL0617", - emdb: null, - pdb: { - dbId: "7CMD", - method: "X-RAY DIFFRACTION", - keywords: "papain like protein;inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CMD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cmd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cmd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UVERBUNNCOKGNZ-CQSZACIVSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: ["Gao, X.", "Cui, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32895623", - title: "Crystal structure of SARS-CoV-2 papain-like protease.", - journal: "Acta Pharm Sin B 11: 237-245 (2021), 2211-3835", - doi: "https://doi.org/10.1016/j.apsb.2020.08.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32895623", - pubDate: "2021", - abstract: "", - authors: [ - "Gao, X.", - "Qin, B.", - "Chen, P.", - "Zhu, K.", - "Hou, P.", - "Wojdyla, J.A.", - "Wang, M.", - "Cui, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cmd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cmd", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2027049478", - emdb: null, - pdb: { - dbId: "5RLY", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RLY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rly_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rly", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "WFEGFRJBAYCOHP-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rly_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rly", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex containing Mg2+ ion", - emdb: null, - pdb: { - dbId: "7MC6", - method: "X-RAY DIFFRACTION", - keywords: "RNA binding, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7MC6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mc6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mc6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Shi, K. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3q_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3q", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z65532537", - emdb: null, - pdb: { - dbId: "5S30", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S30", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s30_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s30", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MMWXPDDADHYFFS-ZCFIWIBFSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s30_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s30", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253H55L and COVOX-75 Fabs", - emdb: null, - pdb: { - dbId: "7BEO", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, antibody, germline, V-gene, receptor-binding-domain, spike, neutralisation, protection, glycosylation, valency, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7BEO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7beo_final.pdb", - externalLink: "https://pdb-redo.eu/db/7beo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - 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sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33756110", - title: - "The antigenic anatomy of SARS-CoV-2 receptor binding domain.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.02.032", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33756110", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Ginn, H.M.", - "Duyvesteyn, H.M.E.", - "Supasa, P.", - "Case, J.B.", - "Zhao, Y.", - "Walter, T.S.", - "Mentzer, A.J.", - "Liu, C.", - "Wang, B.", - "Paesen, G.C.", - "Slon-Campos, J.", - "Lopez-Camacho, C.", - "Kafai, N.M.", - "Bailey, A.L.", - "Chen, R.E.", - "Ying, B.", - "Thompson, C.", - "Bolton, J.", - "Fyfe, A.", - "Gupta, S.", - "Tan, T.K.", - "Gilbert-Jaramillo, J.", - "James, W.", - "Knight, M.", - "Carroll, M.W.", - "Skelly, D.", - "Dold, C.", - "Peng, Y.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Klenerman, P.", - "Temperton, N.", - "Hall, D.R.", - "Williams, M.A.", - "Paterson, N.G.", - "Bertram, F.K.R.", - "Siebert, C.A.", - "Clare, D.K.", - "Howe, A.", - "Radecke, J.", - "Song, Y.", - "Townsend, A.R.", - "Huang, K.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Diamond, M.S.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7beo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7beo", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 macrodomain in complex with ADP-ribose-phosphate (ADP-ribose-2'-phosphate, ADPRP)", - emdb: null, - pdb: { - dbId: "7BF5", - method: "X-RAY DIFFRACTION", - keywords: - "nsp3, macrodomain, SARS-CoV-2, ADP-ribose-phosphate, ADPRP, covid-19, Structural Genomics, Structural Genomics Consortium, SGC, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7BF5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bf5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bf5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "NSP3 macrodomain", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "ICNHOLCERMYLRZ-KEOHHSTQSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Ni, X.", - "Knapp, S.", - "Chaikuad, A.", - "Structural Genomics Consortium (SGC)", - "Structural Genomics Consortium", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33850605", - title: - "Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain.", - journal: "Acs Med.Chem.Lett. 12: 603-609 (2021), 1948-5875", - doi: "https://doi.org/10.1021/acsmedchemlett.0c00684", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33850605", - pubDate: "2021", - abstract: "", - authors: [ - "Ni, X.", - "Schroder, M.", - "Olieric, V.", - "Sharpe, M.E.", - "Hernandez-Olmos, V.", - "Proschak, E.", - "Merk, D.", - "Knapp, S.", - "Chaikuad, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bf5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bf5", - }, - }, - { - title: "Molecular basis for neutralizing antibody 2B11 targeting SARS-CoV-2 RBD", - emdb: null, - pdb: { - dbId: "7E5Y", - method: "X-RAY DIFFRACTION", - keywords: "Complex, Antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7E5Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e5y_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e5y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "2B11 Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "2B11 Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhao, T.", - "Zhou, H.", - "Wang, Q.S.", - "Wu, H. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s18_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s18", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z57446103", - emdb: null, - pdb: { - dbId: "5S3F", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3F", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3f_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3f", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DFAKOYAKHWMEQD-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3f_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3f", - }, - }, - { - title: - "Crystal structure of MG-132 covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2 in absence of DTT.", - emdb: null, - pdb: { - dbId: "7BGP", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Mpro, 3CLpro, EXSCALATE4COV, drug discovery, Elettra, VIRAL PROTEIN, MG-132", - refModels: [ - { - emdbId: null, - pdbId: "7BGP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bgp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bgp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "WUJQMWDTZKIKQZ-VABKMULXSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: ["Costanzi, E.", "Demitri, N.", "Storici, P.", "Giabbai, B."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34769210", - title: - "Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L.", - journal: "Int J Mol Sci 22 (2021), 1422-0067", - doi: "https://doi.org/10.3390/ijms222111779", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34769210", - pubDate: "2021", - abstract: "", - authors: [ - "Costanzi, E.", - "Kuzikov, M. (0000-0001-8771-1865)", - "Esposito, F. (0000-0001-9725-7977)", - "Albani, S. (0000-0002-3560-4539)", - "Demitri, N.", - "Giabbai, B.", - "Camasta, M.", - "Tramontano, E. (0000-0002-4849-0980)", - "Rossetti, G. (0000-0002-2032-4630)", - "Zaliani, A. (0000-0002-1740-8390)", - "Storici, P. (0000-0002-2590-3332)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bgp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bgp", - }, - }, - { - title: - "Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD)", - emdb: null, - pdb: { - dbId: "7L2C", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, Viral protein, Spike glycoprotein, N-terminal domain, NTD, Neutralizing antibody, 2-51, Fab, IMMUNE SYSTEM, IMMUNE SYSTEM-Viral Protein complex", - refModels: [ - { - emdbId: null, - pdbId: "7L2C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l2c_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l2c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "2-51 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "2-51 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "BHPQYMZQTOCNFJ-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "OGGXGZAMXPVRFZ-UHFFFAOYSA-N", - "ZIBGPFATKBEMQZ-UHFFFAOYSA-N", - ], - dbauthors: ["Reddem, E.R.", "Shapiro, L.", "Cerutti, G."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33789084", - title: - "Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.", - journal: "Cell Host Microbe 29: 819-833.e7 (2021), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2021.03.005", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33789084", - pubDate: "2021", - abstract: "", - authors: [ - "Cerutti, G.", - "Guo, Y.", - "Zhou, T.", - "Gorman, J.", - "Lee, M.", - "Rapp, M.", - "Reddem, E.R.", - "Yu, J.", - "Bahna, F.", - "Bimela, J.", - "Huang, Y.", - "Katsamba, P.S.", - "Liu, L.", - "Nair, M.S.", - "Rawi, R.", - "Olia, A.S.", - "Wang, P.", - "Zhang, B.", - "Chuang, G.Y.", - "Ho, D.D.", - "Sheng, Z.", - "Kwong, P.D.", - "Shapiro, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l2c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l2c", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 3CLpro in complex with the non-covalent inhibitor WU-04", - emdb: null, - pdb: { - dbId: "7EN8", - method: "X-RAY DIFFRACTION", - keywords: "Non-covalent, Inhibitor, 3CLpro, Coronavirus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7EN8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7en8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7en8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BPLNOSFMIIASSJ-UXHICEINSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Hou, N. (0000-0003-3489-5271)", - "Peng, C. (0000-0002-4165-5957)", - "Hu, Q. (0000-0001-7803-7821)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36844503", - title: - "Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro.", - journal: "Acs Cent.Sci. 9: 217-227 (2023), 2374-7951", - doi: "https://doi.org/10.1021/acscentsci.2c01359", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36844503", - pubDate: "2023", - abstract: "", - authors: [ - "Hou, N.", - "Shuai, L.", - "Zhang, L.", - "Xie, X.", - "Tang, K.", - "Zhu, Y.", - "Yu, Y.", - "Zhang, W.", - "Tan, Q.", - "Zhong, G.", - "Wen, Z.", - "Wang, C.", - "He, X.", - "Huo, H.", - "Gao, H.", - "Xu, Y.", - "Xue, J.", - "Peng, C.", - "Zou, J.", - "Schindewolf, C.", - "Menachery, V.", - "Su, W.", - "Yuan, Y.", - "Shen, Z.", - "Zhang, R.", - "Yuan, S.", - "Yu, H.", - "Shi, P.Y.", - "Bu, Z.", - "Huang, J.", - "Hu, Q.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7en8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7en8", - }, - }, - { - title: - "Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a potent neutralizing antibody, CV30 Fab", - emdb: null, - pdb: { - dbId: "6XE1", - method: "X-RAY DIFFRACTION", - keywords: - "Antibody, COVID-19, immune system, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "6XE1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xe1_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xe1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "CV30 Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV30 Fab Kappa chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Hurlburt, N.K. 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(0000-0001-5854-2388)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34381460", - title: - "Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies.", - journal: "Front Immunol 12: 719037-719037 (2021), 1664-3224", - doi: "https://doi.org/10.3389/fimmu.2021.719037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381460", - pubDate: "2021", - abstract: "", - authors: ["Ye, Q.", "Lu, S.", "Corbett, K.D."], - }, - { - pmID: "34100017", - title: - "Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.06.01.446591", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34100017", - pubDate: "2021", - abstract: "", - authors: ["Ye, Q.", "Lu, S.", "Corbett, K.D."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n0i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n0i", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI18", - emdb: null, - pdb: { - dbId: "7RVR", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, main protease, reversible covalent inhibitors, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RVR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rvr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rvr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BMXUTPCWTPHBMF-MYGLTJDJSA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35779291", - title: - "A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114570-114570 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114570", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35779291", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, Y.", - "Yang, K.S.", - "Geng, Z.Z.", - "Alugubelli, Y.R.", - "Shaabani, N.", - "Vatansever, E.C.", - "Ma, X.R.", - "Cho, C.C.", - "Khatua, K.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rvr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rvr", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z4718398572", - emdb: null, - pdb: { - dbId: "5SP4", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SP4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sp4_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sp4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QGSVLNUQBAPFJD-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. 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(0000-0002-8711-0012)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32363136", - title: - "Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites.", - journal: "Acta Pharm Sin B 10: 1228-1238 (2020), 2211-3835", - doi: "https://doi.org/10.1016/j.apsb.2020.04.009", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32363136", - pubDate: "2020", - abstract: "", - authors: [ - "Kang, S.", - "Yang, M.", - "Hong, Z.", - "Zhang, L.", - "Huang, Z.", - "Chen, X.", - "He, S.", - "Zhou, Z.", - "Chen, Q.", - "Yan, Y.", - "Zhang, C.", - "Shan, H.", - "Chen, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6m3m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6m3m", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with REAL250000548538 - (R) isomer", - emdb: null, - pdb: { - dbId: "5SQF", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SQF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sqf_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sqf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZNXPXZYKUWUFEH-SECBINFHSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. 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(0000-0002-5416-5789)", - "Li, H. (0000-0002-6964-9962)", - "Galanie, S.", - "Phillips, G.", - "Labbe, A.", - "Weiss, K.L. (0000-0002-6486-8007)", - "Zhang, Q.", - "Arnould, M.A.", - "Clyde, A.", - "Ma, H.", - "Ramanathan, A. (0000-0002-1622-5488)", - "Jonsson, C.B. (0000-0002-2640-7672)", - "Head, M.S.", - "Coates, L. (0000-0003-2342-049X)", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3s_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3s", - }, - }, - { - title: "B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide", - emdb: null, - pdb: { - dbId: "7M53", - method: "X-RAY DIFFRACTION", - keywords: - "Broadly neutralizing antibody, Structural genomics, SSGCID, Center for Structural Genomics of Infectious Diseases, CSGID, ANTIVIRAL PROTEIN, Seattle Structural Genomics Center for Infectious Disease, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7M53", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m53_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m53", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike glycoprotein stem helix peptide", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "B6 antigen-binding (Fab) fragment heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "B6 antigen-binding (Fab) fragment light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Seattle Structural Genomics Center for Infectious Disease (SSGCID)", - "Veesler, D.", - "Park, Y.J.", - "Sauer, M.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33981021", - title: "Structural basis for broad coronavirus neutralization.", - journal: "Nat.Struct.Mol.Biol. 28: 478-486 (2021), 1545-9985", - doi: "https://doi.org/10.1038/s41594-021-00596-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33981021", - pubDate: "2021", - abstract: "", - authors: [ - "Sauer, M.M.", - "Tortorici, M.A. (0000-0002-2260-2577)", - "Park, Y.J. (0000-0003-2901-6949)", - "Walls, A.C. (0000-0002-9636-8330)", - "Homad, L.", - "Acton, O.J.", - "Bowen, J.E. (0000-0003-3590-9727)", - "Wang, C.", - "Xiong, X. (0000-0002-4632-9122)", - "de van der Schueren, W.", - "Quispe, J.", - "Hoffstrom, B.G.", - "Bosch, B.J. (0000-0002-3864-232X)", - "McGuire, A.T. (0000-0003-1841-6859)", - "Veesler, D. (0000-0002-6019-8675)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m53_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m53", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 3", - emdb: null, - pdb: { - dbId: "7AU4", - method: "X-RAY DIFFRACTION", - keywords: "Inhibitor, complex, protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AU4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7au4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7au4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "BIZQWNOTOCHPKD-HNNXBMFYSA-N"], - dbauthors: ["Talibov, V.O. (0000-0002-1135-2744)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35142215", - title: - "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", - journal: "J.Am.Chem.Soc. 144: 2905-2920 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08402", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35142215", - pubDate: "2022", - abstract: "", - authors: [ - "Luttens, A. (0000-0003-2915-7901)", - "Gullberg, H.", - "Abdurakhmanov, E.", - "Vo, D.D.", - "Akaberi, D. (0000-0002-9595-9796)", - "Talibov, V.O.", - "Nekhotiaeva, N.", - "Vangeel, L.", - "De Jonghe, S. (0000-0002-3872-6558)", - "Jochmans, D.", - "Krambrich, J.", - "Tas, A.", - "Lundgren, B.", - "Gravenfors, Y. (0000-0001-6025-4908)", - "Craig, A.J.", - "Atilaw, Y.", - "Sandstrom, A.", - "Moodie, L.W.K. (0000-0002-9500-4535)", - "Lundkvist, A.", - "van Hemert, M.J.", - "Neyts, J.", - "Lennerstrand, J.", - "Kihlberg, J. (0000-0002-4205-6040)", - "Sandberg, K.", - "Danielson, U.H. (0000-0003-2728-0340)", - "Carlsson, J. (0000-0003-4623-2977)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7au4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7au4", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z425387594", - emdb: null, - pdb: { - dbId: "5RLL", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RLL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rll_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rll", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "FBQIUSDQWOLCNY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rll_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rll", - }, - }, - { - title: "SARS-CoV-2 3CL protease (3CLpro) in complex with a covalent inhibitor", - emdb: null, - pdb: { - dbId: "7VVT", - method: "X-RAY DIFFRACTION", - keywords: - "Main protease, covalent inhibitor, VIRAL PROTEIN-INHIBITOR COMPLEX, VIRAL INHIBITOR-COMPLEX complex", - refModels: [ - { - emdbId: null, - pdbId: "7VVT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vvt_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vvt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VFCHONURCHBPEO-GFCCVEGCSA-N"], - dbauthors: ["Li, M.", "Xu, Y.", "Su, H.", "Nie, T."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35114541", - title: - "In silico screening-based discovery of novel covalent inhibitors of the SARS-CoV-2 3CL protease.", - journal: "Eur.J.Med.Chem. 231: 114130-114130 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114130", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35114541", - pubDate: "2022", - abstract: "", - authors: [ - "Xiong, M.", - "Nie, T.", - "Shao, Q.", - "Li, M.", - "Su, H.", - "Xu, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vvt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vvt", - }, - }, - { - title: - "SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19).", - emdb: null, - pdb: { - dbId: "6YB7", - method: "X-RAY DIFFRACTION", - keywords: "protease, cysteine protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6YB7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6yb7_final.pdb", - externalLink: "https://pdb-redo.eu/db/6yb7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "MTHSVFCYNBDYFN-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Stuart, D.I.", - "Hall, D.R.", - "Lukacik, P.", - "Walsh, M.A.", - "Crawshaw, A.D.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Brandao-Neto, J.", - "Powell, A.J.", - "Aragao, D. (0000-0002-6551-4657)", - "Williams, M.", - "Flaig, R.", - "McAuley, K.E.", - "Mazzorana, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "COVID-19 main protease with unliganded active site", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Owen, C.D.", - "Lukacik, P.", - "Strain-Damerell, C.M.", - "Douangamath, A.", - "Powell, A.J.", - "Fearon, D.", - "Brandao-Neto, J.", - "Crawshaw, A.D.", - "Aragao, D.", - "Williams, M.", - "Flaig, R.", - "Hall, D.", - "McAauley, K.", - "Stuart, D.I.", - "von Delft, F.", - "Walsh, M.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6yb7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6yb7", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1101755952", - emdb: null, - pdb: { - dbId: "5RMH", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RMH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rmh_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rmh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ORSJIQSXTAJDMZ-VIFPVBQESA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. 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(0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rmh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rmh", - }, - }, - { - title: "Crystal Structure of VN01H1 Fab in complex with SARS-CoV-2 S fusion peptide", - emdb: null, - pdb: { - dbId: "7SKZ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 spike, COVID-19, fusion peptide, Fab, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID", - refModels: [ - { - emdbId: null, - pdbId: "7SKZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7skz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7skz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "PRO-SER-LYS-ARG-SER-PHE-ILE-GLU-ASP-LEU-LEU-PHE-ASN", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of VN01H1 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of VN01H1 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Seattle Structural Genomics Center for Infectious Disease (SSGCID)", - "Veesler, D.", - "Tortorici, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35857703", - title: - "ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.", - journal: "Science 377: 735-742 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abq2679", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35857703", - pubDate: "2022", - abstract: "", - authors: [ - "Low, J.S.", - "Jerak, J.", - "Tortorici, M.A.", - "McCallum, M.", - "Pinto, D.", - "Cassotta, A.", - "Foglierini, M.", - "Mele, F.", - "Abdelnabi, R.", - "Weynand, B.", - "Noack, J.", - "Montiel-Ruiz, M.", - "Bianchi, S.", - "Benigni, F.", - "Sprugasci, N.", - "Joshi, A.", - "Bowen, J.E.", - "Stewart, C.", - "Rexhepaj, M.", - "Walls, A.C.", - "Jarrossay, D.", - "Morone, D.", - "Paparoditis, P.", - "Garzoni, C.", - "Ferrari, P.", - "Ceschi, A.", - "Neyts, J.", - "Purcell, L.A.", - "Snell, G.", - "Corti, D.", - "Lanzavecchia, A.", - "Veesler, D.", - "Sallusto, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7skz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7skz", - }, - }, - { - title: - "PanDDA analysis group deposition of ground-state model of SARS-CoV-2 main protease screened against DSI poised (Enamine), Fraglites and Peplites (Newcastle university), Mini Frags (Astex), York 3D (York university), electrophile cysteine covalent (Weizman institute) fragment libraries", - emdb: null, - pdb: { - dbId: "5R8T", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5R8T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5r8t_final.pdb", - externalLink: "https://pdb-redo.eu/db/5r8t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition of ground-state model of SARS-CoV-2 main protease fragment screening", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5r8t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5r8t", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 50", - emdb: null, - pdb: { - dbId: "7M90", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7M90", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m90_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m90", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ROLIIXCVQCAWPI-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, C.H.", - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34161756", - title: - "Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.", - journal: "Structure 29 (2021), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2021.06.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34161756", - pubDate: "2021", - abstract: "", - authors: [ - "Deshmukh, M.G.", - "Ippolito, J.A.", - "Zhang, C.H.", - "Stone, E.A.", - "Reilly, R.A.", - "Miller, S.J.", - "Jorgensen, W.L.", - "Anderson, K.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m90_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m90", - }, - }, - { - title: "SARS-CoV-2 Nucleocapsid N-terminal domain (N-NTD) protein", - emdb: null, - pdb: { - dbId: "7SD4", - method: "SOLID-STATE NMR", - keywords: - "COVID-19, SARS-CoV-2, nucleocapsid protein, N-terminal domain, RNA-binding domain, STRUCTURAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Sarkar, S. 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(0000-0002-0346-1131)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35638584", - title: - "Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain.", - journal: "J.Am.Chem.Soc. 144: 10543-10555 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.2c03320", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35638584", - pubDate: "2022", - abstract: "", - authors: [ - "Sarkar, S.", - "Runge, B.", - "Russell, R.W.", - "Movellan, K.T.", - "Calero, D.", - "Zeinalilathori, S.", - "Quinn, C.M.", - "Lu, M.", - "Calero, G.", - "Gronenborn, A.M.", - "Polenova, T.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sd4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sd4", - }, - }, - { - title: "Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 12/13", - emdb: null, - pdb: { - dbId: "7TB2", - method: "X-RAY DIFFRACTION", - keywords: - "Coronavirus, COVID-19, COVID, PROTEASE, DRUG RESISTANCE, COMPLEX, HYDROLASE, DURG DISCOVERY, MAIN PROTEASE, MPRO, SUBSTRATE COMPLEX, NSP 12/13, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TB2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tb2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tb2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Nonstructural protein 12/13", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Shaqra, A.M. 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(0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tb2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tb2", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Isofloxythepin", - emdb: null, - pdb: { - dbId: "7AY7", - method: "X-RAY DIFFRACTION", - keywords: "inhibitor, complex, screen, sars-cov-2, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AY7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ay7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ay7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QEZUZXXLBLAREJ-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "RAXXELZNTBOGNW-UHFFFAOYSA-O", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Reinke, P.Y.A.", - "Lieske, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - { - pmID: "", - title: - "Inhibition of SARS-CoV-2 main protease by allosteric drug-binding", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.11.12.378422", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ay7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ay7", - }, - }, - { - title: - "Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from SARS-CoV-2 spike (S896-904)", - emdb: null, - pdb: { - dbId: "7M8U", - method: "X-RAY DIFFRACTION", - keywords: "TCR, T cell, spike, peptide presentation, immunology, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7M8U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m8u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m8u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q546I9", - organism: "9606", - name: "HLA class I histocompatibility antigen B, alpha chain", - details: "", - altNames: "HLA-B*35:01:01:NEW,MHC class I antigen,MHC class I protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2 peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NBIIXXVUZAFLBC-UHFFFAOYSA-K", "FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: ["Gras, S.", "Szeto, C.", "Nguyen, A.T."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules", - journal: "Biophysica 1 (2021)", - doi: "https://doi.org/10.3390/biophysica1020015", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Nguyen, A.T.", - "Szeto, C.", - "Jayasinghe, D.", - "Lobos, C.A.", - "Halim, H.", - "Chatzileontiadou, D.S.M.", - "Grant, E.J.", - "Gras, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m8u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m8u", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 7c", - emdb: null, - pdb: { - dbId: "7T45", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7T45", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t45_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t45", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UCJPXTXBXDDVDN-UDSSINMLSA-N", "UWHCKJMYHZGTIT-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Kankanamalage, A.C.G.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35638577", - title: - "Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.", - journal: "J.Med.Chem. 65: 7818-7832 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00224", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35638577", - pubDate: "2022", - abstract: "", - authors: [ - "Dampalla, C.S. (0000-0002-8199-2376)", - "Rathnayake, A.D. (0000-0003-2588-7624)", - "Galasiti Kankanamalage, A.C.", - "Kim, Y.", - "Perera, K.D. (0000-0002-3778-4975)", - "Nguyen, H.N.", - "Miller, M.J.", - "Madden, T.K.", - "Picard, H.R.", - "Thurman, H.A.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P. (0000-0003-0833-3259)", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Battaile, K.P.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t45_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t45", - }, - }, - { - title: - "Crystal Structure of the Second Form of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS CoV-2", - emdb: null, - pdb: { - dbId: "6WTC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, co-factor for RNA polymerase NSP12, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WTC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wtc_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wtc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 7", - details: "", - altNames: "nsp7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 8", - details: "", - altNames: "nsp8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QTBSBXVTEAMEQO-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Wilamowski, M.", - "Godzik, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of the Second Form of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Wilamowski, M.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.", - "Endres, M.", - "Godzik, A.", - "Michalska, K.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wtc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wtc", - }, - }, - { - title: - "The crystal structure of SARS-CoV-2 nsp10-nsp16 methyltransferase complex with Sinefungin", - emdb: null, - pdb: { - dbId: "6YZ1", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, viral replication, coronavirus, methyltransferase, sinefungin, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6YZ1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6yz1_final.pdb", - externalLink: "https://pdb-redo.eu/db/6yz1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "nsp16", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "nsp10", - details: "", - altNames: "nsp10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LMXOHSDXUQEUSF-YECHIGJVSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Boura, E. (0000-0002-9652-4065)", - "Krafcikova, P.", - "Silhan, J. (0000-0003-3868-5714)", - "Nencka, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32709887", - title: - "Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin.", - journal: "Nat Commun 11: 3717-3717 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-17495-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32709887", - pubDate: "2020", - abstract: "", - authors: [ - "Krafcikova, P.", - "Silhan, J.", - "Nencka, R.", - "Boura, E. (0000-0002-9652-4065)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6yz1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6yz1", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000332752", - emdb: null, - pdb: { - dbId: "5RTJ", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RTJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rtj_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rtj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FJKROLUGYXJWQN-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rtj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rtj", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 2C02", - emdb: null, - pdb: { - dbId: "7SPP", - method: "X-RAY DIFFRACTION", - keywords: "RBD, VIRAL PROTEIN, VNAR, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7SPP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7spp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7spp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "7797", - name: "VNAR 2C02", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: ["Shi, K. (0000-0003-4175-3714)", "Aihara, H. (0000-0001-7508-6230)"], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34916516", - title: - "Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography.", - journal: "Nat Commun 12: 7325-7325 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-27611-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34916516", - pubDate: "2021", - abstract: "", - authors: [ - "Ubah, O.C. (0000-0001-9011-8405)", - "Lake, E.W.", - "Gunaratne, G.S.", - "Gallant, J.P.", - "Fernie, M.", - "Robertson, A.J.", - "Marchant, J.S. (0000-0001-6592-0877)", - "Bold, T.D.", - "Langlois, R.A.", - "Matchett, W.E. (0000-0001-7515-2226)", - "Thiede, J.M. (0000-0002-6603-281X)", - "Shi, K.", - "Yin, L.", - "Moeller, N.H.", - "Banerjee, S.", - "Ferguson, L.", - "Kovaleva, M.", - "Porter, A.J.", - "Aihara, H. (0000-0001-7508-6230)", - "LeBeau, A.M. (0000-0003-3802-7789)", - "Barelle, C.J. (0000-0003-1872-3373)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7spp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7spp", - }, - }, - { - title: "SARS-CoV-2 Nucleocapsid phosphopeptide 201-210 bound to human 14-3-3 sigma", - emdb: null, - pdb: { - dbId: "7QIP", - method: "X-RAY DIFFRACTION", - keywords: - "phosphopeptide-binding, universal regulatory hub, protein-peptide complex, coronavirus protein fragment, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7QIP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qip_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qip", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P31947", - organism: "9606", - name: "14-3-3 protein sigma", - details: "", - altNames: "Epithelial cell marker protein 1,Stratifin, CLU1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "ARG-GLY-TPO-SER-PRO-ALA-ARG-MET", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Sluchanko, N.N. (0000-0002-8608-1416)", - "Tugaeva, K.V.", - "Smith, J.L.R.", - "Antson, A.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Sluchanko, N.N. (0000-0002-8608-1416)", - "Tugaeva, K.V.", - "Smith, J.L.R.", - "Antson, A.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qip_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qip", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Climbazole", - emdb: null, - pdb: { - dbId: "7AOL", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-!9, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AOL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aol_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aol", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "RAXXELZNTBOGNW-UHFFFAOYSA-O", - "OWEGWHBOCFMBLP-AWEZNQCLSA-N", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Lieske, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7aol_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7aol", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000002506130", - emdb: null, - pdb: { - dbId: "5RVU", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RVU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rvu_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rvu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DLFLQXUYRFIFOK-UHFFFAOYSA-N"], - dbauthors: ["Fraser, J.S.", "Young, I.D.", "Thompson, M.C.", "Correy, G.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5run_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5run", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 8 (P43 crystal form)", - emdb: null, - pdb: { - dbId: "7TWR", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, room temperature diffraction, protein dynamics, water networks, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TWR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7twr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7twr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QTBSBXVTEAMEQO-UHFFFAOYSA-M"], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 8 (P43 crystal form)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. 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(0000-0001-5930-7363)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32541865", - title: - "Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease.", - journal: "Cell Res. (2020), 1001-0602", - doi: "https://doi.org/10.1038/s41422-020-0356-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32541865", - pubDate: "2020", - abstract: "", - authors: [ - "Ma, C. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rvb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rvb", - }, - }, - { - title: - "Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with m7GpppA Cap-0 and SAM Determined by Fixed-Target Serial Crystallography", - emdb: null, - pdb: { - dbId: "7JPE", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, Serial Crystallography, Methyltransferase, m7GpppA, Cap-0, S-adenosylhomomethionine, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7JPE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jpe_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jpe", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QQOHNVHGNZYSBP-XPWFQUROSA-O", - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "SBASPRRECYVBRF-KQYNXXCUSA-O", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Satchell, K.J.F.", - "Michalska, K.", - "Wilamowski, M.", - "Sherrell, D.A.", - "Lavens, A.", - "Chard, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33972410", - title: - "2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography.", - journal: "Proc.Natl.Acad.Sci.USA 118 (2021), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2100170118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33972410", - pubDate: "2021", - abstract: "", - authors: [ - "Wilamowski, M.", - "Sherrell, D.A. (0000-0002-6393-8800)", - "Minasov, G. (0000-0001-5460-3462)", - "Kim, Y. (0000-0002-1610-4889)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Lavens, A. (0000-0002-3856-9919)", - "Chard, R.", - "Maltseva, N. (0000-0002-2871-465X)", - "Jedrzejczak, R.", - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Saint, N.", - "Foster, I.T. (0000-0003-2129-5269)", - "Michalska, K. (0000-0001-7140-3649)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jpe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jpe", - }, - }, - { - title: - "1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5", - emdb: null, - pdb: { - dbId: "7VBF", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Nucleocapsid dimerization domain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VBF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vbf_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vbf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhang, J.", "Li, J.", "Zhou, X.L.", "Zhong, F.L."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zhou, X.L.", "Zhong, F.L.", "Li, J.", "Zhang, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vbf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vbf", - }, - }, - { - title: "crystal structure of SARS-CoV-2 3CL protease", - emdb: null, - pdb: { - dbId: "7V7M", - method: "X-RAY DIFFRACTION", - keywords: "protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7V7M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7v7m_final.pdb", - externalLink: "https://pdb-redo.eu/db/7v7m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Yi, Y. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rtk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rtk", - }, - }, - { - title: - "The co-crystal structure of SARS-CoV-2 main protease with (S)-2-cinnamamido-4-methyl-N-((S)-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)pentanamide", - emdb: null, - pdb: { - dbId: "7DGB", - method: "X-RAY DIFFRACTION", - keywords: "Complex, inhibitor, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7DGB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dgb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dgb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WLXCENLBBWQJML-MRUBZEKTSA-N"], - dbauthors: ["Shang, L.Q. (0000-0003-4424-3162)", "Wang, H. (0000-0002-1916-7092)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35635946", - title: - "The structure-based design of peptidomimetic inhibitors against SARS-CoV-2 3C like protease as Potent anti-viral drug candidate.", - journal: "Eur.J.Med.Chem. 238: 114458-114458 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114458", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35635946", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, H.", - "Pei, R.", - "Li, X.", - "Deng, W.", - "Xing, S.", - "Zhang, Y.", - "Zhang, C.", - "He, S.", - "Sun, H.", - "Xiao, S.", - "Xiong, J.", - "Chen, X.", - "Wang, Y.", - "Guo, Y.", - "Zhang, B.", - "Shang, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dgb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dgb", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 4c", - emdb: null, - pdb: { - dbId: "7T44", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7T44", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t44_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t44", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FMGSKLZLMKYGDP-USOAJAOKSA-N", - "MQSKUPXMBXNALP-FJXLLPKBSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Liu, L.", - "Kim, Y.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35638577", - title: - "Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.", - journal: "J.Med.Chem. 65: 7818-7832 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00224", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35638577", - pubDate: "2022", - abstract: "", - authors: [ - "Dampalla, C.S. (0000-0002-8199-2376)", - "Rathnayake, A.D. (0000-0003-2588-7624)", - "Galasiti Kankanamalage, A.C.", - "Kim, Y.", - "Perera, K.D. (0000-0002-3778-4975)", - "Nguyen, H.N.", - "Miller, M.J.", - "Madden, T.K.", - "Picard, H.R.", - "Thurman, H.A.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P. (0000-0003-0833-3259)", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Battaile, K.P.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t44_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t44", - }, - }, - { - title: - "Crystal Structure of HLA-A*11:01 in complex with NSASFSTFK, an 9-mer epitope from SARS-CoV-2 spike (S370-378)", - emdb: null, - pdb: { - dbId: "7M8T", - method: "X-RAY DIFFRACTION", - keywords: "TCR, T cell, spike, immunology, epitope presentation, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7M8T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m8t_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m8t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q861F7", - organism: "9606", - name: "HLA class I histocompatibility antigen, A alpha chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S1 peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "BHPQYMZQTOCNFJ-UHFFFAOYSA-N", - ], - dbauthors: ["Gras, S.", "Szeto, C.", "Nguyen, A.T."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules", - journal: "Biophysica 1 (2021)", - doi: "https://doi.org/10.3390/biophysica1020015", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Nguyen, A.T.", - "Szeto, C.", - "Jayasinghe, D.", - "Lobos, C.A.", - "Halim, H.", - "Chatzileontiadou, D.S.M.", - "Grant, E.J.", - "Gras, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m8t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m8t", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1220452176", - emdb: null, - pdb: { - dbId: "5R7Z", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5R7Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5r7z_final.pdb", - externalLink: "https://pdb-redo.eu/db/5r7z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "UDLASALUJLTGJV-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Powell, A.J.", - "Wild, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. (0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5r7z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5r7z", - }, - }, - { - title: - "1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "6W4H", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6W4H", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6w4h_final.pdb", - externalLink: "https://pdb-redo.eu/db/6w4h", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LSNNMFCWUKXFEE-UHFFFAOYSA-L", - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "LKDRXBCSQODPBY-ARQDHWQXSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Satchell, K.J.F.", - "Godzik, A.", - "Wiersum, G.", - "Stogios, P.J.", - "Skarina, T.", - "Jaroszewski, L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32994211", - title: - "High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design.", - journal: "Sci.Signal. 13 (2020), 1937-9145", - doi: "https://doi.org/10.1126/scisignal.abe1202", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32994211", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Minasov, G. (0000-0001-5460-3462)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Kiryukhina, O. (0000-0001-5962-8423)", - "Brunzelle, J. (0000-0001-9197-0018)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.L.", - "Kiryukhina, O.", - "Wiersum, G.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Endres, M.", - "Jaroszewski, L.", - "Godzik, A.", - "Joachimiak, A.", - "Satchell, K.J.F.", - ], - }, - { - pmID: "32511376", - title: - "The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.04.17.047498", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32511376", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Minasov, G. (0000-0001-5460-3462)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Kiryukhina, O. (0000-0001-5962-8423)", - "Brunzelle, J. (0000-0001-9197-0018)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.L.", - "Kiryukhina, O.", - "Wiersum, G.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Endres, M.", - "Jaroszewski, L.", - "Godzik, A.", - "Joachimiak, A.", - "Satchell, K.J.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w4h_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w4h", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 14c", - emdb: null, - pdb: { - dbId: "7T4B", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7T4B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t4b_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t4b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "WDYXMIZDWOFVQK-OGNFBWPZSA-N", - "WDYXMIZDWOFVQK-BOSXTWCSSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35638577", - title: - "Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.", - journal: "J.Med.Chem. 65: 7818-7832 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00224", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35638577", - pubDate: "2022", - abstract: "", - authors: [ - "Dampalla, C.S. (0000-0002-8199-2376)", - "Rathnayake, A.D. (0000-0003-2588-7624)", - "Galasiti Kankanamalage, A.C.", - "Kim, Y.", - "Perera, K.D. (0000-0002-3778-4975)", - "Nguyen, H.N.", - "Miller, M.J.", - "Madden, T.K.", - "Picard, H.R.", - "Thurman, H.A.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P. (0000-0003-0833-3259)", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Battaile, K.P.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t4b_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t4b", - }, - }, - { - title: - "Crystallographic structure of neutralizing antibody 10-40 in complex with SARS-CoV-2 spike receptor binding domain", - emdb: null, - pdb: { - dbId: "7SD5", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, Viral protein, Spike glycoprotein, Receptor Binding Protein, RBD, Neutralizing antibody, 10-40, Fab, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7SD5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sd5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sd5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "10-40 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "10-40 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Reddem, E.R. (0000-0003-3054-5506)", - "Shapiro, L. (0000-0001-9943-8819)", - "Casner, R.G. (0000-0002-2910-0908)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35438546", - title: - "An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses.", - journal: "Sci Transl Med 14: eabn6859-eabn6859 (2022), 1946-6242", - doi: "https://doi.org/10.1126/scitranslmed.abn6859", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35438546", - pubDate: "2022", - abstract: "", - authors: [ - "Liu, L. (0000-0003-3128-8513)", - "Iketani, S. (0000-0002-3733-9556)", - "Guo, Y. (0000-0001-5357-660X)", - "Reddem, E.R. (0000-0003-3054-5506)", - "Casner, R.G. (0000-0002-2910-0908)", - "Nair, M.S. (0000-0002-5994-3957)", - "Yu, J. (0000-0001-8604-4538)", - "Chan, J.F. (0000-0001-6336-6657)", - "Wang, M.", - "Cerutti, G. (0000-0002-9081-7561)", - "Li, Z.", - "Morano, N.C. 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(0000-0003-1627-149X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sd5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sd5", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 25", - emdb: null, - pdb: { - dbId: "7M91", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7M91", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m91_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m91", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BHQBUUBHCKLKLD-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, C.H.", - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34161756", - title: - "Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.", - journal: "Structure 29 (2021), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2021.06.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34161756", - pubDate: "2021", - abstract: "", - authors: [ - "Deshmukh, M.G.", - "Ippolito, J.A.", - "Zhang, C.H.", - "Stone, E.A.", - "Reilly, R.A.", - "Miller, S.J.", - "Jorgensen, W.L.", - "Anderson, K.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m91_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m91", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 Omicron main protease (Mpro) in complex with inhibitor GC376", - emdb: null, - pdb: { - dbId: "7TOB", - method: "X-RAY DIFFRACTION", - keywords: - "omicron, main protease, 3cl, 3-chemotrypsin like protease, sars-cov-2, COVID, GC376, inhibitor, covalent, antiviral, NSP5, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TOB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tob_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tob", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N", "MTHSVFCYNBDYFN-UHFFFAOYSA-N"], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M.D."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35292745", - title: - "The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition.", - journal: "Cell Res. 32: 498-500 (2022), 1001-0602", - doi: "https://doi.org/10.1038/s41422-022-00640-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35292745", - pubDate: "2022", - abstract: "", - authors: [ - "Sacco, M.D.", - "Hu, Y.", - "Gongora, M.V.", - "Meilleur, F.", - "Kemp, M.T.", - "Zhang, X.", - "Wang, J.", - "Chen, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tob_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tob", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z31792168", - emdb: null, - pdb: { - dbId: "5R84", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5R84", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5r84_final.pdb", - externalLink: "https://pdb-redo.eu/db/5r84", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SIURWXONEBYXJD-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Powell, A.J.", - "Wild, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5r84_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5r84", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2293643386", - emdb: null, - pdb: { - dbId: "5RLZ", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RLZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rlz_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rlz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "CKOGPKPHDCYLTR-MRVPVSSYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rlz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rlz", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex", - emdb: null, - pdb: { - dbId: "7MC5", - method: "X-RAY DIFFRACTION", - keywords: "RNA binding, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7MC5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mc5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mc5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "FEWJPZIEWOKRBE-JCYAYHJZSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Shi, K. (0000-0003-4175-3714)", - "Aihara, H. (0000-0001-7508-6230)", - "Yin, L.", - "Banerjee, S.", - "Moeller, N.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33821277", - title: - "Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.04.02.438274", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33821277", - pubDate: "2021", - abstract: "", - authors: [ - "Moeller, N.H.", - "Shi, K. (0000-0003-4175-3714)", - "Demir, O. (0000-0002-3317-4731)", - "Belica, C.", - "Banerjee, S. (0000-0002-9414-7163)", - "Yin, L.", - "Durfee, C. (0000-0002-8130-4270)", - "Amaro, R.E. (0000-0002-9275-9553)", - "Aihara, H. (0000-0001-7508-6230)", - "Shi, K.", - "Demir, O.", - "Banerjee, S.", - "Durfee, C.", - "Amaro, R.E.", - "Aihara, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mc5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mc5", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z53860899", - emdb: null, - pdb: { - dbId: "5RMI", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RMI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rmi_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rmi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "UEDUENGHJMELGK-HYDKPPNVSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. 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emdb: null, - pdb: { - dbId: "5RLM", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RLM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rlm_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rlm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "RYRDUZSMONMBBE-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - 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(0000-0002-2996-0326)", - "Tyrrell, D.L.", - "Lemieux, M.J. (0000-0003-4745-9153)", - "Nieman, J.A. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s2a_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s2a", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-88 and COVOX-45 Fabs", - emdb: null, - pdb: { - dbId: "7BEL", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, antibody, germline, V-gene, receptor-binding-domain, spike, neutralisation, protection, glycosylation, valency, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7BEL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bel_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bel", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-45 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-88 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-88 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-45 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: ["Zhao, Y.", "Zhou, D.", "Ren, J.", "Stuart, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33756110", - title: - "The antigenic anatomy of SARS-CoV-2 receptor binding domain.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.02.032", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33756110", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Ginn, H.M.", - "Duyvesteyn, H.M.E.", - "Supasa, P.", - "Case, J.B.", - "Zhao, Y.", - "Walter, T.S.", - "Mentzer, A.J.", - "Liu, C.", - "Wang, B.", - "Paesen, G.C.", - "Slon-Campos, J.", - "Lopez-Camacho, C.", - "Kafai, N.M.", - "Bailey, A.L.", - "Chen, R.E.", - "Ying, B.", - "Thompson, C.", - "Bolton, J.", - "Fyfe, A.", - "Gupta, S.", - "Tan, T.K.", - "Gilbert-Jaramillo, J.", - "James, W.", - "Knight, M.", - "Carroll, M.W.", - "Skelly, D.", - "Dold, C.", - "Peng, Y.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Klenerman, P.", - "Temperton, N.", - "Hall, D.R.", - "Williams, M.A.", - "Paterson, N.G.", - "Bertram, F.K.R.", - "Siebert, C.A.", - "Clare, D.K.", - "Howe, A.", - "Radecke, J.", - "Song, Y.", - "Townsend, A.R.", - "Huang, K.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Diamond, M.S.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bel_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bel", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 macrodomain in complex with remdesivir metabolite GS-441524", - emdb: null, - pdb: { - dbId: "7BF6", - method: "X-RAY DIFFRACTION", - keywords: - "nsp3, macrodomain, SARS-CoV-2, remdesivir, GS-441524, covid-19, Structural Genomics, Structural Genomics Consortium, SGC, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7BF6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bf6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bf6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BRDWIEOJOWJCLU-LTGWCKQJSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Ni, X.", - "Knapp, S.", - "Chaikuad, A.", - "Structural Genomics Consortium (SGC)", - "Structural Genomics Consortium", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33850605", - title: - "Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain.", - journal: "Acs Med.Chem.Lett. 12: 603-609 (2021), 1948-5875", - doi: "https://doi.org/10.1021/acsmedchemlett.0c00684", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33850605", - pubDate: "2021", - abstract: "", - authors: [ - "Ni, X.", - "Schroder, M.", - "Olieric, V.", - "Sharpe, M.E.", - "Hernandez-Olmos, V.", - "Proschak, E.", - "Merk, D.", - "Knapp, S.", - "Chaikuad, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bf6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bf6", - }, - }, - { - title: - "The 1.5 A Crystal Structure of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS CoV-2", - emdb: null, - pdb: { - dbId: "6XIP", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, co-factor for RNA polymerase NSP12, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6XIP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xip_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xip", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 7", - details: "", - altNames: "nsp7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 8", - details: "", - altNames: "nsp8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Wilamowski, M.", - "Godzik, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34197805", - title: - "Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication.", - journal: "Biophys.J. 120: 3152-3165 (2021), 1542-0086", - doi: "https://doi.org/10.1016/j.bpj.2021.06.006", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34197805", - pubDate: "2021", - abstract: "", - authors: [ - "Wilamowski, M.", - "Hammel, M.", - "Leite, W.", - "Zhang, Q.", - "Kim, Y.", - "Weiss, K.L.", - "Jedrzejczak, R.", - "Rosenberg, D.J.", - "Fan, Y.", - "Wower, J.", - "Bierma, J.C.", - "Sarker, A.H.", - "Tsutakawa, S.E.", - "Pingali, S.V.", - "O'Neill, H.M.", - "Joachimiak, A.", - "Hura, G.L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xip_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xip", - }, - }, - { - title: "Membrane bound structure of HR1 domain of SARS-CoV-2 spike protein", - emdb: null, - pdb: { - dbId: "7R95", - method: "SOLUTION NMR", - keywords: - "SARS-Cov-2, Heptad repeat, residual dipolar couplings, bicelles, lipid-water interface, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S2", - details: - "Lysine at N-terminal is used for biochemical assays; two serines were added at N-terminal to increase the peptide solubility in PBS", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Chiliveri, S.C.", "Bax, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34623907", - title: - "Transient lipid-bound states of spike protein heptad repeats provide insights into SARS-CoV-2 membrane fusion.", - journal: "Sci Adv 7: eabk2226-eabk2226 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abk2226", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34623907", - pubDate: "2021", - abstract: "", - authors: [ - "Chiliveri, S.C. 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(0000-0002-6089-5067)", - "Larance, M.", - "Otting, G. (0000-0002-0563-0146)", - "Turville, S.", - "Jackson, C.J.", - "Nitsche, C. (0000-0002-3704-2699)", - "Payne, R.J. (0000-0002-3618-9226)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rnw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rnw", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor Boceprevir at 1.35 A Resolution", - emdb: null, - pdb: { - dbId: "7K40", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Main Protease, 3CLpro/Mpro, Boceprevir, VIRAL PROTEIN, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7K40", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k40_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k40", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FEBWCINGHXXUCV-GFLQDLJJSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Shi, W.", - "McSweeney, S. 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externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k40", - }, - }, - { - title: - "Structure of the hemiacetal complex between the SARS-CoV-2 Main Protease and Leupeptin", - emdb: null, - pdb: { - dbId: "7NEV", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-!9, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NEV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nev_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nev", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "LEUPEPTIN", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - 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isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "OMPJBNCRMGITSC-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5skz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5skz", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 S RBD in complex with BD-515 Fab", - 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(0000-0003-1822-1701)", - "Wei, Y. (0000-0002-2363-4941)", - "Gao, C. (0000-0003-2128-376X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34021265", - title: - "Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines.", - journal: "Cell Res. 31: 732-741 (2021), 1001-0602", - doi: "https://doi.org/10.1038/s41422-021-00514-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34021265", - pubDate: "2021", - abstract: "", - authors: [ - "Cao, Y. (0000-0001-5918-1078)", - "Yisimayi, A.", - "Bai, Y.", - "Huang, W. (0000-0002-4246-8889)", - "Li, X.", - "Zhang, Z.", - "Yuan, T.", - "An, R.", - "Wang, J.", - "Xiao, T.", - "Du, S.", - "Ma, W.", - "Song, L.", - "Li, Y.", - "Song, W.", - "Wu, J.", - "Liu, S.", - "Zhang, Y.", - "Su, B.", - "Guo, X.", - "Wei, Y. (0000-0002-2363-4941)", - "Gao, C. (0000-0002-7654-9476)", - "Zhang, N.", - "Dou, Y.", - "Xu, X.", - "Shi, R.", - "Lu, B.", - "Jin, R.", - "Ma, Y.", - "Qin, C.", - "Wang, Y. (0000-0001-9769-5141)", - "Feng, Y. (0000-0001-5248-0155)", - "Xiao, J. (0000-0003-1822-1701)", - "Xie, X.S. (0000-0001-9281-5239)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e88_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e88", - }, - }, - { - title: - "Crystal structure of chimeric omicron RBD (strain BA.1) complexed with human ACE2", - emdb: null, - pdb: { - dbId: "7U0N", - method: "X-RAY DIFFRACTION", - keywords: "coronavirus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7U0N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u0n_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u0n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, W.", - "Shi, K. (0000-0003-4175-3714)", - "Geng, Q.", - "Ye, G.", - "Aihara, H. (0000-0001-7508-6230)", - "Li, F. (0000-0002-1958-366X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35343765", - title: - "Structural Basis for Human Receptor Recognition by SARS-CoV-2 Omicron Variant BA.1.", - journal: "J.Virol. 96: e0024922-e0024922 (2022), 1098-5514", - doi: "https://doi.org/10.1128/jvi.00249-22", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35343765", - pubDate: "2022", - abstract: "", - authors: [ - "Geng, Q.", - "Shi, K.", - "Ye, G.", - "Zhang, W.", - "Aihara, H.", - "Li, F. (0000-0002-1958-366X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7u0n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7u0n", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 RBD in complex with STE90-C11 Fab", - emdb: null, - pdb: { - dbId: "7B3O", - method: "X-RAY DIFFRACTION", - keywords: "neutralizing antibodies, SARS-CoV-2, RBD, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7B3O", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7b3o_final.pdb", - externalLink: "https://pdb-redo.eu/db/7b3o", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light Chain of Fab Fragment", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy Chain of Fab Fragment", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Kluenemann, T. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. 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(0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. 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(0000-0002-9228-6215)", - "Rabe von Pappenheim, F. (0000-0002-3925-8127)", - "Funk, L.-M. (0000-0003-2443-691X)", - "Tittmann, K. (0000-0001-7891-7108)", - "Chari, A. (0000-0001-6220-9828)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Redox regulation of the SARS-CoV-2 main protease provides new opportunities for drug design", - journal: "Biorxiv (2022)", - doi: "https://doi.org/10.1101/2022.04.18.487732", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Funk, L.M.", - "Poschmann, G.", - "Chari, A.", - "von Pappenheim, F.R.", - "Stegmann, K.M.", - "Dickmanns, A.", - "Eulig, N.", - "Wensien, M.", - "Paknia, E.", - "Heyne, G.", - "Penka, E.", - "Pearson, A.R.", - "Berndt, C.", - "Fritz, T.", - "Bazzi, S.", - "Uranga, J.", - "Mata, R.A.", - "Dobbelstein, M.", - "Hilgenfeld, R.", - "Curth, U.", - "Tittmann, K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zb8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zb8", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with POB0066", - emdb: null, - pdb: { - dbId: "5RMM", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RMM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rmm_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rmm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "UJHLINFGICYWPQ-NWDGAFQWSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. 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(0000-0003-4424-3162)", "Wang, H. (0000-0002-1916-7092)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35635946", - title: - "The structure-based design of peptidomimetic inhibitors against SARS-CoV-2 3C like protease as Potent anti-viral drug candidate.", - journal: "Eur.J.Med.Chem. 238: 114458-114458 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114458", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35635946", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, H.", - "Pei, R.", - "Li, X.", - "Deng, W.", - "Xing, S.", - "Zhang, Y.", - "Zhang, C.", - "He, S.", - "Sun, H.", - "Xiao, S.", - "Xiong, J.", - "Chen, X.", - "Wang, Y.", - "Guo, Y.", - "Zhang, B.", - "Shang, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dgf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dgf", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530724813", - emdb: null, - pdb: { - dbId: "7S3S", - method: "X-RAY DIFFRACTION", - keywords: - "enzyme-inhibitor complex, cysteine protease, homodimer, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S3S", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s3s_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s3s", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DTOSIQBPPRVQHS-UHFFFAOYSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35434531", - title: - "Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.", - journal: "Acs Pharmacol Transl Sci 5: 255-265 (2022), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00026", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35434531", - pubDate: "2022", - abstract: "", - authors: [ - "Glaser, J. (0000-0003-1852-3849)", - "Sedova, A.", - "Galanie, S. (0000-0001-5712-2568)", - "Kneller, D.W.", - "Davidson, R.B.", - "Maradzike, E.", - "Del Galdo, S.", - "Labbe, A.", - "Hsu, D.J.", - "Agarwal, R.", - "Bykov, D.", - "Tharrington, A.", - "Parks, J.M. (0000-0002-3103-9333)", - "Smith, D.M.A.", - "Daidone, I. (0000-0001-8970-8408)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A.", - "Smith, J.C. (0000-0002-2978-3227)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s3s_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s3s", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 main protease in complex with MI-23", - emdb: null, - pdb: { - dbId: "7D3I", - method: "X-RAY DIFFRACTION", - keywords: - "coronavirus, protease, inhibitor, complex, VIRAL PROTEIN., VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7D3I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7d3i_final.pdb", - externalLink: "https://pdb-redo.eu/db/7d3i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZUAZJPLYYVHKFN-NAFADOBPSA-N", "PQYJRMFWJJONBO-UHFFFAOYSA-N"], - dbauthors: [ - "Zeng, R.", - "Lei, J.", - "Wang, Y.F.", - "Qiao, J.X.", - "Li, Y.S.", - "Yang, S.Y.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33602867", - title: - "SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model.", - journal: "Science 371: 1374-1378 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf1611", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33602867", - pubDate: "2021", - abstract: "", - authors: [ - "Qiao, J.", - "Li, Y.S.", - "Zeng, R.", - "Liu, F.L.", - "Luo, R.H.", - "Huang, C.", - "Wang, Y.F.", - "Zhang, J.", - "Quan, B.", - "Shen, C.", - "Mao, X.", - "Liu, X.", - "Sun, W.", - "Yang, W.", - "Ni, X.", - "Wang, K.", - "Xu, L.", - "Duan, Z.L.", - "Zou, Q.C.", - "Zhang, H.L.", - "Qu, W.", - "Long, Y.H.", - "Li, M.H.", - "Yang, R.C.", - "You, J.", - "Zhou, Y.", - "Yao, R.", - "Li, W.P.", - "Liu, J.M.", - "Chen, P.", - "Liu, Y.", - "Lin, G.F.", - "Yang, X.", - "Zou, J.", - "Li, L.", - "Hu, Y.", - "Lu, G.W.", - "Li, W.M.", - "Wei, Y.Q.", - "Zheng, Y.T.", - "Lei, J.", - "Yang, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7d3i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7d3i", - }, - }, - { - title: - "Structure of sybody SR31 in complex with the SARS-CoV-2 S Receptor Binding domain (RBD)", - emdb: null, - pdb: { - dbId: "7D2Z", - method: "X-RAY DIFFRACTION", - keywords: - "coronavirus, Covid-19, nanobody, neutralizing antibody, receptor binding protein, SARS-CoV-2, S protein, synthetic antibody, VHH., PROTEIN BINDING", - refModels: [ - { - emdbId: null, - pdbId: "7D2Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7d2z_final.pdb", - externalLink: "https://pdb-redo.eu/db/7d2z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "32630", - name: "SR31 against SARS-CoV-2 RBD, non neutralizing", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - ], - dbauthors: ["Li, T.", "Li, D.", "Yao, H.", "Cai, H.", "Qin, W."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33657135", - title: - "A high-affinity RBD-targeting nanobody improves fusion partner's potency against SARS-CoV-2.", - journal: "Plos Pathog. 17: e1009328-e1009328 (2021), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1009328", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33657135", - pubDate: "2021", - abstract: "", - authors: [ - "Yao, H. (0000-0002-8588-5877)", - "Cai, H. (0000-0001-7221-8330)", - "Li, T. (0000-0003-3146-2761)", - "Zhou, B. (0000-0002-7753-4065)", - "Qin, W. (0000-0002-8157-6647)", - "Lavillette, D. (0000-0002-4706-1519)", - "Li, D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7d2z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7d2z", - }, - }, - { - title: "Structure of the 2019-nCoV HR2 Domain", - emdb: null, - pdb: { - dbId: "6LVN", - method: "X-RAY DIFFRACTION", - keywords: "2019-nCoV, HR2 domain, VIRUS, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6LVN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6lvn_final.pdb", - externalLink: "https://pdb-redo.eu/db/6lvn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhu, Y.", "Sun, F."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Crystal structure of HR2 domain of 2019-nCoV S2 subunit", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zhu, Y.", "Sun, F."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6lvn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6lvn", - }, - }, - { - title: - "Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1", - emdb: null, - pdb: { - dbId: "7JIB", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, Methyltransferase, m7GpppA, Cap-0, Cap-1, SAH, SAM, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7JIB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jib_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jib", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "QQOHNVHGNZYSBP-XPWFQUROSA-O", - "UFVBPMPLSKDIFV-NAGRZYTCSA-O", - "JOPOQPCBCUIPFX-UHFFFAOYSA-L", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Satchell, K.J.F.", - "Michalska, K.", - "Wilamowski, M.", - "Sherrell, D.A.", - "Lavens, A.", - "Chard, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33972410", - title: - "2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography.", - journal: "Proc.Natl.Acad.Sci.USA 118 (2021), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2100170118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33972410", - pubDate: "2021", - abstract: "", - authors: [ - "Wilamowski, M.", - "Sherrell, D.A. (0000-0002-6393-8800)", - "Minasov, G. (0000-0001-5460-3462)", - "Kim, Y. (0000-0002-1610-4889)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Lavens, A. (0000-0002-3856-9919)", - "Chard, R.", - "Maltseva, N. (0000-0002-2871-465X)", - "Jedrzejczak, R.", - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Saint, N.", - "Foster, I.T. (0000-0003-2129-5269)", - "Michalska, K. (0000-0001-7140-3649)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jib_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jib", - }, - }, - { - title: - "CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 23", - emdb: null, - pdb: { - dbId: "7M8P", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7M8P", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m8p_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m8p", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FBYZCSUBKCAJAK-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, C.H.", - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34161756", - title: - "Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.", - journal: "Structure 29 (2021), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2021.06.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34161756", - pubDate: "2021", - abstract: "", - authors: [ - "Deshmukh, M.G.", - "Ippolito, J.A.", - "Zhang, C.H.", - "Stone, E.A.", - "Reilly, R.A.", - "Miller, S.J.", - "Jorgensen, W.L.", - "Anderson, K.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m8p_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m8p", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Glutathione isopropyl ester", - emdb: null, - pdb: { - dbId: "7AX6", - method: "X-RAY DIFFRACTION", - keywords: "inhibitor, complex, screen, sars-cov-2, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AX6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ax6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ax6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MVNCPACIPXNJIW-DTWKUNHWSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "RAXXELZNTBOGNW-UHFFFAOYSA-O", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - 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(0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5ruk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5ruk", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 6 (P43 crystal form)", - emdb: null, - pdb: { - dbId: "7TWW", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, room temperature diffraction, protein dynamics, water networks, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TWW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tww_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tww", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-ZQSHOCFMSA-N", "KRKNYBCHXYNGOX-UHFFFAOYSA-N"], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 6 (P43 crystal form)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tww_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tww", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI5", - emdb: null, - pdb: { - dbId: "7JQ2", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, main protease, reversible covalent inhibitors, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JQ2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jq2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jq2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LMWONCCZCSKLCL-QORCZRPOSA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33283984", - title: - "A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*.", - journal: "Chemmedchem 16: 942-948 (2021), 1860-7187", - doi: "https://doi.org/10.1002/cmdc.202000924", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33283984", - pubDate: "2021", - abstract: "", - authors: [ - "Yang, K.S.", - "Ma, X.R.", - "Ma, Y.", - "Alugubelli, Y.R.", - "Scott, D.A.", - "Vatansever, E.C.", - "Drelich, A.K.", - "Sankaran, B.", - "Geng, Z.Z.", - "Blankenship, L.R.", - "Ward, H.E.", - "Sheng, Y.J.", - "Hsu, J.C.", - "Kratch, K.C.", - "Zhao, B.", - "Hayatshahi, H.S.", - "Liu, J.", - "Li, P.", - "Fierke, C.A.", - "Tseng, C.K.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jq2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jq2", - }, - }, - { - title: "PLpro-C111S with mISG15", - emdb: null, - pdb: { - dbId: "6YVA", - method: "X-RAY DIFFRACTION", - keywords: - "Deubiquitinase, papain-like-protease, SARS-CoV-2, ISG15, complex, CELL INVASION", - refModels: [ - { - emdbId: null, - pdbId: "6YVA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6yva_final.pdb", - externalLink: "https://pdb-redo.eu/db/6yva", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Replicase polyprotein 1a", - details: "", - altNames: "pp1a,ORF1a polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05161", - organism: "9606", - name: "Ubiquitin-like protein ISG15", - details: "Three N-terminal residues (SNA) are expression tag", - altNames: - "Interferon-induced 15 kDa protein,Interferon-induced 17 kDa protein,IP17,Ubiquitin cross-reactive protein,hUCRP", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: ["Shin, D. (0000-0002-8272-6133)", "Dikic, I. (0000-0001-8156-9511)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32726803", - title: - "Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.", - journal: "Nature 587: 657-662 (2020), 1476-4687", - doi: "https://doi.org/10.1038/s41586-020-2601-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32726803", - pubDate: "2020", - abstract: "", - authors: [ - "Shin, D.", - "Mukherjee, R.", - "Grewe, D.", - "Bojkova, D.", - "Baek, K.", - "Bhattacharya, A.", - "Schulz, L.", - "Widera, M.", - "Mehdipour, A.R.", - "Tascher, G.", - "Geurink, P.P.", - "Wilhelm, A.", - "van der Heden van Noort, G.J.", - "Ovaa, H.", - "Muller, S.", - "Knobeloch, K.P.", - "Rajalingam, K.", - "Schulman, B.A.", - "Cinatl, J.", - "Hummer, G.", - "Ciesek, S.", - "Dikic, I.", - "Shin, D. (0000-0002-8272-6133)", - "Dikic, I. 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(0000-0002-8109-7515)", - "Wang, Y.", - "Li, X. (0000-0003-0896-8713)", - "Yuan, S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "A SARS-CoV-2 neutralizing\nantibody", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Zhang, G.", - "Li, X. (0000-0003-0896-8713)", - "Guo, Y. 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(0000-0001-5904-1905)", - "Gully, B.S. (0000-0002-8197-0871)", - "Rossjohn, J. (0000-0002-2020-7522)", - "Riboldi-Tunnicliffe, A. (0000-0003-2244-2486)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32592996", - title: - "Crystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9.", - journal: "Iscience 23: 101258-101258 (2020), 2589-0042", - doi: "https://doi.org/10.1016/j.isci.2020.101258", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32592996", - pubDate: "2020", - abstract: "", - authors: [ - "Littler, D.R.", - "Gully, B.S.", - "Colson, R.N.", - "Rossjohn, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wxd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wxd", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI6", - emdb: null, - pdb: { - dbId: "7JQ3", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, main protease, reversible covalent inhibitors, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7JQ3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jq3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jq3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AWESOLQTDOBPDY-FFYZIMEISA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33283984", - title: - "A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*.", - journal: "Chemmedchem 16: 942-948 (2021), 1860-7187", - doi: "https://doi.org/10.1002/cmdc.202000924", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33283984", - pubDate: "2021", - abstract: "", - authors: [ - "Yang, K.S.", - "Ma, X.R.", - "Ma, Y.", - "Alugubelli, Y.R.", - "Scott, D.A.", - "Vatansever, E.C.", - "Drelich, A.K.", - "Sankaran, B.", - "Geng, Z.Z.", - "Blankenship, L.R.", - "Ward, H.E.", - "Sheng, Y.J.", - "Hsu, J.C.", - "Kratch, K.C.", - "Zhao, B.", - "Hayatshahi, H.S.", - "Liu, J.", - "Li, P.", - "Fierke, C.A.", - "Tseng, C.K.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jq3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jq3", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 5 (P43 crystal form)", - emdb: null, - pdb: { - dbId: "7TWV", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, room temperature diffraction, protein dynamics, water networks, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7TWV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7twv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7twv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-ZQSHOCFMSA-N", "KRKNYBCHXYNGOX-UHFFFAOYSA-N"], - dbauthors: [ - "Correy, G.J. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rty_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rty", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv", - emdb: null, - pdb: { - dbId: "7DEO", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, RBD, antibody, VIRAL PROTEIN, ANTIVIRAL PROTEIN, VIRAL PROTEIN-ANTIVIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7DEO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7deo_final.pdb", - externalLink: "https://pdb-redo.eu/db/7deo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "antibody scFv", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BHPQYMZQTOCNFJ-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Zhang, G.", - "Rao, Z.", - "Guo, Y. (0000-0002-8109-7515)", - "Li, X. (0000-0003-0896-8713)", - "Fu, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33961621", - title: - "Structural basis for SARS-CoV-2 neutralizing antibodies with novel binding epitopes.", - journal: "Plos Biol. 19: e3001209-e3001209 (2021), 1545-7885", - doi: "https://doi.org/10.1371/journal.pbio.3001209", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33961621", - pubDate: "2021", - abstract: "", - authors: [ - "Fu, D.", - "Zhang, G.", - "Wang, Y.", - "Zhang, Z.", - "Hu, H.", - "Shen, S.", - "Wu, J. (0000-0002-4457-5485)", - "Li, B.", - "Li, X.", - "Fang, Y.", - "Liu, J.", - "Wang, Q.", - "Zhou, Y. (0000-0002-0937-3570)", - "Wang, W.", - "Li, Y.", - "Lu, Z.", - "Wang, X.", - "Nie, C.", - "Tian, Y.", - "Chen, D.", - "Zhou, X.", - "Yu, F.", - "Zhang, C.", - "Deng, C.", - "Zhou, L.", - "Guan, G.", - "Shao, N.", - "Lou, Z.", - "Deng, F.", - "Zhang, H.", - "Chen, X.", - "Wang, M.", - "Liu, L.", - "Rao, Z.", - "Guo, Y. (0000-0002-8109-7515)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7deo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7deo", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to 2-Methyl-1-tetralone.", - emdb: null, - pdb: { - dbId: "6YNQ", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-19, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6YNQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6ynq_final.pdb", - externalLink: "https://pdb-redo.eu/db/6ynq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "GANIBVZSZGNMNB-QMMMGPOBSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Lieske, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - { - pmID: "", - title: - "Inhibition of SARS-CoV-2 main protease by allosteric drug-binding", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.11.12.378422", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. (0000-0002-7329-6653)", - "Reinke, P.Y.A., (0000-0002-7354-0839)", - "Fernandez-Garcia, Y., (0000-0002-9592-2141)", - "Lieske, J.,", - "Lane, T.J.,", - "Ginn, H.M.,", - "Koua, F.H.M.,", - "Ehrt, C.,", - "Ewert, W.,", - "Oberthuer, D.,", - "Yefanov, O.,", - "Meier, S.,", - "Lorenzen, K.,", - "Krichel, B.,", - "Kopicki, J.D., (0000-0001-9806-5352)", - "Gelisio, L.,", - "Brehm, W.,", - "Dunkel , I.,", - "Seychell , B.,", - "Gieseler , H.,", - "Norton-Baker , B.,", - "Escudero-Perez, B.,", - "Domaracky , M.,", - "Saouane, S.,", - "Tolstikova , A.,", - "White, T.A.,", - "Hanle, A.,", - "Groessler , M.,", - "Fleckenstein , H.,", - "Trost , F.,", - "Galchenkova , M.,", - "Gevorkov , Y.,", - "Li , C.,", - "Awel , S.,", - "Barthelmess , M.,", - "Schluenzen , F.,", - "Paulraj , L.X.,", - "Werner , N.,", - "Andaleeb , H.,", - "Ullah , N.,", - "Falke , S.,", - "Srinivasan, V.,", - "Franca , B.,", - "Schwinzer , M.,", - "Brognaro , H.,", - "Rogers , C.,", - "Melo , D.,", - "Doyle , J.J.,", - "Knoska , J.,", - "Pena Murillo, G.E.,", - "Rahmani Mashhour, A.,", - "Guicking , F.,", - "Hennicke , V.,", - "Fischer , P.,", - "Hakanpaeae , J.,", - "Meyer , J.,", - "Gribbon , P.,", - "Ellinger , B.,", - "Kuzikov , M.,", - "Wolf , M.,", - "Burenkov, G.,", - "von Stetten, D.,", - "Pompidor, G.,", - "Bento, I.,", - "Panneerselvam, S.,", - "Karpics, I.,", - "Schneider , T.R.,", - "Garcia Alai, M.,", - "Niebling, S.,", - "Guenther , C.,", - "Schmidt , C.,", - "Schubert , R.,", - "Han , H.,", - "Boger, J.,", - "Monteiro , D.,", - "Zhang, L.,", - "Sun, X.,", - "Pletzer-Zelgert , J.,", - "Wollenhaupt , J.,", - "Feiler , C.,", - "Weiss , M.,", - "Schulz , E.C.,", - "Mehrabi , P.,", - "Karnicar , K.,", - "Usenik, A.,", - "Loboda , J.,", - "Tidow , H.,", - "Chari , A.,", - "Hilgenfeld , R., (0000-0001-8850-2977)", - "Uetrecht , C., (0000-0002-1991-7922)", - "Cox , R.,", - "Zaliani , A.,", - "Beck , T.,", - "Rarey , M.,", - "Guenther , S.,", - "Turk , D., (0000-0003-0205-6609)", - "Hinrichs , W., (0000-0002-0435-4565)", - "Chapman , H.N.,", - "Pearson , A.,", - "Betzel , C.,", - "Meents , A. (0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6ynq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6ynq", - }, - }, - { - title: - "Structure of COVID-19 main protease bound to potent broad-spectrum non-covalent inhibitor X77", - emdb: null, - pdb: { - dbId: "6W63", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS, SARS-CoV-2, SARS-CoV, main protease, 3C-like protease, 3CL protease, 3Clpro, Mpro, broad-spectrum, inhibitor, proteinase, non-covalent, reversible, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, ANTIVIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "6W63", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6w63_final.pdb", - externalLink: "https://pdb-redo.eu/db/6w63", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MUNFBYOTGGMQOS-XMMPIXPASA-N"], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Mesecar, A.D. (0000-0002-1241-2577)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Mesecar, A.D. (0000-0002-1241-2577)"], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w63_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w63", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 complexed with GC376", - emdb: null, - pdb: { - dbId: "7C6U", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7C6U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c6u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c6u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: ["Qi, J.", "Feng, Y.", "Fu, L.", "Gao, F.G."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32887884", - title: - "Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease.", - journal: "Nat Commun 11: 4417-4417 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18233-x", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32887884", - pubDate: "2020", - abstract: "", - authors: [ - "Fu, L. (0000-0003-0431-5424)", - "Ye, F.", - "Feng, Y.", - "Yu, F.", - "Wang, Q.", - "Wu, Y.", - "Zhao, C.", - "Sun, H.", - "Huang, B.", - "Niu, P.", - "Song, H. (0000-0002-2811-0370)", - "Shi, Y. (0000-0002-3053-2687)", - "Li, X. (0000-0001-8903-9793)", - "Tan, W. (0000-0002-5963-1136)", - "Qi, J.", - "Gao, G.F. (0000-0002-3869-615X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7c6u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7c6u", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder495 inhibitor", - emdb: null, - pdb: { - dbId: "7JIT", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7JIT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jit_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jit", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SIBDGNTYRQIIGV-CQSZACIVSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33531496", - title: - "Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.", - journal: "Nat Commun 12: 743-743 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-21060-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33531496", - pubDate: "2021", - abstract: "", - authors: [ - "Osipiuk, J.", - "Azizi, S.A. (0000-0002-9226-9917)", - "Dvorkin, S.", - "Endres, M.", - "Jedrzejczak, R.", - "Jones, K.A. (0000-0003-0711-5516)", - "Kang, S.", - "Kathayat, R.S. (0000-0002-9159-2413)", - "Kim, Y.", - "Lisnyak, V.G. (0000-0002-4406-8440)", - "Maki, S.L. (0000-0001-6917-3602)", - "Nicolaescu, V.", - "Taylor, C.A.", - "Tesar, C.", - "Zhang, Y.A.", - "Zhou, Z. (0000-0002-2792-8429)", - "Randall, G.", - "Michalska, K.", - "Snyder, S.A. (0000-0003-3594-8769)", - "Dickinson, B.C. (0000-0002-9616-1911)", - "Joachimiak, A. (0000-0003-2535-6209)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jit_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jit", - }, - }, - { - title: - "The co-crystal structure of SARS-CoV-2 main protease with (S)-2-cinnamamido-N-((S)-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)hexanamide", - emdb: null, - pdb: { - dbId: "7DGG", - method: "X-RAY DIFFRACTION", - keywords: "Complex, inhibitor, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7DGG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dgg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dgg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GJOOPPJNXSQMMK-BMBPZZTMSA-N"], - dbauthors: ["Shang, L.Q. (0000-0003-4424-3162)", "Wang, H. (0000-0002-1916-7092)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35635946", - title: - "The structure-based design of peptidomimetic inhibitors against SARS-CoV-2 3C like protease as Potent anti-viral drug candidate.", - journal: "Eur.J.Med.Chem. 238: 114458-114458 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114458", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35635946", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, H.", - "Pei, R.", - "Li, X.", - "Deng, W.", - "Xing, S.", - "Zhang, Y.", - "Zhang, C.", - "He, S.", - "Sun, H.", - "Xiao, S.", - "Xiong, J.", - "Chen, X.", - "Wang, Y.", - "Guo, Y.", - "Zhang, B.", - "Shang, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dgg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dgg", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z85956652", - emdb: null, - pdb: { - dbId: "5RML", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RML", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rml_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rml", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "FPQHYOUXKZRHSA-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rml_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rml", - }, - }, - { - title: - "Crystal Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody CT-P59", - emdb: null, - pdb: { - dbId: "7CM4", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-Cov-2, spike, receptor binding domain, RBD, IgG, Fab, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CM4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cm4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cm4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "IgG heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "IgG light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEQPNABPJHWNSG-UHFFFAOYSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.G. (0000-0001-5732-8849)", - "Jeong, J.H. (0000-0003-4286-9911)", - "Bae, J.S. (0000-0001-7484-9048)", - "Lee, J. (0000-0002-8803-7689)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33436577", - title: - "A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein.", - journal: "Nat Commun 12: 288-288 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-20602-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33436577", - pubDate: "2021", - abstract: "", - authors: [ - "Kim, C.", - "Ryu, D.K. (0000-0003-4237-4740)", - "Lee, J. (0000-0002-8803-7689)", - "Kim, Y.I.", - "Seo, J.M.", - "Kim, Y.G.", - "Jeong, J.H.", - "Kim, M.", - "Kim, J.I.", - "Kim, P.", - "Bae, J.S. (0000-0001-7484-9048)", - "Shim, E.Y.", - "Lee, M.S. (0000-0002-2155-3232)", - "Kim, M.S.", - "Noh, H.", - "Park, G.S.", - "Park, J.S.", - "Son, D.", - "An, Y.", - "Lee, J.N.", - "Kwon, K.S.", - "Lee, J.Y.", - "Lee, H.", - "Yang, J.S.", - "Kim, K.C.", - "Kim, S.S.", - "Woo, H.M.", - "Kim, J.W.", - "Park, M.S.", - "Yu, K.M.", - "Kim, S.M.", - "Kim, E.H.", - "Park, S.J.", - "Jeong, S.T.", - "Yu, C.H.", - "Song, Y.", - "Gu, S.H.", - "Oh, H.", - "Koo, B.S.", - "Hong, J.J.", - "Ryu, C.M.", - "Park, W.B.", - "Oh, M.D.", - "Choi, Y.K. (0000-0002-0872-0147)", - "Lee, S.Y. (0000-0002-3306-9333)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cm4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cm4", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2856434778", - emdb: null, - pdb: { - dbId: "5RLH", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RLH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rlh_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rlh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "JMYSPFGUBNENSE-UHFFFAOYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rlh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rlh", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab", - emdb: null, - pdb: { - dbId: "7DK2", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Spike, RBD, Antibody, ADE, VIRUS, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7DK2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dk2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dk2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "MW07 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "MW07 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Wang, J.", - "Zhang, J.", - "Chen, S.", - "Wang, M.", - "Zhang, M.", - "Wang, R.", - "Jiao, S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Architectural versatility of spike neutralization by a SARS-CoV-2 antibody", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Sun, Y.", - "Liu, F.J.", - "Guo, H.T.", - "Wang, J.", - "Wang, R.", - "Zhang, M.", - "Wang, M.", - "Chen, S.", - "Jiao, S.", - ], - }, - { - pmID: "", - title: - "Antibody-dependent enhancement (ADE) of SARS-CoV-2 infection requires FcgammaRIIB-mediated uptake of virus-antibody complex with bivalent interaction", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Sun, Y.", - "Liu, F.J.", - "Guo, H.T.", - "Wang, J.", - "Wang, R.", - "Zhang, M.", - "Wang, M.", - "Chen, S.", - "Jiao, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dk2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dk2", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z1367324110", - emdb: null, - pdb: { - dbId: "5R81", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5R81", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5r81_final.pdb", - externalLink: "https://pdb-redo.eu/db/5r81", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OUJFDUTZTPBMDN-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Powell, A.J.", - "Wild, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5r81_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5r81", - }, - }, - { - title: - "Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7T9W", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-COV-2, COVID-19, NON-STRUCTURAL PROTEIN 3, NSP3, BSM domain, Betacoronavirus-Specific Marker, G2M, group 2 marker, UNKNOWN FUNCTION, STRUCTURAL GENOMICS, CSGID, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, NIAID, NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7T9W", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t9w_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t9w", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Satchell, K.J.F.", - "Stogios, P.J.", - "Skarina, T.", - "Di Leo, R.", - "Savchenko, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Stogios, P.J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t9w_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t9w", - }, - }, - { - title: - "SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp4/5 (P6-P1)", - emdb: null, - pdb: { - dbId: "7MB4", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MB4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mb4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mb4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "THR-SER-ALA-VAL-LEU-GLN", - details: "Cleavage Site Nsp4/5 (P6-P1)", - altNames: "nsp4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35729165", - title: - "Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.", - journal: "Nat Commun 13: 3556-3556 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-31210-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35729165", - pubDate: "2022", - abstract: "", - authors: [ - "Shaqra, A.M.", - "Zvornicanin, S.N.", - "Huang, Q.Y.J. (0000-0001-5107-2336)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Knapp, M.", - "Tandeske, L.", - "Bakan, D.T.", - "Flynn, J. (0000-0002-5490-393X)", - "Bolon, D.N.A.", - "Moquin, S.", - "Dovala, D.", - "Kurt Yilmaz, N. (0000-0002-5036-676X)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mb4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mb4", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 Fab", - emdb: null, - pdb: { - dbId: "7BEI", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, antibody, germline, V-gene, receptor-binding-domain, spike, neutralisation, protection, glycosylation, valency, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7BEI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bei_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bei", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-150 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-150 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NHNBFGGVMKEFGY-UHFFFAOYSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: ["Zhao, Y.", "Zhou, D.", "Ren, J.", "Stuart, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33756110", - title: - "The antigenic anatomy of SARS-CoV-2 receptor binding domain.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.02.032", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33756110", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Ginn, H.M.", - "Duyvesteyn, H.M.E.", - "Supasa, P.", - "Case, J.B.", - "Zhao, Y.", - "Walter, T.S.", - "Mentzer, A.J.", - "Liu, C.", - "Wang, B.", - "Paesen, G.C.", - "Slon-Campos, J.", - "Lopez-Camacho, C.", - "Kafai, N.M.", - "Bailey, A.L.", - "Chen, R.E.", - "Ying, B.", - "Thompson, C.", - "Bolton, J.", - "Fyfe, A.", - "Gupta, S.", - "Tan, T.K.", - "Gilbert-Jaramillo, J.", - "James, W.", - "Knight, M.", - "Carroll, M.W.", - "Skelly, D.", - "Dold, C.", - "Peng, Y.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Klenerman, P.", - "Temperton, N.", - "Hall, D.R.", - "Williams, M.A.", - "Paterson, N.G.", - "Bertram, F.K.R.", - "Siebert, C.A.", - "Clare, D.K.", - "Howe, A.", - "Radecke, J.", - "Song, Y.", - "Townsend, A.R.", - "Huang, K.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Diamond, M.S.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bei_deposited_chain_front_image-200x200.png", - 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"Structural Genomics Consortium", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33850605", - title: - "Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain.", - journal: "Acs Med.Chem.Lett. 12: 603-609 (2021), 1948-5875", - doi: "https://doi.org/10.1021/acsmedchemlett.0c00684", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33850605", - pubDate: "2021", - abstract: "", - authors: [ - "Ni, X.", - "Schroder, M.", - "Olieric, V.", - "Sharpe, M.E.", - "Hernandez-Olmos, V.", - "Proschak, E.", - "Merk, D.", - "Knapp, S.", - "Chaikuad, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bf3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bf3", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z369936976", - emdb: null, - pdb: { - dbId: "5S2D", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S2D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s2d_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s2d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QKUCRJSBLDVNFL-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0002-1135-2744)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35142215", - title: - "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", - journal: "J.Am.Chem.Soc. 144: 2905-2920 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08402", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35142215", - pubDate: "2022", - abstract: "", - authors: [ - "Luttens, A. (0000-0003-2915-7901)", - "Gullberg, H.", - "Abdurakhmanov, E.", - "Vo, D.D.", - "Akaberi, D. (0000-0002-9595-9796)", - "Talibov, V.O.", - "Nekhotiaeva, N.", - "Vangeel, L.", - "De Jonghe, S. (0000-0002-3872-6558)", - "Jochmans, D.", - "Krambrich, J.", - "Tas, A.", - "Lundgren, B.", - "Gravenfors, Y. (0000-0001-6025-4908)", - "Craig, A.J.", - "Atilaw, Y.", - "Sandstrom, A.", - "Moodie, L.W.K. (0000-0002-9500-4535)", - "Lundkvist, A.", - "van Hemert, M.J.", - "Neyts, J.", - "Lennerstrand, J.", - "Kihlberg, J. (0000-0002-4205-6040)", - "Sandberg, K.", - "Danielson, U.H. (0000-0003-2728-0340)", - "Carlsson, J. 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sqb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sqb", - }, - }, - { - title: - "Crystal Structure of Human Fab S24-202 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2", - emdb: null, - pdb: { - dbId: "7N3C", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Coronavirus 2, Nucleocapsid protein, Human antibody Fab, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7N3C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n3c_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n3c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "S24-202 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "S24-202 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "PGLTVOMIXTUURA-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of Human Fab S24-202 in the complex with the N-terminal Domain of Nucleocapsid protein from SARS CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kim, Y.", - "Maltseva, N.", - "Tesar, C.", - "Jedrzejczak, R.", - "Dugan, H.", - "Stamper, C.", - "Wilson, P.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n3c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n3c", - }, - }, - { - title: "Crystal structure of post fusion core of 2019-nCoV S2 subunit", - emdb: null, - pdb: { - dbId: "6M1V", - method: "X-RAY DIFFRACTION", - keywords: "2019-nCoV, spike protein, fusion core, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6M1V", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6m1v_final.pdb", - externalLink: "https://pdb-redo.eu/db/6m1v", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2,Spike protein S2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Sun, H.", - "Song, H. (0000-0002-2811-0370)", - "Wang, Q. (0000-0003-0032-4956)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32482145", - title: - "Structural basis of HCoV-19 fusion core and an effective inhibition peptide against virus entry.", - journal: "Emerg Microbes Infect 9: 1238-1241 (2020), 2222-1751", - doi: "https://doi.org/10.1080/22221751.2020.1770631", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32482145", - pubDate: "2020", - abstract: "", - authors: [ - "Sun, H.", - "Li, Y.", - "Liu, P.", - "Qiao, C.", - "Wang, X.", - "Wu, L.", - "Liu, K.", - "Hu, Y.", - "Su, C.", - "Tan, S. (0000-0002-2599-4959)", - "Zou, S.", - "Wu, G.", - "Yan, J. (0000-0003-0502-3829)", - "Gao, G.F. (0000-0002-3869-615X)", - "Qi, J. (0000-0002-9358-4732)", - "Wang, Q. (0000-0003-3768-0401)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6m1v_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6m1v", - }, - }, - { - title: "The crystal structure of COVID-19 main protease in apo form", - emdb: null, - pdb: { - dbId: "6M03", - method: "X-RAY DIFFRACTION", - keywords: "Coronavirus, COVID-19, viral protease, BIOSYNTHETIC PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6M03", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6m03_final.pdb", - externalLink: "https://pdb-redo.eu/db/6m03", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Liu, X.", "Yang, H.", "Rao, Z.", "Zhang, B.", "Zhao, Y.", "Jin, Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35380892", - title: - "Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2117142119-e2117142119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2117142119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35380892", - pubDate: "2022", - abstract: "", - authors: [ - "Zhao, Y. (0000-0002-2932-2164)", - "Zhu, Y. (0000-0002-7045-4847)", - "Liu, X. (0000-0001-5498-6942)", - "Jin, Z. (0000-0001-6448-820X)", - "Duan, Y.", - "Zhang, Q. (0000-0002-6271-9163)", - "Wu, C. (0000-0001-9178-7467)", - "Feng, L. (0000-0003-1060-6391)", - "Du, X.", - "Zhao, J. (0000-0002-5119-359X)", - "Shao, M. (0000-0002-9762-8608)", - "Zhang, B. (0000-0001-8556-8049)", - "Yang, X. (0000-0003-3443-9815)", - "Wu, L. (0000-0002-2253-0497)", - "Ji, X. (0000-0002-0801-8825)", - "Guddat, L.W. (0000-0002-8204-8408)", - "Yang, K.", - "Rao, Z. (0000-0001-9866-2384)", - "Yang, H. (0000-0002-1875-3268)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6m03_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6m03", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z4718398569", - emdb: null, - pdb: { - dbId: "5SPF", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SPF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5spf_final.pdb", - externalLink: "https://pdb-redo.eu/db/5spf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["INTFUQJSFGYBOV-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. 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(0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sps_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sps", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV503 and COVA1-16", - emdb: null, - pdb: { - dbId: "7LQ7", - method: "X-RAY DIFFRACTION", - keywords: - "antibody, coronavirus, Fab, spike, COVID-19, RBD, receptor binding domain, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7LQ7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lq7_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lq7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV503 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV503 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA1-16 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA1-16 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Wilson, I.A. (0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. (0000-0001-9754-4503)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "pentadecameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34519517", - title: - "Bispecific antibodies targeting distinct regions of the spike protein potently neutralize SARS-CoV-2 variants of concern.", - journal: "Sci Transl Med 13: eabj5413-eabj5413 (2021), 1946-6242", - doi: "https://doi.org/10.1126/scitranslmed.abj5413", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34519517", - pubDate: "2021", - abstract: "", - authors: [ - "Cho, H. (0000-0001-7512-1980)", - "Gonzales-Wartz, K.K. (0000-0001-9131-255X)", - "Huang, D.", - "Yuan, M. (0000-0001-9754-4503)", - "Peterson, M. (0000-0001-6848-8709)", - "Liang, J.", - "Beutler, N. (0000-0003-3240-9524)", - "Torres, J.L. (0000-0003-0137-8497)", - "Cong, Y.", - "Postnikova, E.", - "Bangaru, S. (0000-0001-7994-4693)", - "Talana, C.A. (0000-0002-0313-8502)", - "Shi, W. (0000-0002-4770-6444)", - "Yang, E.S. (0000-0003-3161-1624)", - "Zhang, Y. (0000-0002-8228-2560)", - "Leung, K. (0000-0002-8582-7597)", - "Wang, L. (0000-0002-8404-4910)", - "Peng, L. (0000-0002-3600-2134)", - "Skinner, J. (0000-0001-5697-0442)", - "Li, S. (0000-0003-0998-2082)", - "Wu, N.C. (0000-0002-9078-6697)", - "Liu, H. (0000-0002-2412-7853)", - "Dacon, C. (0000-0003-2347-2740)", - "Moyer, T. (0000-0002-2110-2845)", - "Cohen, M. (0000-0002-4839-9386)", - "Zhao, M. (0000-0002-5700-2950)", - "Lee, F.E. (0000-0002-6133-5942)", - "Weinberg, R.S. (0000-0002-4503-1295)", - "Douagi, I.", - "Gross, R.", - "Schmaljohn, C. (0000-0001-8852-5482)", - "Pegu, A. (0000-0003-3564-6453)", - "Mascola, J.R. (0000-0002-5293-4695)", - "Holbrook, M. (0000-0002-0824-2667)", - "Nemazee, D. (0000-0002-4769-6311)", - "Rogers, T.F. (0000-0001-9756-327X)", - "Ward, A.B. (0000-0001-7153-3769)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Crompton, P.D. (0000-0001-5629-0412)", - "Tan, J. (0000-0002-6661-6372)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lq7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lq7", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 antibody P2C-1F11 with mutated RBD", - emdb: null, - pdb: { - dbId: "7E8M", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 spike, receptor binding domain, antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7E8M", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e8m_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e8m", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "antibody P2C-1F11 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "antibody P2C-1F11 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Ge, J.W.", "Zhang, L.Q.", "Wang, X.Q.", "Lan, J.", "Wang, R.K."], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34166623", - title: - "Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species.", - journal: "Immunity 54: 1611-1621.e5 (2021), 1074-7613", - doi: "https://doi.org/10.1016/j.immuni.2021.06.003", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34166623", - pubDate: "2021", - abstract: "", - authors: [ - "Wang, R.", - "Zhang, Q.", - "Ge, J.", - "Ren, W.", - "Zhang, R.", - "Lan, J.", - "Ju, B.", - "Su, B.", - "Yu, F.", - "Chen, P.", - "Liao, H.", - "Feng, Y.", - "Li, X.", - "Shi, X.", - "Zhang, Z.", - "Zhang, F.", - "Ding, Q.", - "Zhang, T.", - "Wang, X.", - "Zhang, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e8m_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e8m", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z466628048", - emdb: null, - pdb: { - dbId: "5SKY", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SKY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sky_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sky", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "URRZFISTFWQMHO-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sky_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sky", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun9-62-2R", - emdb: null, - pdb: { - dbId: "7RN1", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, inhibitor, main protease, 3cl, SARS, SARS-CoV-2, COVID, COVID-19, VIRAL PROTEIN, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RN1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rn1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rn1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "XQECDPKLDAEYEC-RBTNQOKQSA-N", - ], - dbauthors: ["Chen, Y.", "Sacco, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34860011", - title: - "Discovery of Di- and Trihaloacetamides as Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity.", - journal: "J.Am.Chem.Soc. 143: 20697-20709 (2021), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08060", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34860011", - pubDate: "2021", - abstract: "", - authors: [ - "Ma, C.", - "Xia, Z.", - "Sacco, M.D.", - "Hu, Y.", - "Townsend, J.A.", - "Meng, X.", - "Choza, J.", - "Tan, H.", - "Jang, J.", - "Gongora, M.V.", - "Zhang, X.", - "Zhang, F.", - "Xiang, Y.", - "Marty, M.T. (0000-0001-8115-1772)", - "Chen, Y.", - "Wang, J. (0000-0002-4845-4621)", - "Kitamura, N.", - "Ba, M.", - "Szeto, T.", - "Kukuljac, A.", - "Marty, M.T.", - "Schultz, D.", - "Cherry, S.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rn1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rn1", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z2856434941", - emdb: null, - pdb: { - dbId: "5S34", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S34", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s34_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s34", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VIYPNISBCRFBOV-QMMMGPOBSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-0858-1877)", - "Borisevich, V.", - "Abiona, O. (0000-0002-2745-1691)", - "Belli, H.M. (0000-0002-0816-6844)", - "de Vries, M. (0000-0003-1059-8344)", - "Mohamed, A. (0000-0003-0080-2727)", - "Dittmann, M. (0000-0002-1741-7916)", - "Samanovic, M.I. (0000-0002-6987-2232)", - "Mulligan, M.J.", - "Goldsmith, J.A.", - "Hsieh, C.L. (0000-0002-3665-5717)", - "Johnson, N.V. (0000-0003-4351-125X)", - "Wrapp, D. (0000-0002-0538-9647)", - "McLellan, J.S. (0000-0003-3991-542X)", - "Barnhart, B.C. (0000-0002-5640-1677)", - "Graham, B.S. (0000-0001-8112-0853)", - "Mascola, J.R. (0000-0002-5293-4695)", - "Hansen, C.L.", - "Falconer, E. (0000-0003-1486-5251)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kmi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kmi", - }, - }, - { - title: - "Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-360", - emdb: null, - pdb: { - dbId: "7NP1", - method: "X-RAY DIFFRACTION", - keywords: "Antibody Immune System, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NP1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7np1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7np1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Immunoglobulin gamma-1 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Immunoblobulin light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Hall, G.", "Cowan, R.", "Carr, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34211469", - title: - "Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses.", - journal: "Front Immunol 12: 678570-678570 (2021), 1664-3224", - doi: "https://doi.org/10.3389/fimmu.2021.678570", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34211469", - pubDate: "2021", - abstract: "", - authors: [ - "Bullen, G.", - "Galson, J.D.", - "Hall, G.", - "Villar, P.", - "Moreels, L.", - "Ledsgaard, L.", - "Mattiuzzo, G.", - "Bentley, E.M.", - "Masters, E.W.", - "Tang, D.", - "Millett, S.", - "Tongue, D.", - "Brown, R.", - "Diamantopoulos, I.", - "Parthiban, K.", - "Tebbutt, C.", - "Leah, R.", - "Chaitanya, K.", - "Ergueta-Carballo, S.", - "Pazeraitis, D.", - "Surade, S.B.", - "Ashiru, O.", - "Crippa, L.", - "Cowan, R.", - "Bowler, M.W.", - "Campbell, J.I.", - "Lee, W.J.", - "Carr, M.D.", - "Matthews, D.", - "Pfeffer, P.", - "Hufton, S.E.", - "Sawmynaden, K.", - "Osbourn, J.", - "McCafferty, J.", - "Karatt-Vellatt, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7np1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7np1", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution", - emdb: null, - pdb: { - dbId: "6ZSL", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 Helicase NSP13, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6ZSL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6zsl_final.pdb", - externalLink: "https://pdb-redo.eu/db/6zsl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "SARS-CoV-2 helicase NSP13", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,SARS-CoV-2 helicase NSP13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "NBIIXXVUZAFLBC-UHFFFAOYSA-K"], - dbauthors: [ - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zsl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zsl", - }, - }, - { - title: - "THE 1.28A CRYSTAL STRUCTURE OF 3CL MAINPRO OF SARS-COV-2 WITH OXIDIZED C145 (sulfinic acid cysteine)", - emdb: null, - pdb: { - dbId: "6XKH", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, 3CL main protease, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6XKH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xkh_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xkh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - ], - dbauthors: [ - "Joachimiak, A. (0000-0003-2535-6209)", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Coates, L.", - "Kovalevsky, A.", - "Tan, K. (0000-0002-4003-7903)", - "Maltseva, N.I.", - "Welk, L.F.", - "Jedrzejczak, R.P.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "THE 1.28A CRYSTAL STRUCTURE OF 3CL MAINPRO OF SARS-COV-2 WITH OXIDIZED C145 (sulfinic acid cysteine)", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Tan, K. (0000-0002-4003-7903)", - "Maltseva, N.I.", - "Welk, L.F.", - "Jedrzejczak, R.P.", - "Coates, L.", - "Kovalevsky, A.", - "Joachimiak, A. (0000-0003-2535-6209)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xkh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xkh", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADI-55688", - emdb: null, - pdb: { - dbId: "7U2E", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Coronavirus, Antibody, Spike, RBD, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7U2E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u2e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u2e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "ADI-55688 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "ADI-55688 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Wilson, I.A. (0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. (0000-0001-9754-4503)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35313576", - title: - "A broad and potent neutralization epitope in SARS-related coronaviruses.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.03.13.484037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35313576", - pubDate: "2022", - abstract: "", - authors: [ - "Yuan, M.", - "Zhu, X. (0000-0002-6021-3740)", - "He, W.T.", - "Zhou, P.", - "Kaku, C.I.", - "Capozzola, T. (0000-0002-7269-588X)", - "Zhu, C.Y.", - "Yu, X.", - "Liu, H.", - "Yu, W.", - "Hua, Y.", - "Tien, H.", - "Peng, L.", - "Song, G.", - "Cottrell, C.A. (0000-0002-3364-3083)", - "Schief, W.R. (0000-0002-1120-0150)", - "Nemazee, D. (0000-0002-4769-6311)", - "Walker, L.M.", - "Andrabi, R. (0000-0001-8837-7520)", - "Burton, D.R. (0000-0001-6711-9864)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Yuan, M. (0000-0001-9754-4503)", - "Zhu, X.", - "Zhou, P. (0000-0001-5740-4303)", - "Capozzola, T.", - "Schief, W.R.", - "Andrabi, R.", - "Burton, D.R.", - "Wilson, I.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7u2e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7u2e", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15", - emdb: null, - pdb: { - dbId: "7RBS", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, ISG15, IDP51000, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7RBS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rbs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rbs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05161", - organism: "9606", - name: "Ubiquitin-like protein ISG15", - details: "Three N-terminal residues (SNA) are expression tag", - altNames: - "Interferon-induced 15 kDa protein,Interferon-induced 17 kDa protein,IP17,Ubiquitin cross-reactive protein,hUCRP", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Tesar, C.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Wydorski, P.", - "Joachimiak, L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37185902", - title: - "Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.", - journal: "Nat Commun 14: 2366-2366 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-38031-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37185902", - pubDate: "2023", - abstract: "", - authors: [ - "Wydorski, P.M. (0000-0002-6983-421X)", - "Osipiuk, J.", - "Lanham, B.T.", - "Tesar, C.", - "Endres, M.", - "Engle, E.", - "Jedrzejczak, R.", - "Mullapudi, V. (0000-0002-5346-4242)", - "Michalska, K. (0000-0001-7140-3649)", - "Fidelis, K.", - "Fushman, D.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Joachimiak, L.A. (0000-0003-3061-5850)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rbs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rbs", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z1741966151", - emdb: null, - pdb: { - dbId: "5S3B", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3b_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LULUGSQUPICPQM-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3b_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3b", - }, - }, - { - title: - "Room Temperature Structure of SARS-CoV-2 Nsp10/16 Methyltransferase in a Complex with Cap-0 and SAM Determined by Pink-Beam Serial Crystallography", - emdb: null, - pdb: { - dbId: "7KOA", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, Serial Crystallography, Methyltransferase, m7GpppA, Cap-0, S-adenosylhomometionine, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7KOA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7koa_final.pdb", - externalLink: "https://pdb-redo.eu/db/7koa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QQOHNVHGNZYSBP-XPWFQUROSA-O", - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Satchell, K.J.F.", - "Wilamowski, M.", - "Sherrell, D.A.", - "Lavens, A.", - "Henning, R.", - "Srajer, V.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with Cap-0 and SAM Determined by Pink-Beam Serial Crystallography", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Wilamowski, M.", - "Sherrell, D.A.", - "Minasov, G.", - "Shuvalova, L.", - "Lavens, A.", - "Henning, R.", - "Maltseva, N.", - "Rosas-Lemus, M.", - "Kim, Y.", - "Satchell, K.J.F.", - "Srajer, V.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7koa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7koa", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z44592329", - emdb: null, - pdb: { - dbId: "5S2F", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S2F", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s2f_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s2f", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WBKYYDBHEGTTON-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s2f_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s2f", - }, - }, - { - title: - "1.60 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 3e", - emdb: null, - pdb: { - dbId: "7LKX", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LKX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lkx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lkx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "WZJYVJHLXCYWFV-NFFJHMNLSA-N", - "WZJYVJHLXCYWFV-JBKSVKCVSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Rathnayake, A.D.", - "Baird, M.A.", - "Shadipeni, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34213885", - title: - "Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease.", - journal: "J.Med.Chem. 64: 10047-10058 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00319", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34213885", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Kim, Y.", - "Bickmeier, N.", - "Rathnayake, A.D.", - "Nguyen, H.N.", - "Zheng, J.", - "Kashipathy, M.M.", - "Baird, M.A.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lkx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lkx", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 2)", - emdb: null, - pdb: { - dbId: "7BEK", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, antibody, germline, V-gene, receptor-binding-domain, spike, neutralisation, protection, glycosylation, valency, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7BEK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bek_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bek", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-158 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-158 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PQYJRMFWJJONBO-UHFFFAOYSA-N", - ], - dbauthors: ["Zhao, Y.", "Zhou, D.", "Ren, J.", "Stuart, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33756110", - title: - "The antigenic anatomy of SARS-CoV-2 receptor binding domain.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.02.032", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33756110", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Ginn, H.M.", - "Duyvesteyn, H.M.E.", - "Supasa, P.", - "Case, J.B.", - "Zhao, Y.", - "Walter, T.S.", - "Mentzer, A.J.", - "Liu, C.", - "Wang, B.", - "Paesen, G.C.", - "Slon-Campos, J.", - "Lopez-Camacho, C.", - "Kafai, N.M.", - "Bailey, A.L.", - "Chen, R.E.", - "Ying, B.", - "Thompson, C.", - "Bolton, J.", - "Fyfe, A.", - "Gupta, S.", - "Tan, T.K.", - "Gilbert-Jaramillo, J.", - "James, W.", - "Knight, M.", - "Carroll, M.W.", - "Skelly, D.", - "Dold, C.", - "Peng, Y.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Klenerman, P.", - "Temperton, N.", - "Hall, D.R.", - "Williams, M.A.", - "Paterson, N.G.", - "Bertram, F.K.R.", - "Siebert, C.A.", - "Clare, D.K.", - "Howe, A.", - "Radecke, J.", - "Song, Y.", - "Townsend, A.R.", - "Huang, K.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Diamond, M.S.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bek_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bek", - }, - }, - { - title: - "SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp6/7 (P6-P1)", - emdb: null, - pdb: { - dbId: "7MB6", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, COVID19 PROTEASE, PROTEASE INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "7MB6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mb6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mb6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "LYS-VAL-ALA-THR-VAL-GLN", - details: "Cleavage Site Nsp6/7 (P6-P1)", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Schiffer, C.A. (0000-0003-2270-6613)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35729165", - title: - "Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.", - journal: "Nat Commun 13: 3556-3556 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-31210-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35729165", - pubDate: "2022", - abstract: "", - authors: [ - "Shaqra, A.M.", - "Zvornicanin, S.N.", - "Huang, Q.Y.J. (0000-0001-5107-2336)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Knapp, M.", - "Tandeske, L.", - "Bakan, D.T.", - "Flynn, J. (0000-0002-5490-393X)", - "Bolon, D.N.A.", - "Moquin, S.", - "Dovala, D.", - "Kurt Yilmaz, N. (0000-0002-5036-676X)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mb6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mb6", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1614545742", - emdb: null, - pdb: { - dbId: "5RM8", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RM8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rm8_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rm8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "GVYWVRYDCMRUCE-SFYZADRCSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rm8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rm8", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z44592329", - emdb: null, - pdb: { - dbId: "5R83", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5R83", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5r83_final.pdb", - externalLink: "https://pdb-redo.eu/db/5r83", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "WBKYYDBHEGTTON-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Powell, A.J.", - "Wild, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. (0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5r83_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5r83", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-exoribonuclease domain", - emdb: null, - pdb: { - dbId: "7DIY", - method: "X-RAY DIFFRACTION", - keywords: "exoribonuclease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7DIY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7diy_final.pdb", - externalLink: "https://pdb-redo.eu/db/7diy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "nsp10 protein", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "nsp14-ExoN protein", - details: "", - altNames: "pp1ab,ORF1ab polyprotein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "JLVVSXFLKOJNIY-UHFFFAOYSA-N"], - dbauthors: [ - "Yang, J.", - "Chen, H.", - "Lin, X.", - "Cao, Y.", - "Lu, G.W.", - "Lin, S.", - "Wen, A.", - "Zheng, Y.", - "Ye, F.", - "Sun, H.L.", - "Chen, Z.M.", - "Yang, F.L.", - "Wang, L.L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33956156", - title: - "Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity.", - journal: "Nucleic Acids Res. 49: 5382-5392 (2021), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkab320", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33956156", - pubDate: "2021", - abstract: "", - authors: [ - "Lin, S.", - "Chen, H.", - "Chen, Z.", - "Yang, F.", - "Ye, F.", - "Zheng, Y.", - "Yang, J.", - "Lin, X.", - "Sun, H.", - "Wang, L.", - "Wen, A.", - "Dong, H.", - "Xiao, Q.", - "Deng, D.", - "Cao, Y.", - "Lu, G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7diy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7diy", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 Spike RBD in complex with MW05 Fab", - emdb: null, - pdb: { - dbId: "7DK0", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Spike, RBD, Antibody, ADE, VIRUS, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7DK0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dk0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dk0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "MW05 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "MW05 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Wang, J.", - "Zhang, J.", - "Wang, M.", - "Zhang, M.", - "Wang, R.", - "Jiao, S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35332252", - title: - "Antibody-dependent enhancement (ADE) of SARS-CoV-2 pseudoviral infection requires Fc gamma RIIB and virus-antibody complex with bivalent interaction.", - journal: "Commun Biol 5: 262-262 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03207-0", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35332252", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, S.", - "Wang, J.", - "Yu, X.", - "Jiang, W.", - "Chen, S. (0000-0002-2985-2317)", - "Wang, R.", - "Wang, M.", - "Jiao, S.", - "Yang, Y.", - "Wang, W.", - "Chen, H.", - "Chen, B.", - "Gu, C.", - "Liu, C.", - "Wang, A.", - "Li, G.", - "Guo, C.", - "Liu, D.", - "Zhang, J. (0000-0001-7519-2105)", - "Zhang, M. (0000-0001-9485-6069)", - "Wang, L. (0000-0003-0588-4899)", - "Gui, X. (0000-0002-5070-3527)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dk0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dk0", - }, - }, - { - title: - "The co-crystal structure of SARS-CoV-2 main protease with the peptidomimetic inhibitor (S)-2-cinnamamido-N-((S)-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)propan-2-yl)pent-4-ynamide", - emdb: null, - pdb: { - dbId: "7DHJ", - method: "X-RAY DIFFRACTION", - keywords: "complex, inhibitor, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7DHJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dhj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dhj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QZMKOYAKHMOPIL-GIGACSBGSA-N"], - dbauthors: [ - "Shang, L.Q. (0000-0003-4424-3162)", - "Wang, H. (0000-0002-1916-7092)", - "Deng, W.L. (0000-0001-6806-0307)", - "Xing, S. (0000-0002-9378-649X)", - "Wang, Y.X. (0000-0002-3507-3969)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35635946", - title: - "The structure-based design of peptidomimetic inhibitors against SARS-CoV-2 3C like protease as Potent anti-viral drug candidate.", - journal: "Eur.J.Med.Chem. 238: 114458-114458 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114458", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35635946", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, H.", - "Pei, R.", - "Li, X.", - "Deng, W.", - "Xing, S.", - "Zhang, Y.", - "Zhang, C.", - "He, S.", - "Sun, H.", - "Xiao, S.", - "Xiong, J.", - "Chen, X.", - "Wang, Y.", - "Guo, Y.", - "Zhang, B.", - "Shang, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dhj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dhj", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z1407673036", - emdb: null, - pdb: { - dbId: "5RLJ", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RLJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rlj_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rlj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Helicase", - details: "", - altNames: "Hel, Non-structural protein 13, nsp13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "HXLOQIXEAPZOSG-MRVPVSSYSA-N", - ], - dbauthors: [ - "Fearon, D.", - "von Delft, F.", - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Thompson, W.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Arrowsmith, C.H.", - "Edwards, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rlj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rlj", - }, - }, - { - title: - "Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-5'-Monophosphate", - emdb: null, - pdb: { - dbId: "6WLC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus 2, endoribonuclease, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WLC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wlc_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wlc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "DJJCXFVJDGTHFX-XVFCMESISA-N", - "PQYJRMFWJJONBO-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Godzik, A.", - "Chang, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33564093", - title: - "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.", - journal: "Commun Biol 4: 193-193 (2021), 2399-3642", - doi: "https://doi.org/10.1038/s42003-021-01735-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33564093", - pubDate: "2021", - abstract: "", - authors: [ - "Kim, Y.", - "Wower, J. (0000-0001-8096-7745)", - "Maltseva, N. (0000-0002-2871-465X)", - "Chang, C.", - "Jedrzejczak, R.", - "Wilamowski, M.", - "Kang, S.", - "Nicolaescu, V.", - "Randall, G.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Wower, J.", - "Maltseva, N.", - "Nicolaescu,, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - { - pmID: "", - title: - "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.06.26.173872", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Kim, Y.", - "Wower, J. (0000-0001-8096-7745)", - "Maltseva, N. (0000-0002-2871-465X)", - "Chang, C.", - "Jedrzejczak, R.", - "Wilamowski, M.", - "Kang, S.", - "Nicolaescu, V.", - "Randall, G.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Wower, J.", - "Maltseva, N.", - "Nicolaescu,, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wlc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wlc", - }, - }, - { - title: "LY-CoV1404 neutralizing antibody against SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7MMO", - method: "X-RAY DIFFRACTION", - keywords: - "antibody neutralizing SARS-CoV-2, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7MMO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mmo_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mmo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "LY-CoV1404 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "LY-CoV1404 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Hendle, J. (0000-0001-8857-0216)", - "Pustilnik, A. (0000-0002-3668-4016)", - "Sauder, J.M. (0000-0002-0254-4955)", - "Coleman, K.A. (0000-0002-9424-7025)", - "Boyles, J.S. (0000-0002-0546-3472)", - "Dickinson, C.D. (0000-0003-3410-0096)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33972947", - title: - "LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants.", - journal: "Biorxiv (2022)", - doi: "https://doi.org/10.1101/2021.04.30.442182", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33972947", - pubDate: "2022", - abstract: "", - authors: [ - "Westendorf, K.", - "Wang, L.", - "Zentelis, S.", - "Foster, D.", - "Vaillancourt, P.", - "Wiggin, M.", - "Lovett, E.", - "van der Lee, R.", - "Hendle, J.", - "Pustilnik, A.", - "Sauder, J.M.", - "Kraft, L.", - "Hwang, Y.", - "Siegel, R.W.", - "Chen, J.", - "Heinz, B.A.", - "Higgs, R.E.", - "Kallewaard, N.", - "Jepson, K.", - "Goya, R.", - "Smith, M.A.", - "Collins, D.W.", - "Pellacani, D.", - "Xiang, P.", - "de Puyraimond, V.", - "Ricicova, M.", - "Devorkin, L.", - "Pritchard, C.", - "O'Neill, A.", - "Dalal, K.", - "Panwar, P.", - "Dhupar, H.", - "Garces, F.A.", - "Cohen, C.", - "Dye, J.", - "Huie, K.E.", - "Badger, C.V.", - "Kobasa, D.", - "Audet, J.", - "Freitas, J.J.", - "Hassanali, S.", - "Hughes, I.", - "Munoz, L.", - "Palma, H.C.", - "Ramamurthy, B.", - "Cross, R.W.", - "Geisbert, T.W.", - "Menacherry, V.", - "Lokugamage, K.", - "Borisevich, V.", - "Lanz, I.", - "Anderson, L.", - "Sipahimalani, P.", - "Corbett, K.S.", - "Yang, E.S.", - "Zhang, Y.", - "Shi, W.", - "Zhou, T.", - "Choe, M.", - "Misasi, J.", - "Kwong, P.D.", - "Sullivan, N.J.", - "Graham, B.S.", - "Fernandez, T.L.", - "Hansen, C.L.", - "Falconer, E.", - "Mascola, J.R.", - "Jones, B.E.", - "Barnhart, B.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mmo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mmo", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 3c", - emdb: null, - pdb: { - dbId: "7T43", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7T43", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t43_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t43", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "BUKWXURASAKBCJ-IFXCNKOCSA-N", - "BUKWXURASAKBCJ-QOAPGFADSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Liu, L.", - "Kim, Y.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35638577", - title: - "Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.", - journal: "J.Med.Chem. 65: 7818-7832 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00224", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35638577", - pubDate: "2022", - abstract: "", - authors: [ - "Dampalla, C.S. (0000-0002-8199-2376)", - "Rathnayake, A.D. (0000-0003-2588-7624)", - "Galasiti Kankanamalage, A.C.", - "Kim, Y.", - "Perera, K.D. (0000-0002-3778-4975)", - "Nguyen, H.N.", - "Miller, M.J.", - "Madden, T.K.", - "Picard, H.R.", - "Thurman, H.A.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P. (0000-0003-0833-3259)", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Battaile, K.P.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t43_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t43", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder530 inhibitor", - emdb: null, - pdb: { - dbId: "7JIV", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7JIV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jiv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jiv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QMJFETCLZITVFG-MRXNPFEDSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33531496", - title: - "Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.", - journal: "Nat Commun 12: 743-743 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-21060-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33531496", - pubDate: "2021", - abstract: "", - authors: [ - "Osipiuk, J.", - "Azizi, S.A. (0000-0002-9226-9917)", - "Dvorkin, S.", - "Endres, M.", - "Jedrzejczak, R.", - "Jones, K.A. (0000-0003-0711-5516)", - "Kang, S.", - "Kathayat, R.S. (0000-0002-9159-2413)", - "Kim, Y.", - "Lisnyak, V.G. (0000-0002-4406-8440)", - "Maki, S.L. (0000-0001-6917-3602)", - "Nicolaescu, V.", - "Taylor, C.A.", - "Tesar, C.", - "Zhang, Y.A.", - "Zhou, Z. (0000-0002-2792-8429)", - "Randall, G.", - "Michalska, K.", - "Snyder, S.A. (0000-0003-3594-8769)", - "Dickinson, B.C. (0000-0002-9616-1911)", - "Joachimiak, A. (0000-0003-2535-6209)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jiv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jiv", - }, - }, - { - title: - "1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "6W75", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6W75", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6w75_final.pdb", - externalLink: "https://pdb-redo.eu/db/6w75", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Satchell, K.J.F.", - "Godzik, A.", - "Wiersum, G.", - "Stogios, P.J.", - "Skarina, T.", - "Jaroszewski, L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32994211", - title: - "High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design.", - journal: "Sci.Signal. 13 (2020), 1937-9145", - doi: "https://doi.org/10.1126/scisignal.abe1202", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32994211", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Minasov, G. (0000-0001-5460-3462)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Kiryukhina, O. (0000-0001-5962-8423)", - "Brunzelle, J. (0000-0001-9197-0018)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.L.", - "Kiryukhina, O.", - "Wiersum, G.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Endres, M.", - "Jaroszewski, L.", - "Godzik, A.", - "Joachimiak, A.", - "Satchell, K.J.F.", - ], - }, - { - pmID: "32511376", - title: - "The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.04.17.047498", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32511376", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Minasov, G. (0000-0001-5460-3462)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Kiryukhina, O. (0000-0001-5962-8423)", - "Brunzelle, J. (0000-0001-9197-0018)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.L.", - "Kiryukhina, O.", - "Wiersum, G.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Endres, M.", - "Jaroszewski, L.", - "Godzik, A.", - "Joachimiak, A.", - "Satchell, K.J.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w75_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w75", - }, - }, - { - title: - "Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with 2'-O-methylated m7GpppA Cap-1 and SAH Determined by Fixed-Target Serial Crystallography", - emdb: null, - pdb: { - dbId: "7JHE", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, Serial Crystallography, Methyltransferase, m7GpppA, Cap-1, S-adenosylhomocysteine, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7JHE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jhe_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jhe", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "UFVBPMPLSKDIFV-NAGRZYTCSA-O", - "JOPOQPCBCUIPFX-UHFFFAOYSA-L", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Satchell, K.J.F.", - "Michalska, K.", - "Wilamowski, M.", - "Sherrell, D.A.", - "Lavens, A.", - "Chard, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33972410", - title: - "2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography.", - journal: "Proc.Natl.Acad.Sci.USA 118 (2021), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2100170118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33972410", - pubDate: "2021", - abstract: "", - authors: [ - "Wilamowski, M.", - "Sherrell, D.A. (0000-0002-6393-8800)", - "Minasov, G. (0000-0001-5460-3462)", - "Kim, Y. (0000-0002-1610-4889)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Lavens, A. (0000-0002-3856-9919)", - "Chard, R.", - "Maltseva, N. (0000-0002-2871-465X)", - "Jedrzejczak, R.", - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Saint, N.", - "Foster, I.T. (0000-0003-2129-5269)", - "Michalska, K. (0000-0001-7140-3649)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jhe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jhe", - }, - }, - { - title: - "Crystal Structure of HLA-A*02:01 in complex with KLNDLCFTNV, an 10-mer epitope from SARS-CoV-2 Spike (S386-395)", - emdb: null, - pdb: { - dbId: "7M8S", - method: "X-RAY DIFFRACTION", - keywords: "peptide presentation, TCR, T cell, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7M8S", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m8s_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m8s", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q861F7", - organism: "9606", - name: "HLA class I histocompatibility antigen, A alpha chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: null, - name: "Spike protein S1 peptide", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Gras, S.", "Szeto, C.", "Nguyen, A.T."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules", - journal: "Biophysica 1 (2021)", - doi: "https://doi.org/10.3390/biophysica1020015", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Nguyen, A.T.", - "Szeto, C.", - "Jayasinghe, D.", - "Lobos, C.A.", - "Halim, H.", - "Chatzileontiadou, D.S.M.", - "Grant, E.J.", - "Gras, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m8s_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m8s", - }, - }, - { - title: - "Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2.", - emdb: null, - pdb: { - dbId: "6W61", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus, SAM-dependent methyltransferase, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, NSP16, NSP10, COMPLEX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6W61", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6w61_final.pdb", - externalLink: "https://pdb-redo.eu/db/6w61", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Godzik, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine", - journal: "Biorxiv (2020), 2692-8205", - doi: "https://doi.org/10.1101/2020.04.17.047498", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.L.", - "Kiryukhina, O.", - "Wiersum, G.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Endres, M.", - "Jaroszewski, L.", - "Godzik, A.", - "Joachimiak, A.", - "Satchell, K.J.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w61_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w61", - }, - }, - { - title: - "The crystal structure of COVID-19 main protease in complex with an inhibitor N3", - emdb: null, - pdb: { - dbId: "6LU7", - method: "X-RAY DIFFRACTION", - keywords: "protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6LU7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6lu7_final.pdb", - externalLink: "https://pdb-redo.eu/db/6lu7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: - "N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Liu, X.", "Yang, H.", "Rao, Z.", "Zhang, B.", "Jin, Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32272481", - title: - "Structure of Mprofrom SARS-CoV-2 and discovery of its inhibitors.", - journal: "Nature 582: 289-293 (2020), 1476-4687", - doi: "https://doi.org/10.1038/s41586-020-2223-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32272481", - pubDate: "2020", - abstract: "", - authors: [ - "Jin, Z.", - "Du, X.", - "Xu, Y.", - "Deng, Y.", - "Liu, M.", - "Zhao, Y.", - "Zhang, B.", - "Li, X.", - "Zhang, L.", - "Peng, C.", - "Duan, Y.", - "Yu, J.", - "Wang, L.", - "Yang, K.", - "Liu, F.", - "Jiang, R.", - "Yang, X.", - "You, T.", - "Liu, X.", - "Bai, F.", - "Liu, H.", - "Guddat, L.W.", - "Xu, W.", - "Xiao, G.", - "Qin, C.", - "Shi, Z.", - "Jiang, H.", - "Rao, Z.", - "Yang, H.", - "Jin, Z. (0000-0001-6448-820X)", - "Xu, Y. (0000-0002-1581-6155)", - "Shi, Z. (0000-0001-8089-163X)", - "Jiang, H. (0000-0003-0656-6315)", - "Rao, Z. (0000-0001-9866-2384)", - "Yang, H. (0000-0002-1875-3268)", - "Guddat, L.", - ], - }, - { - pmID: "", - title: - "Structure of Mpro from COVID-19 virus and discovery of its inhibitors.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.02.26.964882", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Jin, Z. (0000-0001-6448-820X)", - "Du, X.", - "Xu, Y. (0000-0002-1581-6155)", - "Deng, Y.", - "Liu, M.", - "Zhao, Y.", - "Zhang, B.", - "Li, X.", - "Zhang, L.", - "Peng, C.", - "Duan, Y.", - "Yu, J.", - "Wang, L.", - "Yang, K.", - "Liu, F.", - "Jiang, R.", - "Yang, X.", - "You, T.", - "Liu, X.", - "Bai, F.", - "Liu, H.", - "Guddat, L.W.", - "Xu, W.", - "Xiao, G.", - "Qin, C.", - "Shi, Z. (0000-0001-8089-163X)", - "Jiang, H. (0000-0003-0656-6315)", - "Rao, Z. (0000-0001-9866-2384)", - "Yang, H. (0000-0002-1875-3268)", - "Jin, Z.", - "Xu, Y.", - "Guddat, L.", - "Shi, Z.", - "Jiang, H.", - "Rao, Z.", - "Yang, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6lu7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6lu7", - }, - }, - { - title: - "Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with Jun9-84-3 inhibitor", - emdb: null, - pdb: { - dbId: "7SQE", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, inhibitor, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7SQE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sqe_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sqe", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SKQKRKDBQBKZJK-MRXNPFEDSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Wang, J.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with Jun9-84-3 inhibitor", - journal: "To be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Wang, J.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sqe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sqe", - }, - }, - { - title: "SARS-CoV-2 Delta RBD and Nb22", - emdb: null, - pdb: { - dbId: "7X7D", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 Delta RBD and Nb22, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7X7D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7x7d_final.pdb", - externalLink: "https://pdb-redo.eu/db/7x7d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9839", - name: "Nb22", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Wang, Y.", "Ye, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Insecta environmental sample", - assembly: "hexameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35371009", - title: - "Short-Term Instantaneous Prophylaxis and Efficient Treatment Against SARS-CoV-2 in hACE2 Mice Conferred by an Intranasal Nanobody (Nb22).", - journal: "Front Immunol 13: 865401-865401 (2022), 1664-3224", - doi: "https://doi.org/10.3389/fimmu.2022.865401", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35371009", - pubDate: "2022", - abstract: "", - authors: [ - "Wu, X.", - "Wang, Y.", - "Cheng, L.", - "Ni, F.", - "Zhu, L.", - "Ma, S.", - "Huang, B.", - "Ji, M.", - "Hu, H.", - "Li, Y.", - "Xu, S.", - "Shi, H.", - "Zhang, D.", - "Liu, L.", - "Nawaz, W.", - "Hu, Q.", - "Ye, S.", - "Liu, Y.", - "Wu, Z.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7x7d_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7x7d", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000263980802", - emdb: null, - pdb: { - dbId: "5RVD", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RVD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rvd_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rvd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BDDRHCCHCFMOJZ-GFCCVEGCSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rvd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rvd", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000159004", - emdb: null, - pdb: { - dbId: "5RVS", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5RVS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rvs_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rvs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VKFXHYRIHRTEIV-UHFFFAOYSA-N"], - dbauthors: ["Fraser, J.S.", "Young, I.D.", "Thompson, M.C.", "Correy, G.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33283984", - title: - "A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*.", - journal: "Chemmedchem 16: 942-948 (2021), 1860-7187", - doi: "https://doi.org/10.1002/cmdc.202000924", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33283984", - pubDate: "2021", - abstract: "", - authors: [ - "Yang, K.S.", - "Ma, X.R.", - "Ma, Y.", - "Alugubelli, Y.R.", - "Scott, D.A.", - "Vatansever, E.C.", - "Drelich, A.K.", - "Sankaran, B.", - "Geng, Z.Z.", - "Blankenship, L.R.", - "Ward, H.E.", - "Sheng, Y.J.", - "Hsu, J.C.", - "Kratch, K.C.", - "Zhao, B.", - "Hayatshahi, H.S.", - "Liu, J.", - "Li, P.", - "Fierke, C.A.", - "Tseng, C.K.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jq1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jq1", - }, - }, - { - title: - "1.45 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "6YUN", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 COVID-19 Nucleocapsid Phosphoprotein, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6YUN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6yun_final.pdb", - externalLink: "https://pdb-redo.eu/db/6yun", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Bracher, A. (0000-0001-8530-7594)", - "Zinzula, L. (0000-0001-6489-7070)", - "Basquin, J. (0000-0003-2151-3991)", - "Nagy, I. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rtm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rtm", - }, - }, - { - title: "Crystal structure of the N-terminal domain of SARS-CoV-2 nucleocapsid protein", - emdb: null, - pdb: { - dbId: "7VNU", - method: "X-RAY DIFFRACTION", - keywords: "coronavirus, nucleocapsid, VIRAL PROTEIN., VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VNU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vnu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vnu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QTBSBXVTEAMEQO-UHFFFAOYSA-M"], - dbauthors: ["Ni, X.C.", "Zhou, R.J.", "Lei, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36806252", - title: - "Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2.", - journal: "Commun Biol 6: 193-193 (2023), 2399-3642", - doi: "https://doi.org/10.1038/s42003-023-04570-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36806252", - pubDate: "2023", - abstract: "", - authors: [ - "Ni, X. (0000-0002-9723-4756)", - "Han, Y.", - "Zhou, R.", - "Zhou, Y.", - "Lei, J. 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(0000-0002-6366-6112)", - "Kutateladze, T.G. (0000-0001-7375-6990)", - "Holt, T.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35716662", - title: - "Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection.", - journal: "Structure 30 (2022), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2022.05.020", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35716662", - pubDate: "2022", - abstract: "", - authors: [ - "Vann, K.R.", - "Acharya, A.", - "Jang, S.M.", - "Lachance, C.", - "Zandian, M.", - "Holt, T.A.", - "Smith, A.L.", - "Pandey, K.", - "Durden, D.L.", - "El-Gamal, D.", - "Cote, J.", - "Byrareddy, S.N.", - "Kutateladze, T.G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tv0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tv0", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 Spike RBD in complex with MW06 Fab", - emdb: null, - pdb: { - dbId: "7DPM", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Spike, RBD, Antibody, ADE, VIRUS, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7DPM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dpm_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dpm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "heavy chain of MW06", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "light chain of MW06", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Wang, J.", - "Zhang, J.", - "Wang, M.", - "Zhang, M.", - "Wang, R.", - "Jiao, S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34313527", - title: - "Characterization of MW06, a human monoclonal antibody with cross-neutralization activity against both SARS-CoV-2 and SARS-CoV.", - journal: "Mabs 13: 1953683-1953683 (2021), 1942-0870", - doi: "https://doi.org/10.1080/19420862.2021.1953683", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34313527", - pubDate: "2021", - abstract: "", - authors: [ - "Jiang, W.", - "Wang, J.", - "Jiao, S.", - "Gu, C.", - "Xu, W.", - "Chen, B.", - "Wang, R.", - "Chen, H.", - "Xie, Y.", - "Wang, A.", - "Li, G.", - "Zeng, D.", - "Zhang, J.", - "Zhang, M.", - "Wang, S.", - "Wang, M.", - "Gui, X. (0000-0002-5070-3527)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dpm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dpm", - }, - }, - { - title: - "The crystal structure of SARS-CoV-2 Omicron BA.1 variant RBD in complex with equine ACE2", - emdb: null, - pdb: { - dbId: "7XBY", - method: "X-RAY DIFFRACTION", - keywords: "complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7XBY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7xby_final.pdb", - externalLink: "https://pdb-redo.eu/db/7xby", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "G1TEF4", - organism: "9986", - name: "Angiotensin-converting enzyme", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "CPELXLSAUQHCOX-UHFFFAOYSA-M", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: ["Han, P.", "Qi, J.X.", "Liu, K.F.", "Xu, Z.P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35729237", - title: - "Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses.", - journal: "Nat Commun 13: 3547-3547 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-31276-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35729237", - pubDate: "2022", - abstract: "", - authors: [ - "Xu, Z.", - "Kang, X.", - "Han, P.", - "Du, P.", - "Li, L.", - "Zheng, A.", - "Deng, C.", - "Qi, J. 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(0000-0001-6994-2416)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35729165", - title: - "Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.", - journal: "Nat Commun 13: 3556-3556 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-31210-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35729165", - pubDate: "2022", - abstract: "", - authors: [ - "Shaqra, A.M.", - "Zvornicanin, S.N.", - "Huang, Q.Y.J. (0000-0001-5107-2336)", - "Lockbaum, G.J. (0000-0003-2720-6984)", - "Knapp, M.", - "Tandeske, L.", - "Bakan, D.T.", - "Flynn, J. (0000-0002-5490-393X)", - "Bolon, D.N.A.", - "Moquin, S.", - "Dovala, D.", - "Kurt Yilmaz, N. (0000-0002-5036-676X)", - "Schiffer, C.A. (0000-0003-2270-6613)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tbt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tbt", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530 inhibitor", - emdb: null, - pdb: { - dbId: "7JIW", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7JIW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jiw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jiw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QMJFETCLZITVFG-MRXNPFEDSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33531496", - title: - "Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.", - journal: "Nat Commun 12: 743-743 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-21060-3", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33531496", - pubDate: "2021", - abstract: "", - authors: [ - "Osipiuk, J.", - "Azizi, S.A. (0000-0002-9226-9917)", - "Dvorkin, S.", - "Endres, M.", - "Jedrzejczak, R.", - "Jones, K.A. (0000-0003-0711-5516)", - "Kang, S.", - "Kathayat, R.S. (0000-0002-9159-2413)", - "Kim, Y.", - "Lisnyak, V.G. (0000-0002-4406-8440)", - "Maki, S.L. (0000-0001-6917-3602)", - "Nicolaescu, V.", - "Taylor, C.A.", - "Tesar, C.", - "Zhang, Y.A.", - "Zhou, Z. (0000-0002-2792-8429)", - "Randall, G.", - "Michalska, K.", - "Snyder, S.A. (0000-0003-3594-8769)", - "Dickinson, B.C. (0000-0002-9616-1911)", - "Joachimiak, A. (0000-0003-2535-6209)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jiw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jiw", - }, - }, - { - title: - "SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19)", - emdb: null, - pdb: { - dbId: "6Y84", - method: "X-RAY DIFFRACTION", - keywords: "protease, cysteine protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6Y84", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6y84_final.pdb", - externalLink: "https://pdb-redo.eu/db/6y84", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Stuart, D.I.", - "Hall, D.R.", - "Lukacik, P.", - "Walsh, M.A.", - "Crawshaw, A.D.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Brandao-Neto, J.", - "Powell, A.J.", - "Aragao, D. (0000-0002-6551-4657)", - "Williams, M.", - "Flaig, R.", - "McAuley, K.E.", - "Mazzorana, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "COVID-19 main protease with unliganded active site", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Owen, C.D.", - "Lukacik, P.", - "Strain-Damerell, C.M.", - "Douangamath, A.", - "Powell, A.J.", - "Fearon, D.", - "Brandao-Neto, J.", - "Crawshaw, A.D.", - "Aragao, D.", - "Williams, M.", - "Flaig, R.", - "Hall, D.", - "McAauley, K.", - "Stuart, D.I.", - "von Delft, F.", - "Walsh, M.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6y84_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6y84", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 2c", - emdb: null, - pdb: { - dbId: "7T42", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7T42", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7t42_final.pdb", - externalLink: "https://pdb-redo.eu/db/7t42", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "HTJCLKWRDFEDBR-JVGYHMDPSA-N", - "HTJCLKWRDFEDBR-ABXWHYIOSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Liu, L.", - "Kim, Y.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35638577", - title: - "Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.", - journal: "J.Med.Chem. 65: 7818-7832 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00224", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35638577", - pubDate: "2022", - abstract: "", - authors: [ - "Dampalla, C.S. (0000-0002-8199-2376)", - "Rathnayake, A.D. (0000-0003-2588-7624)", - "Galasiti Kankanamalage, A.C.", - "Kim, Y.", - "Perera, K.D. (0000-0002-3778-4975)", - "Nguyen, H.N.", - "Miller, M.J.", - "Madden, T.K.", - "Picard, H.R.", - "Thurman, H.A.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P. (0000-0003-0833-3259)", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C. (0000-0001-5248-7912)", - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Battaile, K.P.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7t42_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7t42", - }, - }, - { - title: "Crystal structure of Zinc bound SARS-CoV-2 main protease", - emdb: null, - pdb: { - dbId: "7DK1", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Main protease, Zinc, Mpro-Zinc complex, PEPTIDE BINDING PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7DK1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dk1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dk1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "DHMQDGOQFOQNFH-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "OWMVSZAMULFTJU-UHFFFAOYSA-N", - ], - dbauthors: [ - "Sonkar, K.S. (0000-0002-8382-1140)", - "Panchariya, L. (0000-0002-2194-1323)", - "Kuila, S. (0000-0001-5679-2105)", - "Khan, W.A. (0000-0002-0288-3316)", - "Arockiasamy, A. (0000-0002-4606-8006)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34514483", - title: - "Zinc 2+ ion inhibits SARS-CoV-2 main protease and viral replication in vitro.", - journal: "Chem.Commun.(Camb.) 57: 10083-10086 (2021), 1364-548X", - doi: "https://doi.org/10.1039/d1cc03563k", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34514483", - pubDate: "2021", - abstract: "", - authors: [ - "Panchariya, L. (0000-0002-2194-1323)", - "Khan, W.A. (0000-0002-0288-3316)", - "Kuila, S. (0000-0001-5679-2105)", - "Sonkar, K. (0000-0002-8382-1140)", - "Sahoo, S. (0000-0002-6998-0911)", - "Ghoshal, A.", - "Kumar, A.", - "Verma, D.K. (0000-0002-1806-493X)", - "Hasan, A. 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(0000-0002-0716-7052)", - "Khan, M.A. (0000-0002-0132-8601)", - "Jain, N.", - "Mohapatra, A.K.", - "Das, S.", - "Thakur, J.K.", - "Maiti, S. (0000-0001-9897-1419)", - "Nanda, R.K.", - "Halder, R.", - "Sunil, S.", - "Arockiasamy, A. (0000-0002-4606-8006)", - "Panchariya, L.", - "Sonkar, K.S. 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(0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s2g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s2g", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 1)", - emdb: null, - pdb: { - dbId: "7BEJ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, antibody, germline, V-gene, receptor-binding-domain, spike, neutralisation, protection, glycosylation, valency, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7BEJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bej_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bej", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-158 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-158 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "BDAGIHXWWSANSR-UHFFFAOYSA-N"], - dbauthors: ["Zhao, Y.", "Zhou, D.", "Ren, J.", "Stuart, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33756110", - title: - "The antigenic anatomy of SARS-CoV-2 receptor binding domain.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.02.032", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33756110", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Ginn, H.M.", - "Duyvesteyn, H.M.E.", - "Supasa, P.", - "Case, J.B.", - "Zhao, Y.", - "Walter, T.S.", - "Mentzer, A.J.", - "Liu, C.", - "Wang, B.", - "Paesen, G.C.", - "Slon-Campos, J.", - "Lopez-Camacho, C.", - "Kafai, N.M.", - "Bailey, A.L.", - "Chen, R.E.", - "Ying, B.", - "Thompson, C.", - "Bolton, J.", - "Fyfe, A.", - "Gupta, S.", - "Tan, T.K.", - "Gilbert-Jaramillo, J.", - "James, W.", - "Knight, M.", - "Carroll, M.W.", - "Skelly, D.", - "Dold, C.", - "Peng, Y.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Klenerman, P.", - "Temperton, N.", - "Hall, D.R.", - "Williams, M.A.", - "Paterson, N.G.", - "Bertram, F.K.R.", - "Siebert, C.A.", - "Clare, D.K.", - "Howe, A.", - "Radecke, J.", - "Song, Y.", - "Townsend, A.R.", - "Huang, K.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Diamond, M.S.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bej_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bej", - }, - }, - { - title: - "Room temperature structure of NSP15 Endoribonuclease from SARS CoV-2 solved using SFX.", - emdb: null, - pdb: { - dbId: "7K9P", - method: "X-RAY DIFFRACTION", - keywords: - "Severe acute respiratory syndrome coronavirus 2, room temperature structure, serial femtosecond crystallography, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7K9P", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k9p_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k9p", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N"], - dbauthors: [ - "Botha, S. (0000-0003-4362-7543)", - "Jernigan, R. (0000-0002-0815-8617)", - "Chen, J. (0000-0002-7253-2722)", - "Coleman, M.A. (0000-0003-1389-4018)", - "Frank, M. (0000-0002-5244-0791)", - "Grant, T.D. (0000-0002-8583-3700)", - "Hansen, D.T. (0000-0003-4395-8297)", - "Ketawala, G. (0000-0002-9436-3536)", - "Logeswaran, D. (0000-0002-3522-3883)", - "Martin-Garcia, J. (0000-0002-4558-3858)", - "Nagaratnam, N. (0000-0002-3201-930X)", - "Raj, A.L.L.X. (0000-0003-2397-1021)", - "Shelby, M. (0000-0001-6984-957X)", - "Yang, J.-H. (0000-0002-5811-3724)", - "Yung, M.C. (0000-0003-0534-0728)", - "Fromme, P. (0000-0003-0953-4909)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "hexameric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36630960", - title: - "Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser.", - journal: "Structure (2022), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2022.12.009", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36630960", - pubDate: "2022", - abstract: "", - authors: [ - "Jernigan, R.J.", - "Logeswaran, D.", - "Doppler, D.", - "Nagaratnam, N.", - "Sonker, M.", - "Yang, J.H.", - "Ketawala, G.", - "Martin-Garcia, J.M.", - "Shelby, M.L.", - "Grant, T.D.", - "Mariani, V.", - "Tolstikova, A.", - "Sheikh, M.Z.", - "Yung, M.C.", - "Coleman, M.A.", - "Zaare, S.", - "Kaschner, E.K.", - "Rabbani, M.T.", - "Nazari, R.", - "Zacks, M.A.", - "Hayes, B.", - "Sierra, R.G.", - "Hunter, M.S.", - "Lisova, S.", - "Batyuk, A.", - "Kupitz, C.", - "Boutet, S.", - "Hansen, D.T.", - "Kirian, R.A.", - "Schmidt, M.", - "Fromme, R.", - "Frank, M.", - "Ros, A.", - "Chen, J.J.", - "Botha, S.", - "Fromme, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k9p_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k9p", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z2856434937", - emdb: null, - pdb: { - dbId: "5S3C", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S3C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s3c_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s3c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KMXZEXUYXUMHEQ-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3c", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with a Lys48-linked di-ubiquitin", - emdb: null, - pdb: { - dbId: "7RBR", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, ubiquitin, IDP51000, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7RBR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rbr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rbr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0CG47", - organism: "9606", - name: "Ubiquitin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Wydorski, P.", - "Joachimiak, L.", - "Lanham, B.T.", - "Fushman, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37185902", - title: - "Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.", - journal: "Nat Commun 14: 2366-2366 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-38031-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37185902", - pubDate: "2023", - abstract: "", - authors: [ - "Wydorski, P.M. 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(0000-0003-3061-5850)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rbr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rbr", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADG20", - emdb: null, - pdb: { - dbId: "7U2D", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Coronavirus, Antibody, Spike, RBD, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7U2D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7u2d_final.pdb", - externalLink: "https://pdb-redo.eu/db/7u2d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "ADG20 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "ADG20 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "KRKNYBCHXYNGOX-UHFFFAOYSA-N", - ], - dbauthors: [ - "Wilson, I.A. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s3t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s3t", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z68404778", - emdb: null, - pdb: { - dbId: "5S35", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S35", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s35_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s35", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QAIADKFUCPEVKW-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s35_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s35", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with UAW243", - emdb: null, - pdb: { - dbId: "6XFN", - method: "X-RAY DIFFRACTION", - keywords: - "COVID, COVID19, COVID-19, SARS, SARS COV2, COV, NCOV 19, CORONAVIRUS, MAIN PROTEASE, 3CL, MPRO, PRO, VIRAL PROTEIN, GC376, calpain inhibitor II, calpain inhibitor XII, 12, calpain inhibitor 12, leupeptin, calpain, aldehyde, GC-376, 3cl-like, a-ketoamide, alpheketoamide, alpha, ketoamide, PEPTIDOMIMETIC, PROTEASE, CYSTEINE, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6XFN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xfn_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xfn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "UAW243", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M.", "Ma, C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33158912", - title: - "Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L.", - journal: "Sci Adv 6 (2020), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abe0751", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33158912", - pubDate: "2020", - abstract: "", - authors: [ - "Sacco, M.D.", - "Ma, C.", - "Lagarias, P.", - "Gao, A.", - "Townsend, J.A.", - "Meng, X.", - "Dube, P.", - "Zhang, X.", - "Hu, Y.", - "Kitamura, N.", - "Hurst, B.", - "Tarbet, B.", - "Marty, M.T.", - "Kolocouris, A.", - "Xiang, Y.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xfn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xfn", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun9-57-3R", - emdb: null, - pdb: { - dbId: "7RN0", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, inhibitor, main protease, 3cl, SARS, SARS-CoV-2, COVID, COVID-19, VIRAL PROTEIN, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RN0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rn0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rn0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "JHNKYRWLHFZNLP-RXFWQSSRSA-N"], - dbauthors: ["Chen, Y.", "Sacco, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34860011", - title: - "Discovery of Di- and Trihaloacetamides as Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity.", - journal: "J.Am.Chem.Soc. 143: 20697-20709 (2021), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08060", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34860011", - pubDate: "2021", - abstract: "", - authors: [ - "Ma, C.", - "Xia, Z.", - "Sacco, M.D.", - "Hu, Y.", - "Townsend, J.A.", - "Meng, X.", - "Choza, J.", - "Tan, H.", - "Jang, J.", - "Gongora, M.V.", - "Zhang, X.", - "Zhang, F.", - "Xiang, Y.", - "Marty, M.T. (0000-0001-8115-1772)", - "Chen, Y.", - "Wang, J. (0000-0002-4845-4621)", - "Kitamura, N.", - "Ba, M.", - "Szeto, T.", - "Kukuljac, A.", - "Marty, M.T.", - "Schultz, D.", - "Cherry, S.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rn0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rn0", - }, - }, - { - title: - "Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity", - emdb: null, - pdb: { - dbId: "7L0N", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, variant RBD, viral protein-receptor complex, VIRAL PROTEIN, VIRAL PROTEIN-HYDROLASE complex", - refModels: [ - { - emdbId: null, - pdbId: "7L0N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l0n_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l0n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S309 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S309 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S304 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Monoclonal antibody S304 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "YFNKIDBQEZZDLK-UHFFFAOYSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "ZIBGPFATKBEMQZ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Snell, G.", - "Corti, D.", - "Czudnochowski, N.", - "Nix, J.C.", - "Croll, T.I.", - "Dillen, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "hexameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33621484", - title: - "Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.", - journal: "Cell 184: 1171-1187.e20 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.01.037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33621484", - pubDate: "2021", - abstract: "", - authors: [ - "Thomson, E.C.", - "Rosen, L.E.", - "Shepherd, J.G.", - "Spreafico, R.", - "da Silva Filipe, A.", - "Wojcechowskyj, J.A.", - "Davis, C.", - "Piccoli, L.", - "Pascall, D.J.", - "Dillen, J.", - "Lytras, S.", - "Czudnochowski, N.", - "Shah, R.", - "Meury, M.", - "Jesudason, N.", - "De Marco, A.", - "Li, K.", - "Bassi, J.", - "O'Toole, A.", - "Pinto, D.", - "Colquhoun, R.M.", - "Culap, K.", - "Jackson, B.", - "Zatta, F.", - "Rambaut, A.", - "Jaconi, S.", - "Sreenu, V.B.", - "Nix, J.", - "Zhang, I.", - "Jarrett, R.F.", - "Glass, W.G.", - "Beltramello, M.", - "Nomikou, K.", - "Pizzuto, M.", - "Tong, L.", - "Cameroni, E.", - "Croll, T.I.", - "Johnson, N.", - "Di Iulio, J.", - "Wickenhagen, A.", - "Ceschi, A.", - "Harbison, A.M.", - "Mair, D.", - "Ferrari, P.", - "Smollett, K.", - "Sallusto, F.", - "Carmichael, S.", - "Garzoni, C.", - "Nichols, J.", - "Galli, M.", - "Hughes, J.", - "Riva, A.", - "Ho, A.", - "Schiuma, M.", - "Semple, M.G.", - "Openshaw, P.J.M.", - "Fadda, E.", - "Baillie, J.K.", - "Chodera, J.D.", - "Rihn, S.J.", - "Lycett, S.J.", - "Virgin, H.W.", - "Telenti, A.", - "Corti, D.", - "Robertson, D.L.", - "Snell, G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l0n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l0n", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z126932614", - emdb: null, - pdb: { - dbId: "5SKX", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SKX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5skx_final.pdb", - externalLink: "https://pdb-redo.eu/db/5skx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "WCWTYTQSZZWNEW-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5skx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5skx", - }, - }, - { - title: "Papain-Like Protease of SARS CoV-2 in complex with Jun9-84-3 inhibitor", - emdb: null, - pdb: { - dbId: "7RZC", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, inhibitor, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RZC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rzc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rzc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SKQKRKDBQBKZJK-MRXNPFEDSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Wang, J.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Papain-Like Protease of SARS CoV-2 in complex with Jun9-84-3 inhibitor", - journal: "To be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Wang, J.", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rzc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rzc", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with REAL250002852032 - (S) isomer", - emdb: null, - pdb: { - dbId: "5SPR", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SPR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5spr_final.pdb", - externalLink: "https://pdb-redo.eu/db/5spr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OHVACHOAZRWEJX-QMMMGPOBSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5spr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5spr", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINCn500000bifGU", - emdb: null, - pdb: { - dbId: "5SSI", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SSI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5ssi_final.pdb", - externalLink: "https://pdb-redo.eu/db/5ssi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DQMGMSFESKLRGX-MRVPVSSYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5ssi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5ssi", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000450476923 - (S,R) isomer", - emdb: null, - pdb: { - dbId: "5SP3", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SP3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sp3_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sp3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SSHCMXMCAMBDLI-MNOVXSKESA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sp3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sp3", - }, - }, - { - title: "Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI23", - emdb: null, - pdb: { - dbId: "7RVW", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, main protease, reversible covalent inhibitors, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7RVW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rvw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rvw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PNFAFEUIIJFEIL-VABKMULXSA-N"], - dbauthors: ["Yang, K. (0000-0002-1890-4169)", "Liu, W. (0000-0002-7078-6534)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35779291", - title: - "A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.", - journal: "Eur.J.Med.Chem. 240: 114570-114570 (2022), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2022.114570", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35779291", - pubDate: "2022", - abstract: "", - authors: [ - "Ma, Y.", - "Yang, K.S.", - "Geng, Z.Z.", - "Alugubelli, Y.R.", - "Shaabani, N.", - "Vatansever, E.C.", - "Ma, X.R.", - "Cho, C.C.", - "Khatua, K.", - "Xiao, J.", - "Blankenship, L.R.", - "Yu, G.", - "Sankaran, B.", - "Li, P.", - "Allen, R.", - "Ji, H.", - "Xu, S.", - "Liu, W.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rvw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rvw", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5010894399 - (S,S) isomer", - emdb: null, - pdb: { - dbId: "5SQV", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SQV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sqv_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sqv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PYDRNAYFUJBXAX-AZUAARDMSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. 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(0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5spe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5spe", - }, - }, - { - title: "SARS-CoV-2 3CL protease (3CL pro) in complex with a novel inhibitor", - emdb: null, - pdb: { - dbId: "6M2N", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, 3CL pro, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6M2N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6m2n_final.pdb", - externalLink: "https://pdb-redo.eu/db/6m2n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FXNFHKRTJBSTCS-UHFFFAOYSA-N"], - dbauthors: ["Li, M.J.", "Xie, H.", "Su, H.X.", "Zhao, W.F.", "Xu, Y.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32737471", - title: - "Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients.", - journal: "Acta Pharmacol.Sin. 41: 1167-1177 (2020), 1745-7254", - doi: "https://doi.org/10.1038/s41401-020-0483-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32737471", - pubDate: "2020", - abstract: "", - authors: [ - "Su, H.X.", - "Yao, S.", - "Zhao, W.F.", - "Li, M.J.", - "Liu, J.", - "Shang, W.J.", - "Xie, H.", - "Ke, C.Q.", - "Hu, H.C.", - "Gao, M.N.", - "Yu, K.Q.", - "Liu, H.", - "Shen, J.S.", - "Tang, W.", - "Zhang, L.K.", - "Xiao, G.F.", - "Ni, L.", - "Wang, D.W.", - "Zuo, J.P.", - "Jiang, H.L.", - "Bai, F.", - "Wu, Y.", - "Ye, Y.", - "Xu, Y.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6m2n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6m2n", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5281440906 - (R,S) and (S,R) isomers", - emdb: null, - pdb: { - dbId: "5SRZ", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SRZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5srz_final.pdb", - externalLink: "https://pdb-redo.eu/db/5srz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VLGDVQRYEOXYDY-NEPJUHHUSA-N", "VLGDVQRYEOXYDY-NWDGAFQWSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "Ligand screen against SARS-CoV-2 NSP3 macrodomain", - journal: "To be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Correy, G.J.", "Fraser, J.S."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5srz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5srz", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5010894395 - (R,R) and (S,S) isomers", - emdb: null, - pdb: { - dbId: "5SQA", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SQA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sqa_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sqa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NPDVANGOGQJPGW-PXAZEXFGSA-N", "NPDVANGOGQJPGW-YVEFUNNKSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sqa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sqa", - }, - }, - { - title: - "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 20b (deuterated analog of 19b)", - emdb: null, - pdb: { - dbId: "7LZW", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LZW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lzw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lzw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SXLHHGJXSMBQOQ-JWWIWJDOSA-N", "SXLHHGJXSMBQOQ-VERUCKTNSA-N"], - dbauthors: [ - "Miller, M.J.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Perera, K.D.", - "Rathnayake, A.D.", - "Jesri, A.R.M.", - "Baird, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34865476", - title: - "Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.", - journal: "J.Med.Chem. 64: 17846-17865 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34865476", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Jesri, A.M.", - "Nguyen, H.N.", - "Miller, M.J.", - "Thurman, H.A.", - "Zheng, J.", - "Kashipathy, M.M.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Kim, Y.", - "Groutas, W.C.", - "Chang, K.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lzw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lzw", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with the HCV NS3/4A inhibitor telaprevir", - emdb: null, - pdb: { - dbId: "7NBS", - method: "X-RAY DIFFRACTION", - keywords: - "Coronavirus, main protease, drug repurposing, hepatitis C virus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NBS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nbs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nbs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M", "FTZGWEAUHOMNIG-FJRGXGLZSA-N"], - dbauthors: [ - "Hilgenfeld, R. 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(0000-0001-8850-2977)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nbs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nbs", - }, - }, - { - title: - "Identification of low micromolar SARS-CoV-2 Mpro inhibitors from hits identified by in silico screens", - emdb: null, - pdb: { - dbId: "7P2G", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Mpro, inhibitor, protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7P2G", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7p2g_final.pdb", - externalLink: "https://pdb-redo.eu/db/7p2g", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DDBKMCQLKKZOJH-CYBMUJFWSA-N"], - dbauthors: [ - "Rempel, S. (0000-0003-3569-8229)", - "Halazonetis, T.D. (0000-0001-8384-5030)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35169179", - title: - "Non-covalent SARS-CoV-2 M pro inhibitors developed from in silico screen hits.", - journal: "Sci Rep 12: 2505-2505 (2022), 2045-2322", - doi: "https://doi.org/10.1038/s41598-022-06306-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35169179", - pubDate: "2022", - abstract: "", - authors: [ - "Rossetti, G.G.", - "Ossorio, M.A.", - "Rempel, S.", - "Kratzel, A.", - "Dionellis, V.S.", - "Barriot, S.", - "Tropia, L.", - "Gorgulla, C.", - "Arthanari, H.", - "Thiel, V.", - "Mohr, P.", - "Gamboni, R.", - "Halazonetis, T.D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7p2g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7p2g", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike glycoprotein in complex with its receptor human ACE2", - emdb: null, - pdb: { - dbId: "7WBQ", - method: "X-RAY DIFFRACTION", - keywords: "Complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WBQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wbq_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wbq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: ["Han, P.", "Qi, J. (0000-0002-9358-4732)"], - details: [ - { - sample: { - name: "", - exprSystem: "Insect cell expression vector pTIE1", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35093192", - title: - "Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2.", - journal: "Cell 185: 630-640.e10 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.01.001", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35093192", - pubDate: "2022", - abstract: "", - authors: [ - "Han, P.", - "Li, L.", - "Liu, S.", - "Wang, Q.", - "Zhang, D.", - "Xu, Z.", - "Li, X.", - "Peng, Q.", - "Su, C.", - "Huang, B.", - "Li, D.", - "Zhang, R.", - "Tian, M.", - "Fu, L.", - "Gao, Y.", - "Zhao, X.", - "Liu, K.", - "Qi, J.", - "Gao, G.F.", - "Wang, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wbq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wbq", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 helicase in complex with Z2327226104", - emdb: null, - pdb: { - dbId: "7NNG", - method: "X-RAY DIFFRACTION", - keywords: "NSP13, Helicase, SARS-CoV-2, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7NNG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nng_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nng", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "SARS-CoV-2 helicase NSP13", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,SARS-CoV-2 helicase NSP13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "DAYJQFRBEKQYDR-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. 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(0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nng_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nng", - }, - }, - { - title: - "AALALL segment from the Nucleoprotein of SARS-CoV-2, residues 217-222, crystal form 2", - emdb: null, - pdb: { - dbId: "7LUX", - method: "X-RAY DIFFRACTION", - keywords: "amyloid fibril, PROTEIN FIBRIL", - refModels: [ - { - emdbId: null, - pdbId: "7LUX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lux_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lux", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein AALALL", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UWHCKJMYHZGTIT-UHFFFAOYSA-N"], - dbauthors: [ - "Lu, J. (0000-0002-4941-3098)", - "Zee, C.-T. (0000-0002-6630-706X)", - "Sawaya, M.R. (0000-0003-0874-9043)", - "Rodriguez, J.A. (0000-0001-8471-2504)", - "Eisenberg, D.S. (0000-0003-2432-5419)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "33688654", - title: - "Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.05.434000", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33688654", - pubDate: "2021", - abstract: "", - authors: [ - "Tayeb-Fligelman, E.", - "Cheng, X.", - "Tai, C.", - "Bowler, J.T.", - "Griner, S.", - "Sawaya, M.R.", - "Seidler, P.M.", - "Jiang, Y.X.", - "Lu, J.", - "Rosenberg, G.M.", - "Salwinski, L.", - "Abskharon, R.", - "Zee, C.T.", - "Hou, K.", - "Li, Y.", - "Boyer, D.R.", - "Murray, K.A.", - "Falcon, G.", - "Anderson, D.H.", - "Cascio, D.", - "Saelices, L.", - "Damoiseaux, R.", - "Guo, F.", - "Eisenberg, D.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lux_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lux", - }, - }, - { - title: "Structure of the SARS-CoV-2 3CL protease in complex with rupintrivir", - emdb: null, - pdb: { - dbId: "7P35", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Inhibitor, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7P35", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7p35_final.pdb", - externalLink: "https://pdb-redo.eu/db/7p35", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LMIUALQNZXJHOG-IFILWLFVSA-N"], - dbauthors: [ - "Fabrega-Ferrer, M. (0000-0001-9471-0473)", - "Herrera-Morande, A.", - "Perez-Saavedra, J. (0000-0003-0829-6056)", - "Coll, M. (0000-0003-4471-8674)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36336176", - title: - "Structure and inhibition of SARS-CoV-1 and SARS-CoV-2 main proteases by oral antiviral compound AG7404.", - journal: "Antiviral Res. 208: 105458-105458 (2022), 0166-3542", - doi: "https://doi.org/10.1016/j.antiviral.2022.105458", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36336176", - pubDate: "2022", - abstract: "", - authors: [ - "Fabrega-Ferrer, M.", - "Herrera-Morande, A.", - "Muriel-Goni, S.", - "Perez-Saavedra, J.", - "Bueno, P.", - "Castro, V.", - "Garaigorta, U.", - "Gastaminza, P.", - "Coll, M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7p35_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7p35", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z54615640", - emdb: null, - pdb: { - dbId: "5SLL", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sll_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sll", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "LMUYJJAKMZKBHS-SECBINFHSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sll_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sll", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) at 1.2 A Resolution and a Possible Capture of Zinc Binding Intermediate", - emdb: null, - pdb: { - dbId: "7K3T", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Main Protease, 3CLpro/Mpro, Intermediate, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7K3T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k3t_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k3t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Shi, W.", - "McSweeney, S. (0000-0002-3758-3161)", - "Fuchs, M.R.", - "Kreitler, D.F.", - "Soares, A.S.", - "Jakoncic, J.", - "Keereetaweep, J.", - "Shanklin, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35842458", - title: - "Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.", - journal: "Sci Rep 12: 12197-12197 (2022), 2045-2322", - doi: "https://doi.org/10.1038/s41598-022-15930-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35842458", - pubDate: "2022", - abstract: "", - authors: [ - "Andi, B.", - "Kumaran, D.", - "Kreitler, D.F.", - "Soares, A.S.", - "Keereetaweep, J.", - "Jakoncic, J.", - "Lazo, E.O.", - "Shi, W.", - "Fuchs, M.R.", - "Sweet, R.M.", - "Shanklin, J.", - "Adams, P.D.", - "Schmidt, J.G.", - "Head, M.S.", - "McSweeney, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k3t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k3t", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000118179920", - emdb: null, - pdb: { - dbId: "5SOW", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sow_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sow", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OYAIJZAKIFCNCV-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. 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(0000-0002-2412-7853)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. (0000-0001-9754-4503)", - "Wu, N.C. (0000-0002-9078-6697)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32661058", - title: - "Structural basis of a shared antibody response to SARS-CoV-2.", - journal: "Science 369: 1119-1123 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abd2321", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32661058", - pubDate: "2020", - abstract: "", - authors: [ - "Yuan, M. (0000-0001-9754-4503)", - "Liu, H. (0000-0002-2412-7853)", - "Wu, N.C. (0000-0002-9078-6697)", - "Lee, C.D. (0000-0002-5470-2484)", - "Zhu, X. (0000-0002-6021-3740)", - "Zhao, F. (0000-0002-3172-1340)", - "Huang, D. (0000-0002-6989-639X)", - "Yu, W. (0000-0002-4025-2646)", - "Hua, Y.", - "Tien, H. (0000-0001-7584-5989)", - "Rogers, T.F. 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(0000-0002-6469-2419)", - "Yuan, M.", - "Liu, H.", - "Wu, N.C.", - "Lee, C.D.", - "Zhu, X.", - "Zhao, F.", - "Huang, D.", - "Yu, W.", - "Tien, H.", - "Rogers, T.F.", - "Landais, E.", - "Sok, D.", - "Jardine, J.G.", - "Burton, D.R.", - "Wilson, I.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xc3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xc3", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2856434938", - emdb: null, - pdb: { - dbId: "5SMH", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SMH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5smh_final.pdb", - externalLink: "https://pdb-redo.eu/db/5smh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - 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"Mentzer, A.J.", - "Wang, B.", - "Case, J.B.", - "Zhao, Y.", - "Skelly, D.T.", - "Chen, R.E.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Malik, T.", - "Temperton, N.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Clare, D.K.", - "Howe, A.", - "Goulder, P.J.R.", - "Fry, E.E.", - "Diamond, M.S.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Afonine, P.V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7prz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7prz", - }, - }, - { - title: "SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-69", - emdb: null, - pdb: { - dbId: "7LLZ", - method: "X-RAY DIFFRACTION", - keywords: - "coronavirus inhibitor, SARS-CoV-2, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LLZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7llz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7llz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "XOTUFJPCITWJHW-QGZVFWFLSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: [ - "Ratia, K.M. (0000-0002-4834-9207)", - "Xiong, R. (0000-0002-6350-9037)", - "Thatcher, G.R. (0000-0002-7757-1739)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33594371", - title: - "Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.02.13.431008", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33594371", - pubDate: "2021", - abstract: "", - authors: [ - "Shen, Z.", - "Ratia, K.", - "Cooper, L.", - "Kong, D.", - "Lee, H.", - "Kwon, Y.", - "Li, Y.", - "Alqarni, S.", - "Huang, F.", - "Dubrovskyi, O.", - "Rong, L.", - "Thatcher, G.R.", - "Xiong, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7llz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7llz", - }, - }, - { - title: - "Structure of SARS-CoV-2 spike receptor-binding domain in complex with high affinity ACE2 mutant (S19W,N330Y)", - emdb: null, - pdb: { - dbId: "7EFP", - method: "X-RAY DIFFRACTION", - keywords: "receptor-binding domain, angiotensin converting enzyme 2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7EFP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7efp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7efp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Processed angiotensin-converting enzyme 2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Lin, X.", "Lu, G.W.", "Ye, F."], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34531369", - title: - "S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis.", - journal: - "Signal Transduct Target Ther 6: 343-343 (2021), 2059-3635", - doi: "https://doi.org/10.1038/s41392-021-00756-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34531369", - pubDate: "2021", - abstract: "", - authors: [ - "Ye, F.", - "Lin, X.", - "Chen, Z.", - "Yang, F.", - "Lin, S.", - "Yang, J.", - "Chen, H.", - "Sun, H.", - "Wang, L.", - "Wen, A.", - "Zhang, X.", - "Dai, Y.", - "Cao, Y.", - "Shen, G.", - "Yang, L.", - "Li, J.", - "Wang, Z.", - "Wang, W. (0000-0001-7788-1895)", - "Wei, X. (0000-0002-6513-6422)", - "Lu, G. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s46_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s46", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Triglycidyl isocyanurate.", - emdb: null, - pdb: { - dbId: "7AQJ", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-!9, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AQJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aqj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aqj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MRWWCVUTOFNJLM-HLTSFMKQSA-N", "OUPZKGBUJRBPGC-CIUDSAMLSA-N"], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Lieske, J.", - "Ewert, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - { - pmID: "", - title: - "Inhibition of SARS-CoV-2 main protease by allosteric drug-binding", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.11.12.378422", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7aqj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7aqj", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1129289650 (Mpro-x2646)", - emdb: null, - pdb: { - dbId: "5RH2", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RH2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rh2_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rh2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZROFBWFSOGSOQG-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rh2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rh2", - }, - }, - { - title: - "Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)", - emdb: null, - pdb: { - dbId: "6Y2F", - method: "X-RAY DIFFRACTION", - keywords: - "Novel coronavirus, alpha-ketoamide, antiviral, drug design, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6Y2F", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6y2f_final.pdb", - externalLink: "https://pdb-redo.eu/db/6y2f", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "FRACPXUHUTXLCX-BELIEFIBSA-N"], - dbauthors: [ - "Hilgenfeld, R. (0000-0001-8850-2977)", - "Zhang, L. (0000-0002-4642-9617)", - "Lin, D. (0000-0002-4271-5739)", - "Sun, X. (0000-0002-2761-2862)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32198291", - title: - "Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.", - journal: "Science 368: 409-412 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abb3405", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32198291", - pubDate: "2020", - abstract: "", - authors: [ - "Zhang, L.", - "Lin, D.", - "Sun, X.", - "Curth, U.", - "Drosten, C.", - "Sauerhering, L.", - "Becker, S.", - "Rox, K.", - "Hilgenfeld, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6y2f_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6y2f", - }, - }, - { - title: "SARS-CoV-2 Beta RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs", - emdb: null, - pdb: { - dbId: "7ZFC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Beta, Omicron, BA.1, BA.2, RBD, antibody, Fab, Omi-18, Omi-31, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZFC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zfc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zfc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Omi-31 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-31 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody C1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-18 heavy chain", - details: "", - altNames: "", - 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"Tuekprakhon, A.", - "Ginn, H.M.", - "Supasa, P.", - "Liu, C.", - "Huo, J.", - "Mentzer, A.J.", - "Duyvesteyn, H.M.E.", - "Dijokaite-Guraliuc, A.", - "Skelly, D.", - "Ritter, T.G.", - "Amini, A.", - "Bibi, S.", - "Adele, S.", - "Johnson, S.A.", - "Constantinides, B.", - "Webster, H.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Goulder, P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Mongkolsapaya, J.", - "Fry, E.E.", - "Dejnirattisai, W.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zfc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zfc", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to thioglucose.", - emdb: null, - pdb: { - dbId: "7ARF", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-19, PEPTIDE BINDING PROTEIN, Hydrolase", - 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7arf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7arf", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with SF013 (Mpro-x2193)", - emdb: null, - pdb: { - dbId: "5RHD", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "5RHD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rhd_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rhd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "KNQFDOLIXOOIGX-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Keseru, G.M.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - "Keeley, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34045440", - title: - "Exploring protein hotspots by optimized fragment pharmacophores.", - journal: "Nat Commun 12: 3201-3201 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23443-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34045440", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgk", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a highly potent antibody J08 Fab", - emdb: null, - pdb: { - dbId: "7SBU", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Antibody, Spike, Coronavirus, COVID-19, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex, neutralizing antibody, receptor binding domain", - refModels: [ - { - emdbId: null, - pdbId: "7SBU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sbu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sbu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "J08 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "J08 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Liu, H. (0000-0002-2412-7853)", "Wilson, I.A. (0000-0002-6469-2419)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35549549", - title: - "Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2120976119-e2120976119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2120976119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35549549", - pubDate: "2022", - abstract: "", - authors: [ - "Torres, J.L. (0000-0003-0137-8497)", - "Ozorowski, G. (0000-0002-9695-8138)", - "Andreano, E. (0000-0003-0088-5788)", - "Liu, H.", - "Copps, J. (0000-0003-4793-7258)", - "Piccini, G. (0000-0001-8090-7910)", - "Donnici, L. (0000-0002-9153-9102)", - "Conti, M. (0000-0003-3109-4073)", - "Planchais, C. (0000-0002-5142-7253)", - "Planas, D.", - "Manganaro, N. (0000-0001-8512-4704)", - "Pantano, E.", - "Paciello, I.", - "Pileri, P. (0000-0002-2888-8748)", - "Bruel, T. (0000-0002-3952-4261)", - "Montomoli, E. (0000-0001-7595-4974)", - "Mouquet, H. (0000-0002-4230-610X)", - "Schwartz, O.", - "Sala, C.", - "De Francesco, R.", - "Wilson, I.A. (0000-0002-6469-2419)", - "Rappuoli, R. (0000-0002-8827-254X)", - "Ward, A.B. (0000-0001-7153-3769)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sbu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sbu", - }, - }, - { - title: "The crystal structure of COVID-2019 main protease in the apo state", - emdb: null, - pdb: { - dbId: "7C2Y", - method: "X-RAY DIFFRACTION", - keywords: "COVID-2019, protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7C2Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c2y_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c2y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhang, J.", - "Zhou, H.", - "Li, J.", - "Hu, X.H.", - 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(0000-0002-9078-6697)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33027617", - title: - "An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain.", - journal: "Cell Rep 33: 108274-108274 (2020), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2020.108274", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33027617", - pubDate: "2020", - abstract: "", - authors: [ - "Wu, N.C.", - "Yuan, M.", - "Liu, H.", - "Lee, C.D.", - "Zhu, X.", - "Bangaru, S.", - "Torres, J.L.", - "Caniels, T.G.", - "Brouwer, P.J.M.", - "van Gils, M.J.", - "Sanders, R.W.", - "Ward, A.B.", - "Wilson, I.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jmo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jmo", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1587220559", - emdb: null, - pdb: { - dbId: "5REC", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5REC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rec_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rec", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "OCDMDLRMBVJKCG-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rec_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rec", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z217038356", - emdb: null, - pdb: { - dbId: "5RF9", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RF9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rf9_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rf9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "YJMLTHJLDUBVIC-VIFPVBQESA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rf9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rf9", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102254", - emdb: null, - pdb: { - dbId: "5RFX", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfx_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "AVCQLYXAEKNILW-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rfx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rfx", - }, - }, - { - title: - "Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 5c", - emdb: null, - pdb: { - dbId: "7TQ3", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TQ3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tq3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tq3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AGVPPNJLOUOQLP-XYYCENQHSA-N"], - dbauthors: [ - "Madden, T.K.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - "Picard, H.R.", - "Thruman, H.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36654747", - title: - "Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.", - journal: "Acs Pharmacol Transl Sci 6: 181-194 (2023), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00206", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36654747", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Nguyen, H.N.", - "Rathnayake, A.D.", - "Kim, Y.", - "Perera, K.D.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tq3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tq3", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000064576", - emdb: null, - pdb: { - dbId: "5RSN", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsn_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WQINSVOOIJDOLJ-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsn", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1) and S-Adenosyl-L-homocysteine (SAH).", - emdb: null, - pdb: { - dbId: "7JZ0", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, VIRAL PROTEIN, SAH, Cap-1, VIRAL PROTEIN-RNA complex", - refModels: [ - { - emdbId: null, - pdbId: "7JZ0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jz0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jz0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*U)-3')", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Brunzelle, J.S.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Structure of SARS-CoV-2 2'-O-methyltransferase heterodimer with RNA Cap analog and sulfates bound reveals new strategies for structure-based inhibitor design", - journal: "Biorxiv (2020), 2692-8205", - doi: "https://doi.org/10.1101/2020.08.03.234716", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.", - "Kiryukhina, O.", - "Brunzelle, J.", - "Satchell, K.J.F.", - ], - }, - { - pmID: "", - title: - "Structure of SARS-CoV-2 2′- O -methyltransferase heterodimer with RNA Cap analog and sulfates bound reveals new strategies for structure-based inhibitor design", - journal: "Biorxiv (2020), 2692-8205", - doi: "https://doi.org/10.1101/2020.08.03.234716", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.", - "Kiryukhina, O.", - "Brunzelle, J.", - "Satchell, K.J.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jz0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jz0", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000004787230", - emdb: null, - pdb: { - dbId: "5RSY", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsy_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DATDARDTUZHWMK-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsy", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000001601", - emdb: null, - pdb: { - dbId: "5RS8", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RS8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rs8_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rs8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QANMHLXAZMSUEX-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rs8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rs8", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Mpro at 1.90 A resolution-7", - emdb: null, - pdb: { - dbId: "7VJZ", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, SFX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VJZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vjz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vjz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["DeMirci, H. (0000-0002-9135-5397)", "Tokay, N. (0000-0003-4934-4173)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography", - journal: "Crystals 11 (2021), 2073-4352", - doi: "https://doi.org/10.3390/cryst11121579", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Guven, O.", - "Gul, M.", - "Ayan, E.", - "Johnson, J.A.", - "Cakilkaya, B.", - "Usta, G.", - "Ertem, F.B.", - "Tokay, N.", - "Yuksel, B.", - "Gocenler, O.", - "Buyukdag, C.", - "Botha, S.", - "Ketawala, G.", - "Su, Z.", - "Hayes, B.", - "Poitevin, F.", - "Batyuk, A.", - "Yoon, C.H.", - "Kupitz, C.", - "Durdagi, S.", - "Sierra, R.G.", - "DeMirci, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vjz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vjz", - }, - }, - { - title: "PALS1/MPP5 PDZ domain in complex with SARS-CoV-2_E PBM peptide", - emdb: null, - pdb: { - dbId: "7QCS", - method: "X-RAY DIFFRACTION", - keywords: - "PALS1-MPP5 PDZ domain in complex with SARS-CoV-2_E PBM peptide, CELL ADHESION", - refModels: [ - { - emdbId: null, - pdbId: "7QCS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qcs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qcs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q8N3R9", - organism: "9606", - name: "Protein PALS1", - details: "", - altNames: - "MAGUK p55 subfamily member 5,Membrane protein,palmitoylated 5,Protein associated with Lin-7 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC4", - organism: "2697049", - name: "Envelope small membrane protein", - details: "", - altNames: "E,sM protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhu, Y. (0000-0002-6841-0298)", - "Alvarez, F. (0000-0003-2950-7035)", - "Haouz, A. (0000-0003-1196-1635)", - "Mechaly, A. (0000-0002-5305-7495)", - "Caillet-Saguy, C. (0000-0001-5066-0435)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "pentameric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35283834", - title: - "Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins.", - journal: "Front Microbiol 13: 829094-829094 (2022), 1664-302X", - doi: "https://doi.org/10.3389/fmicb.2022.829094", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35283834", - pubDate: "2022", - abstract: "", - authors: [ - "Zhu, Y.", - "Alvarez, F.", - "Wolff, N.", - "Mechaly, A.", - "Brule, S.", - "Neitthoffer, B.", - "Etienne-Manneville, S.", - "Haouz, A.", - "Boeda, B.", - "Caillet-Saguy, C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qcs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qcs", - }, - }, - { - title: "Structure of SARS-CoV-2 ORF8 accessory protein", - emdb: null, - pdb: { - dbId: "7JTL", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, SARS2, Covid-19, coronavirus, accessory protein, host-factor restriction, RNA virus, immune evasion, MHC-I, open reading frame 8, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7JTL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jtl_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jtl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC8", - organism: "2697049", - name: "ORF8 protein", - details: "", - altNames: "ORF8, Non-structural protein 8, ns8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: [ - "Flower, T.G. (0000-0002-7890-6473)", - "Buffalo, C.Z. (0000-0002-8187-4660)", - "Hooy, R.M. (0000-0001-8917-0249)", - "Allaire, M.", - "Ren, X. (0000-0002-4822-4316)", - "Hurley, J.H. (0000-0001-5054-5445)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33361333", - title: - "Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein.", - journal: "Proc.Natl.Acad.Sci.USA 118 (2021), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2021785118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33361333", - pubDate: "2021", - abstract: "", - authors: [ - "Flower, T.G. (0000-0002-7890-6473)", - "Buffalo, C.Z. (0000-0002-8187-4660)", - "Hooy, R.M. (0000-0001-8917-0249)", - "Allaire, M. (0000-0002-4786-2420)", - "Ren, X. (0000-0002-4822-4316)", - "Hurley, J.H. (0000-0001-5054-5445)", - "Flower, T.G.", - "Buffalo, C.Z.", - "Hooy, R.M.", - "Allaire, M.", - "Ren, X.", - "Hurley, J.H.", - ], - }, - { - pmID: "32869027", - title: - "Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.08.27.270637", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32869027", - pubDate: "2020", - abstract: "", - authors: [ - "Flower, T.G. (0000-0002-7890-6473)", - "Buffalo, C.Z. (0000-0002-8187-4660)", - "Hooy, R.M. (0000-0001-8917-0249)", - "Allaire, M. (0000-0002-4786-2420)", - "Ren, X. (0000-0002-4822-4316)", - "Hurley, J.H. 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(0000-0002-6841-0298)", - "Haouz, A. (0000-0003-1196-1635)", - "Mechaly, A. (0000-0002-5305-7495)", - "Caillet-Saguy, C. (0000-0001-5066-0435)", - "Alvarez, F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35283834", - title: - "Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins.", - journal: "Front Microbiol 13: 829094-829094 (2022), 1664-302X", - doi: "https://doi.org/10.3389/fmicb.2022.829094", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35283834", - pubDate: "2022", - abstract: "", - authors: [ - "Zhu, Y.", - "Alvarez, F.", - "Wolff, N.", - "Mechaly, A.", - "Brule, S.", - "Neitthoffer, B.", - "Etienne-Manneville, S.", - "Haouz, A.", - "Boeda, B.", - "Caillet-Saguy, C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qcr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qcr", - }, - }, - { - title: "SARS Coronavirus-2 Main Protease 3CL-pro binding Ascorbate", - emdb: null, - pdb: { - dbId: "7MPB", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Coronavirus-2 Main Protease, 3CL-PRO, 3CLP, SARS-COV-2 MAIN PROTEASE, VIRAL PROTEIN, Hydrolase", - refModels: [ - { - emdbId: null, - pdbId: "7MPB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mpb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mpb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CIWBSHSKHKDKBQ-JLAZNSOCSA-N", "RHQDFWAXVIIEBN-UHFFFAOYSA-N"], - dbauthors: ["Schmidt, M.", "Pandey, S.", "Malla, T.N.", "Stojkovic, E.A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Vitamin C inhibits SARS coronavirus-2 main protease essential for viral replication", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.05.02.442358", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Malla, T.N.", - "Pandey, S.", - "Poudyal, I.", - "Aldama, L.", - "Feliz, D.", - "Noda, M.", - "Phillips, G.N.", - "Stojkovic, E.A.", - "Schmidt, M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mpb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mpb", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000007636250", - emdb: null, - pdb: { - dbId: "5RS9", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RS9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rs9_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rs9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IMQBKTYGTJTOGV-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rs9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rs9", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000388262", - emdb: null, - pdb: { - dbId: "5RSX", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsx_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QRMZSPFSDQBLIX-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsx", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000000226", - emdb: null, - pdb: { - dbId: "5RSO", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rso_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rso", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QCXJEYYXVJIFCE-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rso_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rso", - }, - }, - { - title: - "Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 1c", - emdb: null, - pdb: { - dbId: "7TQ2", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TQ2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tq2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tq2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["HUKBDAJESLCQRJ-SXYSDOLCSA-N"], - dbauthors: [ - "Madden, T.K.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Picard, H.R.", - "Thruman, H.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36654747", - title: - "Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.", - journal: "Acs Pharmacol Transl Sci 6: 181-194 (2023), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00206", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36654747", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Nguyen, H.N.", - "Rathnayake, A.D.", - "Kim, Y.", - "Perera, K.D.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tq2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tq2", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102974", - emdb: null, - pdb: { - dbId: "5RFY", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfy_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "CELKOAKJTFSHIV-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0002-3869-615X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32454512", - title: - "A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2.", - journal: "Nature 584: 120-124 (2020), 1476-4687", - doi: "https://doi.org/10.1038/s41586-020-2381-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32454512", - pubDate: "2020", - abstract: "", - authors: [ - "Shi, R.", - "Shan, C.", - "Duan, X.", - "Chen, Z.", - "Liu, P.", - "Song, J.", - "Song, T.", - "Bi, X.", - "Han, C.", - "Wu, L.", - "Gao, G.", - "Hu, X.", - "Zhang, Y.", - "Tong, Z.", - "Huang, W.", - "Liu, W.J.", - "Wu, G.", - "Zhang, B.", - "Wang, L.", - "Qi, J.", - "Feng, H.", - "Wang, F.S.", - "Wang, Q.", - "Gao, G.F.", - "Yuan, Z.", - "Yan, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7c01_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7c01", - }, - }, - { - title: "The crystal structure of COVID-19 main protease treated by GA", - emdb: null, - pdb: { - dbId: "7DAU", - method: "X-RAY DIFFRACTION", - keywords: "PROTEASE, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7DAU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dau_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dau", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "COVID-19 MAIN PROTEASE", - details: "", - altNames: "main protease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZBKIUFWVEIBQRT-UHFFFAOYSA-N"], - dbauthors: [ - "He, B.", - "Gong, Y.", - "He, Z.S.", - "Cao, P.", - "Jiang, H.D.", - "Gao, X.Y.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster.", - journal: "Nano Today 44 (2022), 1878-044X", - doi: "https://doi.org/10.1016/j.nantod.2022.101468", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "He, Z.", - "Ye, F.", - "Zhang, C.", - "Fan, J.", - "Du, Z.", - "Zhao, W.", - "Yuan, Q.", - "Niu, W.", - "Gao, F.", - "He, B.", - "Cao, P.", - "Zhao, L.", - "Gao, X.", - "Sun, B.", - "Dong, Y.", - "Zhao, J.", - "Qi, J.", - "Liang, X.J.", - "Jiang, H.", - "Gong, Y.", - "Tan, W.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dau_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dau", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102395", - emdb: null, - pdb: { - dbId: "5REU", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5REU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5reu_final.pdb", - externalLink: "https://pdb-redo.eu/db/5reu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "GOCXXCRVJCAULM-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgj", - }, - }, - { - title: "SARS-CoV-2 Omicron RBD in complex with Omi-9 Fab and nanobody F2", - emdb: null, - pdb: { - dbId: "7ZF4", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Omicron, RBD, antibody, Fab, Omi-3, EY6A, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZF4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zf4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zf4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody F2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-9 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-9 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I.", "Huo, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35662412", - title: - "Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.", - journal: "Cell 185: 2116-2131.e18 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.05.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35662412", - pubDate: "2022", - abstract: "", - authors: [ - "Nutalai, R.", - "Zhou, D.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Supasa, P.", - "Liu, C.", - "Huo, J.", - "Mentzer, A.J.", - "Duyvesteyn, H.M.E.", - "Dijokaite-Guraliuc, A.", - "Skelly, D.", - "Ritter, T.G.", - "Amini, A.", - "Bibi, S.", - "Adele, S.", - "Johnson, S.A.", - "Constantinides, B.", - "Webster, H.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Goulder, P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Mongkolsapaya, J.", - "Fry, E.E.", - "Dejnirattisai, W.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zf4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zf4", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with PG-COV-42 (Mpro-x2052)", - emdb: null, - pdb: { - dbId: "5RHE", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, Hydrolase-Hydrolase Inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5RHE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rhe_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rhe", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZIGOYOFMTWMITB-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. (0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rhe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rhe", - }, - }, - { - title: "Nanobody H11 and F2 bound to RBD", - emdb: null, - pdb: { - dbId: "7Z1A", - method: "X-RAY DIFFRACTION", - keywords: "spike, nanobody, high affinity, antiviral protein", - refModels: [ - { - emdbId: null, - pdbId: "7Z1A", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7z1a_final.pdb", - externalLink: "https://pdb-redo.eu/db/7z1a", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "F2 Nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "H11 Nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Naismith, J.H. (0000-0001-6744-5061)", - "Mikolajek, H. (0000-0003-0776-9974)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35858383", - title: - "Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2205412119-e2205412119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2205412119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35858383", - pubDate: "2022", - abstract: "", - authors: [ - "Mikolajek, H. (0000-0003-0776-9974)", - "Weckener, M. (0000-0002-1419-9378)", - "Brotzakis, Z.F.", - "Huo, J.", - "Dalietou, E.V.", - "Le Bas, A.", - "Sormanni, P. (0000-0002-6228-2221)", - "Harrison, P.J.", - "Ward, P.N. (0000-0003-2546-3426)", - "Truong, S. (0000-0001-9624-4461)", - "Moynie, L. (0000-0002-4097-4331)", - "Clare, D.K.", - "Dumoux, M.", - "Dormon, J.", - "Norman, C.", - "Hussain, N. (0000-0002-5170-0061)", - "Vogirala, V. (0000-0002-8534-3736)", - "Owens, R.J. (0000-0002-3705-2993)", - "Vendruscolo, M. (0000-0002-3616-1610)", - "Naismith, J.H. (0000-0001-6744-5061)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z1a_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z1a", - }, - }, - { - title: - "Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)", - emdb: null, - pdb: { - dbId: "6Y2G", - method: "X-RAY DIFFRACTION", - keywords: - "Novel coronavirus, alpha-ketoamide, antiviral, drug design, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6Y2G", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6y2g_final.pdb", - externalLink: "https://pdb-redo.eu/db/6y2g", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DHMQDGOQFOQNFH-UHFFFAOYSA-N", "FRACPXUHUTXLCX-BELIEFIBSA-N"], - dbauthors: [ - "Hilgenfeld, R. (0000-0001-8850-2977)", - "Zhang, L. (0000-0002-4642-9617)", - "Lin, D. (0000-0002-4271-5739)", - "Sun, X. (0000-0002-2761-2862)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32198291", - title: - "Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.", - journal: "Science 368: 409-412 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abb3405", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32198291", - pubDate: "2020", - abstract: "", - authors: [ - "Zhang, L.", - "Lin, D.", - "Sun, X.", - "Curth, U.", - "Drosten, C.", - "Sauerhering, L.", - "Becker, S.", - "Rox, K.", - "Hilgenfeld, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6y2g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6y2g", - }, - }, - { - title: "SARS-CoV-2 Omicron RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs", - emdb: null, - pdb: { - dbId: "7ZFB", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Omicron, BA.1, BA.2, RBD, antibody, Fab, Omi-18, Omi-31, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZFB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zfb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zfb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody C1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-31 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-31 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-18 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-18 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I.", "Huo, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35662412", - title: - "Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.", - journal: "Cell 185: 2116-2131.e18 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.05.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35662412", - pubDate: "2022", - abstract: "", - authors: [ - "Nutalai, R.", - "Zhou, D.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Supasa, P.", - "Liu, C.", - "Huo, J.", - "Mentzer, A.J.", - "Duyvesteyn, H.M.E.", - "Dijokaite-Guraliuc, A.", - "Skelly, D.", - "Ritter, T.G.", - "Amini, A.", - "Bibi, S.", - "Adele, S.", - "Johnson, S.A.", - "Constantinides, B.", - "Webster, H.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Goulder, P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Mongkolsapaya, J.", - "Fry, E.E.", - "Dejnirattisai, W.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zfb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zfb", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB46", - emdb: null, - pdb: { - dbId: "7TIU", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TIU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tiu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tiu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "YPCVDTHFTGPBJP-VERUCKTNSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Liu, H.", - "Huang, Y.", - "Li, W.", - "Lee, S.", - "Ho, D.D.", - "Hurst, B.", - "Forouhar, F.", - "Iketani, S.", - "Zack, A.", - "Khanizeman, N.", - "Bednarova, E.", - "Fowler, B.", - "Hong, S.J.", - "Mohri, H.", - "Nair, M.S.", - "Tay, N.E.S.", - "Karan, C.", - "Resnick, S.J.", - "Quinn, C.", - "Shion, H.", - "Jurtschenko, C.", - "Lauber, M.A.", - "McDonald, T.", - "Rovis, T.", - 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4a_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4a", - }, - }, - { - title: "Structure of the SARS-COV-2 main protease with 337 inhibitor", - emdb: null, - pdb: { - dbId: "7WYM", - method: "X-RAY DIFFRACTION", - keywords: - "Structure of the SARS-COV-2 main protease with 337 inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WYM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wym_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wym", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZPJNBQRFMJDXHX-UHFFFAOYSA-N"], - dbauthors: ["Gao, X.", "Qin, B.", "Cui, S.", "Hou, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35702321", - title: - "Acrylamide fragment inhibitors that induce unprecedented conformational distortions in enterovirus 71 3C and SARS-CoV-2 main protease.", - journal: "Acta Pharm Sin B 12: 3924-3933 (2022), 2211-3835", - doi: "https://doi.org/10.1016/j.apsb.2022.06.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35702321", - pubDate: "2022", - abstract: "", - authors: [ - "Qin, B.", - "Craven, G.B.", - "Hou, P.", - "Chesti, J.", - "Lu, X.", - "Child, E.S.", - "Morgan, R.M.L.", - "Niu, W.", - "Zhao, L.", - "Armstrong, A.", - "Mann, D.J.", - "Cui, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wym_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wym", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2072621991", - emdb: null, - pdb: { - dbId: "5SLZ", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slz_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "GFKMUMPBDKROCT-OCAPTIKFSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slz", - }, - }, - { - title: - "Improved Feline Drugs as SARS-CoV-2 Mpro Inhibitors: Structure-Activity Studies & Micellar Solubilization for Enhanced Bioavailability", - emdb: null, - pdb: { - dbId: "7LCT", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, 3CLpro, coronavirus, main protease, kinetics, SARS, VIRAL PROTEIN, Hydrolase-Hydrolase Inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LCT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lct_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lct", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["TTWGQXYYGIKZJA-WNHJNPCNSA-N"], - dbauthors: [ - "Khan, M.B. (0000-0002-4164-9573)", - "Lemieux, M.J. (0000-0003-4745-9153)", - "Arutyunova, E.", - "Young, H.S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli O103:H2", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34118724", - title: - "Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies.", - journal: "Eur.J.Med.Chem. 222: 113584-113584 (2021), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2021.113584", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34118724", - pubDate: "2021", - abstract: "", - authors: [ - "Vuong, W.", - "Fischer, C.", - "Khan, M.B.", - "van Belkum, M.J.", - "Lamer, T.", - "Willoughby, K.D.", - "Lu, J.", - "Arutyunova, E.", - "Joyce, M.A.", - "Saffran, H.A.", - "Shields, J.A.", - "Young, H.S.", - "Nieman, J.A.", - "Tyrrell, D.L.", - "Lemieux, M.J.", - "Vederas, J.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lct_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lct", - }, - }, - { - title: - "The crystal structure of SARS-CoV-2 Main Protease in complex with demethylated analog of masitinib", - emdb: null, - pdb: { - dbId: "7L5D", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-COV-2, COVID-19, 3CL, MAIN PROTEASE, MASITINIB, demethylation, analog, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7L5D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l5d_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l5d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LBWSNUMFQJZFGI-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Joachimiak, A. (0000-0003-2535-6209)", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Tan, K. 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"Lima, G.M.A.", - "Rosa, H.V.D.", - "Pereira, H.D.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "Freire, M.C.L.C.", - "Fearon, D.", - "Douangamath, A.", - "von Delft, F.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kfi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kfi", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z71580604", - emdb: null, - pdb: { - dbId: "5SMI", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SMI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5smi_final.pdb", - externalLink: "https://pdb-redo.eu/db/5smi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - 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(0000-0002-6989-639X)", - "Yu, W. (0000-0002-4025-2646)", - "Hua, Y.", - "Tien, H. (0000-0001-7584-5989)", - "Rogers, T.F. (0000-0001-9756-327X)", - "Landais, E. (0000-0002-8183-5565)", - "Sok, D. (0000-0002-9354-1740)", - "Jardine, J.G. (0000-0001-8951-1074)", - "Burton, D.R. (0000-0001-6711-9864)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Yuan, M.", - "Liu, H.", - "Wu, N.C.", - "Lee, C.D.", - "Zhu, X.", - "Zhao, F.", - "Huang, D.", - "Yu, W.", - "Tien, H.", - "Rogers, T.F.", - "Landais, E.", - "Sok, D.", - "Jardine, J.G.", - "Burton, D.R.", - "Wilson, I.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xc2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xc2", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000893191027 - (S) and (R) isomers", - emdb: null, - pdb: { - dbId: "5SOV", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sov_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sov", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KOOLXXAPHSXXFR-NSHDSACASA-N", "KOOLXXAPHSXXFR-LLVKDONJSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sov_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sov", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z28290384", - emdb: null, - pdb: { - dbId: "5SLM", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slm_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "GIUMGIOTJZLCCG-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slm", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 helicase in complex with AMP-PNP", - emdb: null, - pdb: { - dbId: "7NN0", - method: "X-RAY DIFFRACTION", - keywords: "NSP13, Helicase, SARS-CoV-2, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7NN0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nn0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nn0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "SARS-CoV-2 helicase NSP13", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,SARS-CoV-2 helicase NSP13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PVKSNHVPLWYQGJ-KQYNXXCUSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Yosaatmadja, Y.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - "Douangamath, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34381037", - title: - "Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.", - journal: "Nat Commun 12: 4848-4848 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-25166-6", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34381037", - pubDate: "2021", - abstract: "", - authors: [ - "Newman, J.A. (0000-0003-4488-0516)", - "Douangamath, A. (0000-0002-9196-8644)", - "Yadzani, S. (0000-0002-9205-4318)", - "Yosaatmadja, Y. (0000-0003-2875-5993)", - "Aimon, A. (0000-0002-9135-129X)", - "Brandao-Neto, J.", - "Dunnett, L.", - "Gorrie-Stone, T.", - "Skyner, R. (0000-0003-3614-6661)", - "Fearon, D. (0000-0003-3529-7863)", - "Schapira, M. (0000-0002-1047-3309)", - "von Delft, F.", - "Gileadi, O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nn0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nn0", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, methylated)", - emdb: null, - pdb: { - dbId: "7KQW", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7KQW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kqw_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kqw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Young, I.D. (0000-0003-4713-9504)", - "Thompson, M.C. (0000-0002-6099-2027)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kqw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kqw", - }, - }, - { - title: - "Room-temperature X-ray structure of SARS-CoV-2 main protease (3CL Mpro) in complex with a non-covalent inhibitor Mcule-5948770040", - emdb: null, - pdb: { - dbId: "7LTJ", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, viral protease, SARS-CoV-2, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LTJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ltj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ltj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XREZIAMDGRLMGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34793155", - title: - "High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor.", - journal: "J.Chem.Inf.Model. 62: 116-128 (2022), 1549-960X", - doi: "https://doi.org/10.1021/acs.jcim.1c00851", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34793155", - pubDate: "2022", - abstract: "", - authors: [ - "Clyde, A.", - "Galanie, S.", - "Kneller, D.W. (0000-0002-5416-5789)", - "Ma, H.", - "Babuji, Y.", - "Blaiszik, B.", - "Brace, A.", - "Brettin, T.", - "Chard, K.", - "Chard, R.", - "Coates, L. (0000-0003-2342-049X)", - "Foster, I.", - "Hauner, D.", - "Kertesz, V. (0000-0003-0186-5797)", - "Kumar, N. (0000-0001-6713-2129)", - "Lee, H.", - "Li, Z.", - "Merzky, A.", - "Schmidt, J.G.", - "Tan, L.", - "Titov, M.", - "Trifan, A.", - "Turilli, M.", - "Van Dam, H.", - "Chennubhotla, S.C.", - "Jha, S.", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Ramanathan, A. (0000-0002-1622-5488)", - "Head, M.S.", - "Stevens, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ltj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ltj", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with its receptor human ACE2", - emdb: null, - pdb: { - dbId: "7WBP", - method: "X-RAY DIFFRACTION", - keywords: "Complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WBP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wbp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wbp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: ["Han, P.", "Qi, J. (0000-0002-9358-4732)"], - details: [ - { - sample: { - name: "", - exprSystem: "Insect cell expression vector pTIE1", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35093192", - title: - "Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2.", - journal: "Cell 185: 630-640.e10 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.01.001", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35093192", - pubDate: "2022", - abstract: "", - authors: [ - "Han, P.", - "Li, L.", - "Liu, S.", - "Wang, Q.", - "Zhang, D.", - "Xu, Z.", - "Li, X.", - "Peng, Q.", - "Su, C.", - "Huang, B.", - "Li, D.", - "Zhang, R.", - "Tian, M.", - "Fu, L.", - "Gao, Y.", - "Zhao, X.", - "Liu, K.", - "Qi, J.", - "Gao, G.F.", - "Wang, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wbp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wbp", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with the HCV NS3/4A inhibitor boceprevir", - emdb: null, - pdb: { - dbId: "7NBR", - method: "X-RAY DIFFRACTION", - keywords: - "Coronavirus, main protease, drug repurposing, hepatitis C virus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NBR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nbr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nbr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FEBWCINGHXXUCV-GFLQDLJJSA-N", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Hilgenfeld, R. (0000-0001-8850-2977)", - "Zhang, L. (0000-0002-4642-9617)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-CoV-2 main protease (Mpro) in complex with the HCV NS3/4A inhibitor boceprevir", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Zhang, L. (0000-0002-4642-9617)", - "Hilgenfeld, R. (0000-0001-8850-2977)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nbr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nbr", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 19b", - emdb: null, - pdb: { - dbId: "7LZV", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LZV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lzv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lzv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SXLHHGJXSMBQOQ-JWWIWJDOSA-N", - "SXLHHGJXSMBQOQ-VERUCKTNSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Miller, M.J.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Perera, K.D.", - "Rathnayake, A.D.", - "Jesri, A.R.M.", - "Baird, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34865476", - title: - "Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.", - journal: "J.Med.Chem. 64: 17846-17865 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34865476", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Jesri, A.M.", - "Nguyen, H.N.", - "Miller, M.J.", - "Thurman, H.A.", - "Zheng, J.", - "Kashipathy, M.M.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Kim, Y.", - "Groutas, W.C.", - "Chang, K.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lzv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lzv", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 NendoU in complex with Z18197050", - emdb: null, - pdb: { - dbId: "7N7Y", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7N7Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n7y_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n7y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XLOVNJUCAFIANM-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n7y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n7y", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (2019-NCoV) main protease in complex with 5-(3-{3-chloro-5-[(5-methyl-1,3-thiazol-4-yl)methoxy]phenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl)pyrimidine-2,4(1H,3H)-dione (compound 13)", - emdb: null, - pdb: { - dbId: "7N44", - method: "X-RAY DIFFRACTION", - keywords: "novel coronavirus, antiviral, drug design, viral protein, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7N44", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n44_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n44", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RJHJFSODWKKAIP-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, C.H.", - "Deshmukh, M.G. (0000-0002-3704-3229)", - "Ippolito, J.A. (0000-0002-1461-3372)", - "Jorgensen, W.L. (0000-0002-3993-9520)", - "Anderson, K.S. (0000-0003-3433-0780)", - "Reilly, R.A. (0000-0001-7488-0088)", - "Hollander, K. (0000-0002-4718-6557)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34408808", - title: - "Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency.", - journal: "Acs Med.Chem.Lett. 12: 1325-1332 (2021), 1948-5875", - doi: "https://doi.org/10.1021/acsmedchemlett.1c00326", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34408808", - pubDate: "2021", - abstract: "", - authors: [ - "Zhang, C.H.", - "Spasov, K.A.", - "Reilly, R.A.", - "Hollander, K.", - "Stone, E.A.", - "Ippolito, J.A.", - "Liosi, M.E.", - "Deshmukh, M.G.", - "Tirado-Rives, J.", - "Zhang, S.", - "Liang, Z.", - "Miller, S.J.", - "Isaacs, F.", - "Lindenbach, B.D.", - "Anderson, K.S.", - "Jorgensen, W.L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n44_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n44", - }, - }, - { - title: "SARS-CoV-2 Macrodomain in complex with ADP-ribose", - emdb: null, - pdb: { - dbId: "6Z5T", - method: "X-RAY DIFFRACTION", - keywords: - "Viral Macrodomain, ADP-ribose binding module, ADP-ribosylhydrolase, ADP-ribosylation, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6Z5T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6z5t_final.pdb", - externalLink: "https://pdb-redo.eu/db/6z5t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-KEOHHSTQSA-N", "FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: [ - "Ahel, I. (0000-0002-9446-3756)", - "Zorzini, V. (0000-0002-8727-309X)", - "Rack, J. (0000-0001-8341-6439)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33202171", - title: - "Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential.", - journal: "Open Biology 10: 200237-200237 (2020), 2046-2441", - doi: "https://doi.org/10.1098/rsob.200237", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33202171", - pubDate: "2020", - abstract: "", - authors: [ - "Rack, J.G.M.", - "Zorzini, V.", - "Zhu, Z.", - "Schuller, M.", - "Ahel, D.", - "Ahel, I.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6z5t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6z5t", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 8b", - emdb: null, - pdb: { - dbId: "7LZT", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LZT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lzt_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lzt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "ZJKUZJJPWZXFHP-LIUHCEAOSA-N", - "ZJKUZJJPWZXFHP-VUGRZMFUSA-N", - ], - dbauthors: [ - "Miller, M.J.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Perera, K.D.", - "Rathnayake, A.D.", - "Jesri, A.R.M.", - "Baird, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34865476", - title: - "Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.", - journal: "J.Med.Chem. 64: 17846-17865 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34865476", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Jesri, A.M.", - "Nguyen, H.N.", - "Miller, M.J.", - "Thurman, H.A.", - "Zheng, J.", - "Kashipathy, M.M.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Kim, Y.", - "Groutas, W.C.", - "Chang, K.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lzt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lzt", - }, - }, - { - title: - "Joint X-ray/neutron structure of SARS-CoV-2 main protease (Mpro) in complex with Mcule5948770040", - emdb: null, - pdb: { - dbId: "7N8C", - method: "X-RAY DIFFRACTION", - keywords: "cysteine protease, inhibitor complex, protonation states, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7N8C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n8c_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n8c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XREZIAMDGRLMGZ-UHFFFAOYSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34705466", - title: - "Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.", - journal: "J.Med.Chem. 64: 17366-17383 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01475", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34705466", - pubDate: "2021", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Li, H. (0000-0002-6964-9962)", - "Galanie, S.", - "Phillips, G.", - "Labbe, A.", - "Weiss, K.L. (0000-0002-6486-8007)", - "Zhang, Q.", - "Arnould, M.A.", - "Clyde, A.", - "Ma, H.", - "Ramanathan, A. (0000-0002-1622-5488)", - "Jonsson, C.B. (0000-0002-2640-7672)", - "Head, M.S.", - "Coates, L. (0000-0003-2342-049X)", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n8c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n8c", - }, - }, - { - title: "PanDDA analysis group deposition of ground-state model of SARS-CoV-2 NSP14", - emdb: null, - pdb: { - dbId: "5SMK", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5SMK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5smk_final.pdb", - externalLink: "https://pdb-redo.eu/db/5smk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "NBIIXXVUZAFLBC-UHFFFAOYSA-K"], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition of ground-state model", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Newman, J.A.", - "Yosaatmadja, Y.", - "Douangamath, A.", - "Aimon, A.", - "Powell, A.J.", - "Dias, A.", - "Fearon, D.", - "Dunnett, L.", - "Brandao-Neto, J.", - "Krojer, T.", - "Skyner, R.", - "Gorrie-Stone, T.", - "Thompson, W.", - "von Delft, F.", - "Arrowsmith, C.H.", - "Edwards, A.", - "Bountra, C.", - "Gileadi, O.", - "Imprachim, N.", - "von-Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5smk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5smk", - }, - }, - { - title: "Crystal structure from SARS-COV2 NendoU NSP15", - emdb: null, - pdb: { - dbId: "7KEG", - method: "X-RAY DIFFRACTION", - keywords: - "NSP15, NendoU, covid-19, covid, sars, sars-cov-2, endoribonuclease, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7KEG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7keg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7keg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NBIIXXVUZAFLBC-UHFFFAOYSA-K"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Oliveira, K.I.Z.", - "Pereira, H.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7keg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7keg", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z56983806", - emdb: null, - pdb: { - dbId: "5SLO", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slo_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "MLUHWTUFJZKUST-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slo", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000292637864 - (R) and (S) isomers", - emdb: null, - pdb: { - dbId: "5SOT", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sot_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sot", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ASNUGOSBOWLSJV-LLVKDONJSA-N", "ASNUGOSBOWLSJV-NSHDSACASA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sot_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sot", - }, - }, - { - title: "SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-89", - emdb: null, - pdb: { - dbId: "7LBR", - method: "X-RAY DIFFRACTION", - keywords: - "papain-like protease, coronavirus inhibitor, SARS-CoV-2, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LBR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lbr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lbr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "IGVYCVBUHQMNRZ-RZTXVSJASA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Ratia, K.M. (0000-0002-4834-9207)", - "Xiong, R. (0000-0002-6350-9037)", - "Thatcher, G.R. (0000-0002-7757-1739)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33594371", - title: - "Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.02.13.431008", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33594371", - pubDate: "2021", - abstract: "", - authors: [ - "Shen, Z.", - "Ratia, K.", - "Cooper, L.", - "Kong, D.", - "Lee, H.", - "Kwon, Y.", - "Li, Y.", - "Alqarni, S.", - "Huang, F.", - "Dubrovskyi, O.", - "Rong, L.", - "Thatcher, G.R.", - "Xiong, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lbr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lbr", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with COVOX-45 and beta-6 Fabs", - emdb: null, - pdb: { - dbId: "7PRY", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 alpha variant, beta variant, gamma variant, delta variant, B.1.1.7, B.1.351, P.1, B.1.617.2, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7PRY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7pry_final.pdb", - externalLink: "https://pdb-redo.eu/db/7pry", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-45 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-45 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-6 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Beta-6 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34921776", - title: - "The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.", - journal: "Cell Host Microbe 30 (2022), 1934-6069", - doi: "https://doi.org/10.1016/j.chom.2021.11.013", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34921776", - pubDate: "2022", - abstract: "", - authors: [ - "Liu, C.", - "Zhou, D.", - "Nutalai, R.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Dejnirattisai, W.", - "Supasa, P.", - "Mentzer, A.J.", - "Wang, B.", - "Case, J.B.", - "Zhao, Y.", - "Skelly, D.T.", - "Chen, R.E.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Malik, T.", - "Temperton, N.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Clare, D.K.", - "Howe, A.", - "Goulder, P.J.R.", - "Fry, E.E.", - "Diamond, M.S.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Afonine, P.V.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7pry_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7pry", - }, - }, - { - title: "Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N351-359", - emdb: null, - pdb: { - dbId: "7KGO", - method: "X-RAY DIFFRACTION", - keywords: - "HLA-A*0201, T cell, SARS-CoV-2, COVID-19, viral peptide, TCR, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "7KGO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kgo_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kgo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PXHVJJICTQNCMI-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "WLZRMCYVCSSEQC-UHFFFAOYSA-N", - ], - dbauthors: [ - "Gras, S.", - "Chatzileontiadou, D.S.M.", - "Szeto, C.", - "Riboldi-Tunnicliffe, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33521593", - title: - "The presentation of SARS-CoV-2 peptides by the common HLA-A * 02:01 molecule.", - journal: "Iscience 24: 102096-102096 (2021), 2589-0042", - doi: "https://doi.org/10.1016/j.isci.2021.102096", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33521593", - pubDate: "2021", - abstract: "", - authors: [ - "Szeto, C.", - "Chatzileontiadou, D.S.M.", - "Nguyen, A.T.", - "Sloane, H.", - "Lobos, C.A.", - "Jayasinghe, D.", - "Halim, H.", - "Smith, C.", - "Riboldi-Tunnicliffe, A.", - "Grant, E.J.", - "Gras, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kgo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kgo", - }, - }, - { - title: - "Structure of SARS-CoV-2 Gamma variant spike receptor-binding domain complexed with human ACE2", - emdb: null, - pdb: { - dbId: "7EKC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, spike, RBD, 501Y.V3, ACE2, VIRAL PROTEIN, HYDROLASE-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7EKC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ekc_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ekc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Gao, G.F. (0000-0002-3869-615X)", - "Su, C. (0000-0002-5824-7968)", - "Qi, J.X. (0000-0002-9358-4732)", - "Han, P.C. (0000-0002-4551-6209)", - "Zhang, Y.F. (0000-0003-3026-3357)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34671049", - title: - "Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.", - journal: "Nat Commun 12: 6103-6103 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-26401-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34671049", - pubDate: "2021", - abstract: "", - authors: [ - "Han, P.", - "Su, C. (0000-0002-5824-7968)", - "Zhang, Y.", - "Bai, C.", - "Zheng, A.", - "Qiao, C.", - "Wang, Q.", - "Niu, S.", - "Chen, Q.", - "Li, W.", - "Liao, H.", - "Li, J.", - "Zhang, Z.", - "Cho, H.", - "Yang, M.", - "Rong, X.", - "Hu, Y.", - "Huang, N. (0000-0002-6912-033X)", - "Yan, J. (0000-0003-0502-3829)", - "Wang, Q. (0000-0003-3768-0401)", - "Zhao, X. (0000-0002-2001-1343)", - "Gao, G.F. (0000-0002-3869-615X)", - "Qi, J. 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emdb: null, - pdb: { - dbId: "5SLX", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slx_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "WFXLRLQSHRNHCE-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slx", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-100112", - emdb: null, - pdb: { - dbId: "5SAH", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SAH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sah_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sah", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VQKHNWPVBIRRNP-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sah_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sah", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z1954800348", - emdb: null, - pdb: { - dbId: "5S4C", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S4C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s4c_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s4c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEHDFSFYZKSKGH-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4c", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody nCoV617", - emdb: null, - pdb: { - dbId: "7E3O", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, S-RBD, RBS-C, native human monoclonal antibody, therapeutic antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7E3O", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e3o_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e3o", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "nCoV617 Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "nCoV617 Heigh Chain", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Yang, M.", "Chen, S.D."], - details: [ - { - sample: { - name: "", - exprSystem: "Mammalian expression vector HA-MCS-pcDNA3.1", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34643438", - title: - "Structural Basis of a Human Neutralizing Antibody Specific to the SARS-CoV-2 Spike Protein Receptor-Binding Domain.", - journal: "Microbiol Spectr 9: e0135221-e0135221 (2021), 2165-0497", - doi: "https://doi.org/10.1128/Spectrum.01352-21", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34643438", - pubDate: "2021", - abstract: "", - authors: [ - "Yang, M.", - "Li, J.", - "Huang, Z.", - "Li, H.", - "Wang, Y.", - "Wang, X.", - "Kang, S.", - "Huang, X.", - "Wu, C.", - "Liu, T.", - "Jia, Z.", - "Liang, J.", - "Yuan, X.", - "He, S.", - "Chen, X.", - "Zhou, Z.", - "Chen, Q.", - "Liu, S.", - "Zheng, H.", - "Liu, X.", - "Li, K.", - "Yao, X.", - "Lang, B.", - "Liu, L.", - "Liao, H.X.", - "Chen, S. (0000-0002-7634-2141)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e3o_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e3o", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with NCL-00024773", - emdb: null, - pdb: { - dbId: "5S45", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S45", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s45_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s45", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["INCAMIFWGMKSNK-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s45_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s45", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 8", - emdb: null, - pdb: { - dbId: "7B77", - method: "X-RAY DIFFRACTION", - keywords: "Inhibitor, complex, protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7B77", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7b77_final.pdb", - externalLink: "https://pdb-redo.eu/db/7b77", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "IKYIQYHISJXELQ-UHFFFAOYSA-N"], - dbauthors: ["Talibov, V.O. (0000-0002-1135-2744)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35142215", - title: - "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", - journal: "J.Am.Chem.Soc. 144: 2905-2920 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08402", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35142215", - pubDate: "2022", - abstract: "", - authors: [ - "Luttens, A. (0000-0003-2915-7901)", - "Gullberg, H.", - "Abdurakhmanov, E.", - "Vo, D.D.", - "Akaberi, D. (0000-0002-9595-9796)", - "Talibov, V.O.", - "Nekhotiaeva, N.", - "Vangeel, L.", - "De Jonghe, S. (0000-0002-3872-6558)", - "Jochmans, D.", - "Krambrich, J.", - "Tas, A.", - "Lundgren, B.", - "Gravenfors, Y. (0000-0001-6025-4908)", - "Craig, A.J.", - "Atilaw, Y.", - "Sandstrom, A.", - "Moodie, L.W.K. (0000-0002-9500-4535)", - "Lundkvist, A.", - "van Hemert, M.J.", - "Neyts, J.", - "Lennerstrand, J.", - "Kihlberg, J. (0000-0002-4205-6040)", - "Sandberg, K.", - "Danielson, U.H. (0000-0003-2728-0340)", - "Carlsson, J. 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(0000-0002-5214-1572)", - "Iketani, S. (0000-0002-3733-9556)", - "Zask, A.", - "Khanizeman, N.", - "Bednarova, E.", - "Forouhar, F.", - "Fowler, B.", - "Hong, S.J.", - "Mohri, H.", - "Nair, M.S. (0000-0002-5994-3957)", - "Huang, Y. (0000-0001-6270-1644)", - "Tay, N.E.S.", - "Lee, S.", - "Karan, C.", - "Resnick, S.J.", - "Quinn, C.", - "Li, W.", - "Shion, H.", - "Xia, X.", - "Daniels, J.D.", - "Bartolo-Cruz, M.", - "Farina, M.", - "Rajbhandari, P.", - "Jurtschenko, C.", - "Lauber, M.A.", - "McDonald, T.", - "Stokes, M.E.", - "Hurst, B.L. (0000-0003-1025-5878)", - "Rovis, T. (0000-0001-6287-8669)", - "Chavez, A. (0000-0001-5626-7140)", - "Ho, D.D. (0000-0003-1627-149X)", - "Stockwell, B.R. (0000-0002-3532-3868)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tiw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tiw", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with ebselen", - emdb: null, - pdb: { - dbId: "7M1Y", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7M1Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7m1y_final.pdb", - externalLink: "https://pdb-redo.eu/db/7m1y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "KWTUCBZCJBVRTM-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "PGLTVOMIXTUURA-UHFFFAOYSA-N", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Maltseva, N.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with ebselen", - journal: "to be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Maltseva, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m1y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m1y", - }, - }, - { - title: "Nanobody H11-B5 and H11-F2 bound to RBD", - emdb: null, - pdb: { - dbId: "7Z1C", - method: "X-RAY DIFFRACTION", - keywords: "spike, nanobody, high affinity, antiviral protein", - refModels: [ - { - emdbId: null, - pdbId: "7Z1C", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7z1c_final.pdb", - externalLink: "https://pdb-redo.eu/db/7z1c", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody F2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody B5", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "MTHSVFCYNBDYFN-UHFFFAOYSA-N"], - dbauthors: [ - "Naismith, J.H. (0000-0001-6744-5061)", - "Mikolajek, H. (0000-0003-0776-9974)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35858383", - title: - "Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2205412119-e2205412119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2205412119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35858383", - pubDate: "2022", - abstract: "", - authors: [ - "Mikolajek, H. (0000-0003-0776-9974)", - "Weckener, M. (0000-0002-1419-9378)", - "Brotzakis, Z.F.", - "Huo, J.", - "Dalietou, E.V.", - "Le Bas, A.", - "Sormanni, P. (0000-0002-6228-2221)", - "Harrison, P.J.", - "Ward, P.N. (0000-0003-2546-3426)", - "Truong, S. (0000-0001-9624-4461)", - "Moynie, L. (0000-0002-4097-4331)", - "Clare, D.K.", - "Dumoux, M.", - "Dormon, J.", - "Norman, C.", - "Hussain, N. (0000-0002-5170-0061)", - "Vogirala, V. (0000-0002-8534-3736)", - "Owens, R.J. (0000-0002-3705-2993)", - "Vendruscolo, M. (0000-0002-3616-1610)", - "Naismith, J.H. (0000-0001-6744-5061)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z1c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z1c", - }, - }, - { - title: "Room temperature In-situ SARS-CoV-2 MPRO with bound ABT-957", - emdb: null, - pdb: { - dbId: "7QT8", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Dimer, Main protease, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7QT8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qt8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qt8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LGWQYJCCERJRJX-MZKUHISZSA-N"], - dbauthors: [ - "Owen, C.D. (0000-0001-5774-8202)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Lukacik, P.", - "Strain-Damerell, C.", - "Horrell, S. (0000-0001-6355-8640)", - "Gildae, R.J. (0000-0001-5038-6958)", - "Axford, D.", - "Owen, R.L. (0000-0002-2104-7057)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35647922", - title: "xia2.multiplex: a multi-crystal data-analysis pipeline.", - journal: - "Acta Crystallogr D Struct Biol 78: 752-769 (2022), 2059-7983", - doi: "https://doi.org/10.1107/S2059798322004399", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35647922", - pubDate: "2022", - abstract: "", - authors: [ - "Gildea, R.J. (0000-0001-5038-6958)", - "Beilsten-Edmands, J.", - "Axford, D. (0000-0001-7694-8525)", - "Horrell, S. (0000-0001-6355-8640)", - "Aller, P. (0000-0002-1793-7030)", - "Sandy, J. (0000-0002-6271-2084)", - "Sanchez-Weatherby, J. (0000-0001-5893-9641)", - "Owen, C.D.", - "Lukacik, P.", - "Strain-Damerell, C.", - "Owen, R.L. 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(0000-0001-9366-1470)", - "Wang, R. (0000-0002-8040-7913)", - "Ju, B.", - "Zhang, Q.", - "Sun, J.", - "Chen, P. (0000-0002-9041-8392)", - "Zhang, S. (0000-0003-1703-3848)", - "Tian, Y. (0000-0001-9343-4024)", - "Shan, S. (0000-0002-7184-6818)", - "Cheng, L.", - "Zhou, B.", - "Song, S.", - "Zhao, J.", - "Wang, H.", - "Shi, X.", - "Ding, Q. (0000-0002-6226-869X)", - "Liu, L.", - "Zhao, J. (0000-0003-2515-5589)", - "Zhang, Z. (0000-0002-3544-1389)", - "Wang, X.", - "Zhang, L. 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(0000-0003-3782-5279)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33264373", - title: - "Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein.", - journal: "Plos Pathog. 16: e1009100-e1009100 (2020), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1009100", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33264373", - pubDate: "2020", - abstract: "", - authors: [ - "Dinesh, D.C. (0000-0001-9125-4775)", - "Chalupska, D. (0000-0002-9666-4228)", - "Silhan, J.", - "Koutna, E.", - "Nencka, R. (0000-0001-6167-0380)", - "Veverka, V. (0000-0003-3782-5279)", - "Boura, E. 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(0000-0002-3426-4210)", - "Duyvesteyn, H.M.", - "Openshaw, P.J.", - "Huang, K.Y.A.", - ], - }, - { - pmID: "34981049", - title: - "Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.", - journal: "Biorxiv (2021), 2692-8205", - doi: "https://doi.org/10.1101/2021.12.03.471045", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34981049", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Huo, J.", - "Zhou, D.", - "Zahradnik, J.", - "Supasa, P.", - "Liu, C.", - "Duyvesteyn, H.M.E.", - "Ginn, H.M.", - "Mentzer, A.J.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Dijokaite, A.", - "Khan, S.", - "Avinoam, O.", - "Bahar, M.", - "Skelly, D.", - "Adele, S.", - "Johnson, S.A.", - "Amini, A.", - "Ritter, T.G.", - "Mason, C.", - "Dold, C.", - "Pan, D.", - "Assadi, S.", - "Bellass, A.", - "Omo-Dare, N.", - "Koeckerling, D.", - "Flaxman, A.", - "Jenkin, D.", - "Aley, P.K.", - "Voysey, M.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Baillie, V.", - "Serafin, N.", - "Kwatra, G.", - "Da Silva, K.", - "Madhi, S.A.", - "Nunes, M.C.", - "Malik, T.", - "Openshaw, P.J.M.", - "Baillie, J.K.", - "Semple, M.G.", - "Townsend, A.R.", - "Huang, K.A.", - "Tan, T.K.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Constantinides, B.", - "Webster, H.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Schreiber, G.", - "Stuart, D.I.", - "Screaton, G.R.", - "Ritter, T.", - "Voysey, M. (0000-0001-6324-6559)", - "Resende, P.C. (0000-0002-2884-3662)", - "Ditse, Z.", - "Silva, K.D.", - "Madhi, S.", - "Openshaw, P.J. (0000-0002-7220-2555)", - "Baillie, J.K. (0000-0001-5258-793X)", - "Semple, M.G. (0000-0001-9700-0418)", - "Townsend, A.R. (0000-0002-3702-0107)", - "Tan, T.K. (0000-0001-8746-8308)", - "Stuart, D.I. (0000-0002-3426-4210)", - "Duyvesteyn, H.M.", - "Openshaw, P.J.", - "Huang, K.Y.A.", - ], - }, - { - pmID: "", - title: - "SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses", - journal: "Cell(Cambridge,Mass.) (2022), 0092-8674", - doi: "https://doi.org/10.1016/j.cell.2021.12.046", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Huo, J.", - "Zhou, D.", - "Zahradnik, J.", - "Supasa, P.", - "Liu, C.", - "Duyvesteyn, H.M.E.", - "Ginn, H.M.", - "Mentzer, A.J.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Dijokaite, A.", - "Khan, S.", - "Avinoam, O.", - "Bahar, M.", - "Skelly, D.", - "Adele, S.", - "Johnson, S.A.", - "Amini, A.", - "Ritter, T.G.", - "Mason, C.", - "Dold, C.", - "Pan, D.", - "Assadi, S.", - "Bellass, A.", - "Omo-Dare, N.", - "Koeckerling, D.", - "Flaxman, A.", - "Jenkin, D.", - "Aley, P.K.", - "Voysey, M.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Baillie, V.", - "Serafin, N.", - "Kwatra, G.", - "Da Silva, K.", - "Madhi, S.A.", - "Nunes, M.C.", - "Malik, T.", - "Openshaw, P.J.M.", - "Baillie, J.K.", - "Semple, M.G.", - "Townsend, A.R.", - "Huang, K.A.", - "Tan, T.K.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Constantinides, B.", - "Webster, H.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Schreiber, G.", - "Stuart, D.I.", - "Screaton, G.R.", - "Ritter, T.", - "Voysey, M. (0000-0001-6324-6559)", - "Resende, P.C. (0000-0002-2884-3662)", - "Ditse, Z.", - "Silva, K.D.", - "Madhi, S.", - "Openshaw, P.J. (0000-0002-7220-2555)", - "Baillie, J.K. (0000-0001-5258-793X)", - "Semple, M.G. (0000-0001-9700-0418)", - "Townsend, A.R. (0000-0002-3702-0107)", - "Tan, T.K. (0000-0001-8746-8308)", - "Stuart, D.I. (0000-0002-3426-4210)", - "Duyvesteyn, H.M.", - "Openshaw, P.J.", - "Huang, K.Y.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qnw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qnw", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K398.22", - emdb: null, - pdb: { - dbId: "7TP4", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, antibody, neutralizing antibody, Fab, COVID-19, coronavirus, receptor-binding domain, RBD, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7TP4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tp4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tp4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9544", - name: "K398.22 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9544", - name: "K398.22 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Wilson, I.A. (0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. (0000-0001-9754-4503)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35947674", - title: - "Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques.", - journal: "Sci Transl Med 14: eabl9605-eabl9605 (2022), 1946-6242", - doi: "https://doi.org/10.1126/scitranslmed.abl9605", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35947674", - pubDate: "2022", - abstract: "", - authors: [ - "He, W.T. (0000-0003-4692-3516)", - "Yuan, M. (0000-0001-9754-4503)", - "Callaghan, S. (0000-0003-2966-994X)", - "Musharrafieh, R.", - "Song, G. (0000-0001-7306-3510)", - "Silva, M. (0000-0003-4668-6290)", - "Beutler, N. (0000-0003-3240-9524)", - "Lee, W.H. (0000-0001-9445-6671)", - "Yong, P. (0000-0002-4899-3270)", - "Torres, J.L. 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(0000-0001-8837-7520)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tp4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tp4", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000001099", - emdb: null, - pdb: { - dbId: "5RSM", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsm_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UCAGLBKTLXCODC-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsm", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000004218283", - emdb: null, - pdb: { - dbId: "5RSZ", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsz_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZROILLPDIUNLSE-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsz", - }, - }, - { - title: "Crystal Structure of Sars-Cov-2 Mpro at 1.90 A resolution-1", - emdb: null, - pdb: { - dbId: "7VJY", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main protease, SFX, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7VJY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7vjy_final.pdb", - externalLink: "https://pdb-redo.eu/db/7vjy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "DeMirci, H. (0000-0002-9135-5397)", - "Johnson, A.J. (0000-0002-8553-2465)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography", - journal: "Crystals 11 (2021), 2073-4352", - doi: "https://doi.org/10.3390/cryst11121579", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Guven, O.", - "Gul, M.", - "Ayan, E.", - "Johnson, J.A.", - "Cakilkaya, B.", - "Usta, G.", - "Ertem, F.B.", - "Tokay, N.", - "Yuksel, B.", - "Gocenler, O.", - "Buyukdag, C.", - "Botha, S.", - "Ketawala, G.", - "Su, Z.", - "Hayes, B.", - "Poitevin, F.", - "Batyuk, A.", - "Yoon, C.H.", - "Kupitz, C.", - "Durdagi, S.", - "Sierra, R.G.", - "DeMirci, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vjy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vjy", - }, - }, - { - title: "Structure Determination of the NB1B11-RBD Complex", - emdb: null, - pdb: { - dbId: "7FAU", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, RBD, Nanobody, STRUCTURAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7FAU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7fau_final.pdb", - externalLink: "https://pdb-redo.eu/db/7fau", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9835", - name: "NB_1B11", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Zhang, X.", - "Sun, Z.C.", - "Shi, Z.Z.", - "Li, X.X.", - "Wang, L. (0000-0001-6336-5806)", - "Zhang, H.W.", - "Chen, X.C.", - "Cui, Q.Q.", - "Qiao, H.R.", - "Lan, Z.Y.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35276082", - title: - "Structural basis of nanobodies neutralizing SARS-CoV-2 variants.", - journal: "Structure 30: 707-720.e5 (2022), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2022.02.011", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35276082", - pubDate: "2022", - abstract: "", - authors: [ - "Shi, Z.", - "Li, X.", - "Wang, L.", - "Sun, Z.", - "Zhang, H.", - "Chen, X.", - "Cui, Q.", - "Qiao, H.", - "Lan, Z.", - "Zhang, X.", - "Li, L.", - "Xu, J.", - "Gong, R.", - "Fan, C.", - "Geng, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7fau_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7fau", - }, - }, - { - title: "SARS-CoV-2 S protein RBD in complex with A5-10 Fab", - emdb: null, - pdb: { - dbId: "7F7E", - method: "X-RAY DIFFRACTION", - keywords: "Antibody, SARS-CoV-2, VIRUS, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7F7E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7f7e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7f7e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of A5-10 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of A5-10 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Wang, K.", "Wang, X.", "Liu, P.", "Dou, Y.", "Lu, B."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35060840", - title: - "Etesevimab in combination with JS026 neutralizing SARS-CoV-2 and its variants.", - journal: "Emerg Microbes Infect 11: 548-551 (2022), 2222-1751", - doi: "https://doi.org/10.1080/22221751.2022.2032374", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35060840", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, F.", - "Li, L.", - "Dou, Y.", - "Shi, R.", - "Duan, X.", - "Liu, H.", - "Zhang, J.", - "Liu, D.", - "Wu, J.", - "He, Y.", - "Lan, J.", - "Lu, B.", - "Feng, H.", - "Yan, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7f7e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7f7e", - }, - }, - { - title: - "Structure of SARS-CoV-2 Papain-like Protease bound to N-(2-pyrrolidyl)-3,4,5-trihydroxybenzoylhydrazone", - emdb: null, - pdb: { - dbId: "7QCG", - method: "X-RAY DIFFRACTION", - keywords: - "Cystein-Protease, Inhibitor, SARS-CoV-2, Hydrazone, Deubiquitination, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7QCG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7qcg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7qcg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "RPKVALFTHLQJDU-MKMNVTDBSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - ], - dbauthors: [ - "Reinke, P.", - "Hinrichs, W.", - "Han, H.", - "Srinivasan, V.", - "Lorenzen, K.", - "Betzel, C.", - "Meents, A.", - "Falke, S.", - "Gunther, S.", - "Lieske, J.", - "Ewert, W.", - "Niebling, S.", - "Miglioli, F.", - "Carcelli, M.", - "Guenther, C.", - "Garcia-Alai, M.", - "Rogolino, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35480391", - title: - "Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease.", - journal: "Front Chem 10: 832431-832431 (2022), 2296-2646", - doi: "https://doi.org/10.3389/fchem.2022.832431", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35480391", - pubDate: "2022", - abstract: "", - authors: [ - "Ewert, W.", - "Gunther, S.", - "Miglioli, F.", - "Falke, S.", - "Reinke, P.Y.A.", - "Niebling, S.", - "Gunther, C.", - "Han, H.", - "Srinivasan, V.", - "Brognaro, H.", - "Lieske, J.", - "Lorenzen, K.", - "Garcia-Alai, M.M.", - "Betzel, C.", - "Carcelli, M.", - "Hinrichs, W.", - "Rogolino, D.", - "Meents, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qcg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qcg", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Fusidic Acid.", - emdb: null, - pdb: { - dbId: "7A1U", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, MPro, COVID-19, PEPTIDE BINDING PROTEIN, virus protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7A1U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7a1u_final.pdb", - externalLink: "https://pdb-redo.eu/db/7a1u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "IECPWNUMDGFDKC-MZJAQBGESA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - 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(0000-0002-1135-2744)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35142215", - title: - "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", - journal: "J.Am.Chem.Soc. 144: 2905-2920 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08402", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35142215", - pubDate: "2022", - abstract: "", - authors: [ - "Luttens, A. (0000-0003-2915-7901)", - "Gullberg, H.", - "Abdurakhmanov, E.", - "Vo, D.D.", - "Akaberi, D. (0000-0002-9595-9796)", - "Talibov, V.O.", - "Nekhotiaeva, N.", - "Vangeel, L.", - "De Jonghe, S. (0000-0002-3872-6558)", - "Jochmans, D.", - "Krambrich, J.", - "Tas, A.", - "Lundgren, B.", - "Gravenfors, Y. (0000-0001-6025-4908)", - "Craig, A.J.", - "Atilaw, Y.", - "Sandstrom, A.", - "Moodie, L.W.K. (0000-0002-9500-4535)", - "Lundkvist, A.", - "van Hemert, M.J.", - "Neyts, J.", - "Lennerstrand, J.", - "Kihlberg, J. (0000-0002-4205-6040)", - "Sandberg, K.", - "Danielson, U.H. (0000-0003-2728-0340)", - "Carlsson, J. 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(0000-0001-7131-1154)", - "Xia, W. (0000-0001-6480-3265)", - "Tao, X. (0000-0001-7275-3536)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35255411", - title: - "Inhibition of SARS-CoV-2 replication by zinc gluconate in combination with hinokitiol.", - journal: "J.Inorg.Biochem. 231: 111777-111777 (2022), 0162-0134", - doi: "https://doi.org/10.1016/j.jinorgbio.2022.111777", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35255411", - pubDate: "2022", - abstract: "", - authors: [ - "Tao, X.", - "Zhang, L.", - "Du, L.", - "Lu, K.", - "Zhao, Z.", - "Xie, Y.", - "Li, X.", - "Huang, S.", - "Wang, P.H.", - "Pan, J.A.", - "Xia, W.", - "Dai, J.", - "Mao, Z.W.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7d64_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7d64", - }, - }, - { - title: - "Ensemble refinement structure of SARS-CoV-2 main protease (Mpro) at 298 K at high humidity", - emdb: null, - pdb: { - dbId: "7MHP", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Coronavirus, main protease, 3CLpro, Mpro, hydrolase, ensemble refinement, temperature series, temperature, multitemperature, humidity", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro )", - journal: "Iucrj 9: 682-694 (2022), 2052-2525", - doi: "https://doi.org/10.1107/S2052252522007497", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Ebrahim, A. (0000-0003-2661-381X)", - "Riley, B.T. (0000-0003-2176-0503)", - "Kumaran, D.", - "Andi, B. (0000-0002-7666-639X)", - "Fuchs, M.R. (0000-0001-9784-0927)", - "McSweeney, S. (0000-0002-3758-3161)", - "Keedy, D.A. (0000-0002-9184-7586)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mhp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mhp", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102274", - emdb: null, - pdb: { - dbId: "5RFZ", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfz_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "KWZIDENWDCKKPW-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0001-6744-5061)", - "Mikolajek, H. (0000-0003-0776-9974)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35858383", - title: - "Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2205412119-e2205412119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2205412119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35858383", - pubDate: "2022", - abstract: "", - authors: [ - "Mikolajek, H. (0000-0003-0776-9974)", - "Weckener, M. (0000-0002-1419-9378)", - "Brotzakis, Z.F.", - "Huo, J.", - "Dalietou, E.V.", - "Le Bas, A.", - "Sormanni, P. (0000-0002-6228-2221)", - "Harrison, P.J.", - "Ward, P.N. (0000-0003-2546-3426)", - "Truong, S. (0000-0001-9624-4461)", - "Moynie, L. (0000-0002-4097-4331)", - "Clare, D.K.", - "Dumoux, M.", - "Dormon, J.", - "Norman, C.", - "Hussain, N. (0000-0002-5170-0061)", - "Vogirala, V. (0000-0002-8534-3736)", - "Owens, R.J. (0000-0002-3705-2993)", - "Vendruscolo, M. (0000-0002-3616-1610)", - "Naismith, J.H. 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(0000-0002-3532-3868)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tiv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tiv", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1286870272 (Mpro-x2608)", - emdb: null, - pdb: { - dbId: "5RH0", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RH0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rh0_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rh0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OCXJDZBTSLHCNX-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rh0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rh0", - }, - }, - { - title: "SARS-CoV-2 Omicron RBD in complex with Omi-6 and COVOX-150 Fabs", - emdb: null, - pdb: { - dbId: "7ZFA", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Omicron, BA.1, BA.2, RBD, antibody, Fab, Omi-6, COVOX-150, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZFA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zfa_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zfa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-6 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-6 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-150 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-150 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I.", "Huo, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35662412", - title: - "Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.", - journal: "Cell 185: 2116-2131.e18 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.05.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35662412", - pubDate: "2022", - abstract: "", - authors: [ - "Nutalai, R.", - "Zhou, D.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Supasa, P.", - "Liu, C.", - "Huo, J.", - "Mentzer, A.J.", - "Duyvesteyn, H.M.E.", - "Dijokaite-Guraliuc, A.", - "Skelly, D.", - "Ritter, T.G.", - "Amini, A.", - "Bibi, S.", - "Adele, S.", - "Johnson, S.A.", - "Constantinides, B.", - "Webster, H.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Goulder, P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Mongkolsapaya, J.", - "Fry, E.E.", - "Dejnirattisai, W.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zfa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zfa", - }, - }, - { - title: - "Structure of SARS-CoV-2 spike receptor-binding domain complexed with high affinity ACE2 mutant 3N39", - emdb: null, - pdb: { - dbId: "7DMU", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, COVID-19, ACE2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7DMU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dmu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dmu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: [ - "Arimori, T. (0000-0002-6063-5572)", - "Takagi, J. (0000-0002-1219-475X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34155214", - title: - "Engineered ACE2 receptor therapy overcomes mutational escape of SARS-CoV-2.", - journal: "Nat Commun 12: 3802-3802 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-24013-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34155214", - pubDate: "2021", - abstract: "", - authors: [ - "Higuchi, Y.", - "Suzuki, T.", - "Arimori, T. (0000-0002-6063-5572)", - "Ikemura, N.", - "Mihara, E. (0000-0002-9127-8643)", - "Kirita, Y. (0000-0002-5240-5531)", - "Ohgitani, E.", - "Mazda, O. (0000-0001-9489-3556)", - "Motooka, D.", - "Nakamura, S.", - "Sakai, Y. (0000-0003-0531-8256)", - "Itoh, Y.", - "Sugihara, F.", - "Matsuura, Y. (0000-0001-9091-8285)", - "Matoba, S. (0000-0002-9373-4331)", - "Okamoto, T. (0000-0003-4000-3102)", - "Takagi, J. (0000-0002-1219-475X)", - "Hoshino, A. (0000-0002-4015-1319)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dmu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dmu", - }, - }, - { - title: "PALS1 PDZ1 domain with SARS-CoV-2_E PBM complex", - emdb: null, - pdb: { - dbId: "7NTK", - method: "X-RAY DIFFRACTION", - keywords: "cell polarity, PALS1, SARS-CoV-2_E, CELL ADHESION", - refModels: [ - { - emdbId: null, - pdbId: "7NTK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ntk_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ntk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q8N3R9", - organism: "9606", - name: "MAGUK p55 subfamily member 5", - details: - "At the n-terminal of chain A,B,D,F, sequence GPLGS is part of the expression tag", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC4", - organism: "2697049", - name: "Envelope small membrane protein", - details: "", - altNames: "E,sM protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RFHAOTPXVQNOHP-UHFFFAOYSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Javorsky, A. (0000-0002-5893-6990)", - "Kvansakul, M. (0000-0003-2639-2498)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34117354", - title: - "Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain.", - journal: "Commun Biol 4: 724-724 (2021), 2399-3642", - doi: "https://doi.org/10.1038/s42003-021-02250-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34117354", - pubDate: "2021", - abstract: "", - authors: [ - "Javorsky, A.", - "Humbert, P.O. (0000-0002-1366-6691)", - "Kvansakul, M. (0000-0003-2639-2498)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ntk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ntk", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike protein N-terminal domain in complex with biliverdin", - emdb: null, - pdb: { - dbId: "7B62", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, COVID19, Biliverdin, coronavirus, NTD, green, spike, glycoprotein, S1, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7B62", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7b62_final.pdb", - externalLink: "https://pdb-redo.eu/db/7b62", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "RCNSAJSGRJSBKK-NSQVQWHSSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "ZIBGPFATKBEMQZ-UHFFFAOYSA-N", - "JLFNLZLINWHATN-UHFFFAOYSA-N", - ], - dbauthors: ["Rosa, A.", "Pye, V.E.", "Cherepanov, P.", "Roustan, C."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33888467", - title: - "SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abg7607", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33888467", - pubDate: "2021", - abstract: "", - authors: [ - "Rosa, A.", - "Pye, V.E.", - "Graham, C.", - "Muir, L.", - "Seow, J.", - "Ng, K.W.", - "Cook, N.J.", - "Rees-Spear, C.", - "Parker, E.", - "Dos Santos, M.S.", - "Rosadas, C.", - "Susana, A.", - "Rhys, H.", - "Nans, A.", - "Masino, L.", - "Roustan, C.", - "Christodoulou, E.", - "Ulferts, R.", - "Wrobel, A.G.", - "Short, C.E.", - "Fertleman, M.", - "Sanders, R.W.", - "Heaney, J.", - "Spyer, M.", - "Kjaer, S.", - "Riddell, A.", - "Malim, M.H.", - "Beale, R.", - "MacRae, J.I.", - "Taylor, G.P.", - "Nastouli, E.", - "van Gils, M.J.", - "Rosenthal, P.B.", - "Pizzato, M.", - "McClure, M.O.", - "Tedder, R.S.", - "Kassiotis, G.", - "McCoy, L.E.", - "Doores, K.J.", - "Cherepanov, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7b62_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7b62", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with NCL-00024890", - emdb: null, - pdb: { - dbId: "5S44", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S44", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s44_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s44", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WRXIKBHQDRMYJJ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s44_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s44", - }, - }, - { - title: - "Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 15d", - emdb: null, - pdb: { - dbId: "8CZW", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8CZW", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8czw_final.pdb", - externalLink: "https://pdb-redo.eu/db/8czw", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VKRZPHPWNNQDHJ-MWOXCZGJSA-O", - "VKRZPHPWNNQDHJ-HUWCRECTSA-O", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Madden, T.K.", - "Kim, Y.", - "Nguyen, H.N.", - "Machen, A.J.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - "Picard, H.R.", - "Thruman, H.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36654747", - title: - "Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.", - journal: "Acs Pharmacol Transl Sci 6: 181-194 (2023), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00206", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36654747", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Nguyen, H.N.", - "Rathnayake, A.D.", - "Kim, Y.", - "Perera, K.D.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8czw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8czw", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1424343998", - emdb: null, - pdb: { - dbId: "5SAI", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SAI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sai_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sai", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JMNHFNZOQMCQHZ-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sai_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sai", - }, - }, - { - title: - "Structure of SARS-CoV-2 spike receptor-binding domain in complex with high affinity ACE2 mutant (T27W,N330Y)", - emdb: null, - pdb: { - dbId: "7EFR", - method: "X-RAY DIFFRACTION", - keywords: "receptor-binding domain, angiotensin converting enzyme 2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7EFR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7efr_final.pdb", - externalLink: "https://pdb-redo.eu/db/7efr", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Processed angiotensin-converting enzyme 2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Lin, X.", "Lu, G.W.", "Ye, F."], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34531369", - title: - "S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis.", - journal: - "Signal Transduct Target Ther 6: 343-343 (2021), 2059-3635", - doi: "https://doi.org/10.1038/s41392-021-00756-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34531369", - pubDate: "2021", - abstract: "", - authors: [ - "Ye, F.", - "Lin, X.", - "Chen, Z.", - "Yang, F.", - "Lin, S.", - "Yang, J.", - "Chen, H.", - "Sun, H.", - "Wang, L.", - "Wen, A.", - "Zhang, X.", - "Dai, Y.", - "Cao, Y.", - "Shen, G.", - "Yang, L.", - "Li, J.", - "Wang, Z.", - "Wang, W. (0000-0001-7788-1895)", - "Wei, X. (0000-0002-6513-6422)", - "Lu, G. (0000-0001-7568-592X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7efr_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7efr", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z3219959731", - emdb: null, - pdb: { - dbId: "5S4B", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S4B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s4b_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s4b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AAILEWXSEQLMNI-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4b_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4b", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1526504764", - emdb: null, - pdb: { - dbId: "5SLY", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sly_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sly", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "IPBXAQNEXLMXRW-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sly_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sly", - }, - }, - { - title: "Structure of SARS-CoV2 NSP5 (3C-like proteinase) determined in-house", - emdb: null, - pdb: { - dbId: "7NXH", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV2, NSP5, 3C-like proteinase, coronavirus, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NXH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nxh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nxh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Grifagni, D.", - "Cantini, F.", - "Banci, L.", - "Calderone, V. (0000-0002-7963-6241)", - "Fragai, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34278402", - title: - "SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design.", - journal: "Chem.Commun.(Camb.) 57: 7910-7913 (2021), 1364-548X", - doi: "https://doi.org/10.1039/d1cc02956h", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34278402", - pubDate: "2021", - abstract: "", - authors: [ - "Grifagni, D. (0000-0001-5402-6781)", - "Calderone, V. (0000-0002-7963-6241)", - "Giuntini, S.", - "Cantini, F. (0000-0003-0526-6732)", - "Fragai, M. (0000-0002-8440-1690)", - "Banci, L. (0000-0003-0562-5774)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nxh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nxh", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2856434762", - emdb: null, - pdb: { - dbId: "5SL8", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SL8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sl8_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sl8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "VHYFNPMBLIVWCW-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sl8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sl8", - }, - }, - { - title: "SARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargylamide", - emdb: null, - pdb: { - dbId: "6XA9", - method: "X-RAY DIFFRACTION", - keywords: - "SARS CoV-2, papain-like protease, ISG15CTD activity based probe, COVID19, HYDROLASE-SUBSTRATE complex", - refModels: [ - { - emdbId: null, - pdbId: "6XA9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xa9_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xa9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05161", - organism: "9606", - name: "ISG15 CTD-propargylamide", - details: "", - altNames: - "Interferon-induced 15 kDa protein,Interferon-induced 17 kDa protein,IP17,Ubiquitin cross-reactive protein,hUCRP", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Klemm, T. (0000-0002-2847-3550)", - "Calleja, D.J. (0000-0002-8306-0900)", - "Richardson, L.W. (0000-0001-8877-1376)", - "Lechtenberg, B.C. (0000-0002-5674-6894)", - "Komander, D. (0000-0002-8092-4320)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32845033", - title: - "Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2.", - journal: "Embo J. 39: e106275-e106275 (2020), 1460-2075", - doi: "https://doi.org/10.15252/embj.2020106275", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32845033", - pubDate: "2020", - abstract: "", - authors: [ - "Klemm, T. (0000-0002-2847-3550)", - "Ebert, G.", - "Calleja, D.J. (0000-0002-8306-0900)", - "Allison, C.C.", - "Richardson, L.W. (0000-0001-8877-1376)", - "Bernardini, J.P. (0000-0002-5767-7624)", - "Lu, B.G. (0000-0001-8044-9710)", - "Kuchel, N.W.", - "Grohmann, C.", - "Shibata, Y.", - "Gan, Z.Y. (0000-0001-5755-7780)", - "Cooney, J.P. (0000-0003-3680-4644)", - "Doerflinger, M. (0000-0001-9159-3021)", - "Au, A.E. (0000-0003-3656-2673)", - "Blackmore, T.R. (0000-0001-7079-676X)", - "van der Heden van Noort, G.J. (0000-0001-5955-6431)", - "Geurink, P.P.", - "Ovaa, H.", - "Newman, J. (0000-0003-2666-3219)", - "Riboldi-Tunnicliffe, A. (0000-0003-2244-2486)", - "Czabotar, P.E.", - "Mitchell, J.P.", - "Feltham, R.", - "Lechtenberg, B.C. (0000-0002-5674-6894)", - "Lowes, K.N.", - "Dewson, G. (0000-0003-4251-8898)", - "Pellegrini, M. (0000-0003-3627-3126)", - "Lessene, G. (0000-0002-1193-8147)", - "Komander, D. (0000-0002-8092-4320)", - "Adams, P.D.", - "Afonine, P.V.", - "Bunkoczi, G.", - "Chen, V.B.", - "Davis, I.W.", - "Echols, N.", - "Headd, J.J.", - "Hung, L.W.", - "Kapral, G.J.", - "Grosse-Kunstleve, R.W.", - "McCoy, A.J.", - "Moriarty, N.W.", - "Oeffner, R.", - "Read, R.J.", - "Richardson, D.C.", - "Richardson, J.S.", - "Terwilliger, T.C.", - "Zwart, P.H.", - ], - }, - { - pmID: "20124702", - title: - "PHENIX: a comprehensive Python-based system for macromolecular structure solution.", - journal: - "Acta Crystallogr. D Biol. Crystallogr. 66: 213-221 (2010), 1399-0047", - doi: "https://doi.org/10.1107/S0907444909052925", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/20124702", - pubDate: "2010", - abstract: "", - authors: [ - "Anson, B. (0000-0003-2670-974X)", - "Ghosh, A.K.", - "Mesecar, A. (0000-0002-1241-2577)", - "Afonine, P.V.", - "Grosse-Kunstleve, R.W.", - "Echols, N.", - "Headd, J.J.", - "Moriarty, N.W.", - "Mustyakimov, M.", - "Terwilliger, T.C.", - "Urzhumtsev, A.", - "Zwart, P.H.", - "Adams, P.D.", - "Bunkoczi, G.", - "Chen, V.B.", - "Davis, I.W.", - "Hung, L.W.", - "Kapral, G.J.", - "McCoy, A.J.", - "Oeffner, R.", - "Read, R.J.", - "Richardson, D.C.", - "Richardson, J.S.", - "Klemm, T. (0000-0002-2847-3550)", - "Ebert, G.", - "Calleja, D.J. (0000-0002-8306-0900)", - "Allison, C.C.", - "Richardson, L.W. (0000-0001-8877-1376)", - "Bernardini, J.P. (0000-0002-5767-7624)", - "Lu, B.G. (0000-0001-8044-9710)", - "Kuchel, N.W.", - "Grohmann, C.", - "Shibata, Y.", - "Gan, Z.Y. (0000-0001-5755-7780)", - "Cooney, J.P. (0000-0003-3680-4644)", - "Doerflinger, M. (0000-0001-9159-3021)", - "Au, A.E. (0000-0003-3656-2673)", - "Blackmore, T.R. (0000-0001-7079-676X)", - "van der Heden van Noort, G.J. (0000-0001-5955-6431)", - "Geurink, P.P.", - "Ovaa, H.", - "Newman, J. (0000-0003-2666-3219)", - "Riboldi-Tunnicliffe, A. (0000-0003-2244-2486)", - "Czabotar, P.E.", - "Mitchell, J.P.", - "Feltham, R.", - "Lechtenberg, B.C. (0000-0002-5674-6894)", - "Lowes, K.N.", - "Dewson, G. (0000-0003-4251-8898)", - "Pellegrini, M. (0000-0003-3627-3126)", - "Lessene, G. (0000-0002-1193-8147)", - "Komander, D. (0000-0002-8092-4320)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xa9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xa9", - }, - }, - { - title: "SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-24", - emdb: null, - pdb: { - dbId: "7LBS", - method: "X-RAY DIFFRACTION", - keywords: - "papain-like protease, coronavirus inhibitor, SARS-CoV-2, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LBS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lbs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lbs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ZTKSBNLNPMUGBL-HXUWFJFHSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "KGBXLFKZBHKPEV-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Ratia, K.M. (0000-0002-4834-9207)", - "Xiong, R. (0000-0002-6350-9037)", - "Thatcher, G.R. (0000-0002-7757-1739)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33594371", - title: - "Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.02.13.431008", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33594371", - pubDate: "2021", - abstract: "", - authors: [ - "Shen, Z.", - "Ratia, K.", - "Cooper, L.", - "Kong, D.", - "Lee, H.", - "Kwon, Y.", - "Li, Y.", - "Alqarni, S.", - "Huang, F.", - "Dubrovskyi, O.", - "Rong, L.", - "Thatcher, G.R.", - "Xiong, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lbs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lbs", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000285507655 - (R) and (S) isomers", - emdb: null, - pdb: { - dbId: "5SOU", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sou_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sou", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FSJZPCQWTVULBE-MRVPVSSYSA-N", "FSJZPCQWTVULBE-QMMMGPOBSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sou_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sou", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z57299529", - emdb: null, - pdb: { - dbId: "5SLN", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sln_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sln", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "OWETVOGOOABRTJ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sln_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sln", - }, - }, - { - title: - "Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of Cap-1 analog (m7GpppAmU) and SAH", - emdb: null, - pdb: { - dbId: "7LW3", - method: "X-RAY DIFFRACTION", - keywords: "product complex, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7LW3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lw3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lw3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "POOGENYSODSFCS-SWDLWUBYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Qi, S.", - "Gupta, Y.K. (0000-0001-6372-5007)", - "Viswanathan, T.", - "Misra, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34078893", - title: - "A metal ion orients SARS-CoV-2 mRNA to ensure accurate 2'-O methylation of its first nucleotide.", - journal: "Nat Commun 12: 3287-3287 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23594-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34078893", - pubDate: "2021", - abstract: "", - authors: [ - "Viswanathan, T. (0000-0001-9817-6730)", - "Misra, A.", - "Chan, S.H. (0000-0002-9554-7273)", - "Qi, S. (0000-0003-0175-6267)", - "Dai, N. (0000-0003-3268-1835)", - "Arya, S. (0000-0002-7689-7411)", - "Martinez-Sobrido, L. (0000-0001-7084-0804)", - "Gupta, Y.K. (0000-0001-6372-5007)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lw3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lw3", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder441 inhibitor", - emdb: null, - pdb: { - dbId: "7KRX", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7KRX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7krx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7krx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PZEBTCMUWPLVEX-CQSZACIVSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder441", - journal: "to be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Lisnyak, V.", - "Maki, S.", - "Taylor, C.", - "Zhang, Y.", - "Zhou, Z.", - "Azizi, S.A.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - "Dickinson, B.C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7krx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7krx", - }, - }, - { - title: "GQTVTK segment from the Nucleoprotein of SARS-CoV-2, residues 243-248", - emdb: null, - pdb: { - dbId: "7LUZ", - method: "X-RAY DIFFRACTION", - keywords: "amyloid fibril, PROTEIN FIBRIL", - refModels: [ - { - emdbId: null, - pdbId: "7LUZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7luz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7luz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein GQTVTK", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Sawaya, M.R. (0000-0003-0874-9043)", - "Eisenberg, D.S. (0000-0003-2432-5419)", - "Balbirnie, M. (0000-0003-3497-392X)", - "Cascio, D. (0000-0002-3877-6803)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "33688654", - title: - "Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.05.434000", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33688654", - pubDate: "2021", - abstract: "", - authors: [ - "Tayeb-Fligelman, E.", - "Cheng, X.", - "Tai, C.", - "Bowler, J.T.", - "Griner, S.", - "Sawaya, M.R.", - "Seidler, P.M.", - "Jiang, Y.X.", - "Lu, J.", - "Rosenberg, G.M.", - "Salwinski, L.", - "Abskharon, R.", - "Zee, C.T.", - "Hou, K.", - "Li, Y.", - "Boyer, D.R.", - "Murray, K.A.", - "Falcon, G.", - "Anderson, D.H.", - "Cascio, D.", - "Saelices, L.", - "Damoiseaux, R.", - "Guo, F.", - "Eisenberg, D.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7luz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7luz", - }, - }, - { - title: "Structure of SARS-CoV-2 3CL protease in complex with inhibitor 12b", - emdb: null, - pdb: { - dbId: "7LZU", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LZU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lzu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lzu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "YRNJEPAFOLVHMN-GINSCSNVSA-N", - "YRNJEPAFOLVHMN-ZZKADIETSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Miller, M.J.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Chamandi, S.D.", - "Perera, K.D.", - "Rathnayake, A.D.", - "Jesri, A.R.M.", - "Baird, M.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34865476", - title: - "Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.", - journal: "J.Med.Chem. 64: 17846-17865 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c01037", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34865476", - pubDate: "2021", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Rathnayake, A.D.", - "Perera, K.D.", - "Jesri, A.M.", - "Nguyen, H.N.", - "Miller, M.J.", - "Thurman, H.A.", - "Zheng, J.", - "Kashipathy, M.M.", - "Battaile, K.P.", - "Lovell, S.", - "Perlman, S.", - "Kim, Y.", - "Groutas, W.C.", - "Chang, K.O.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lzu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lzu", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin", - emdb: null, - pdb: { - dbId: "7UV5", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, ubiquitin, IDP51000, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7UV5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uv5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uv5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0CG47", - organism: "9606", - name: "Ubiquitin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Wydorski, P.", - "Joachimiak, L.", - "Lanham, B.T.", - "Fushman, D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37185902", - title: - "Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.", - journal: "Nat Commun 14: 2366-2366 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-38031-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37185902", - pubDate: "2023", - abstract: "", - authors: [ - "Wydorski, P.M. (0000-0002-6983-421X)", - "Osipiuk, J.", - "Lanham, B.T.", - "Tesar, C.", - "Endres, M.", - "Engle, E.", - "Jedrzejczak, R.", - "Mullapudi, V. (0000-0002-5346-4242)", - "Michalska, K. (0000-0001-7140-3649)", - "Fidelis, K.", - "Fushman, D.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Joachimiak, L.A. (0000-0003-3061-5850)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uv5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uv5", - }, - }, - { - title: "crystal structure of SARS-CoV-2 antibody with RBD", - emdb: null, - pdb: { - dbId: "7BWJ", - method: "X-RAY DIFFRACTION", - keywords: "spike, receptor binding domain, antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7BWJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7bwj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7bwj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "antibody light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "antibody heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Wang, X.", "Ge, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32454513", - title: - "Human neutralizing antibodies elicited by SARS-CoV-2 infection.", - journal: "Nature 584: 115-119 (2020), 1476-4687", - doi: "https://doi.org/10.1038/s41586-020-2380-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32454513", - pubDate: "2020", - abstract: "", - authors: [ - "Ju, B.", - "Zhang, Q.", - "Ge, J.", - "Wang, R.", - "Sun, J.", - "Ge, X.", - "Yu, J.", - "Shan, S.", - "Zhou, B.", - "Song, S.", - "Tang, X.", - "Lan, J.", - "Yuan, J.", - "Wang, H.", - "Zhao, J.", - "Zhang, S.", - "Wang, Y.", - "Shi, X.", - "Liu, L.", - "Wang, X.", - "Zhang, Z.", - "Zhang, L.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7bwj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7bwj", - }, - }, - { - title: "SARS-CoV-2 frameshifting pseudoknot RNA", - emdb: null, - pdb: { - dbId: "7LYJ", - method: "X-RAY DIFFRACTION", - keywords: - "Pseudoknot, tetraloop, triple, SARS, virus, COVID, coronavirus, severe acute respiratory syndrome, frameshift, RNA", - refModels: [ - { - emdbId: null, - pdbId: "7LYJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lyj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lyj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "RNA (66-MER)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "DZCQSPMFVDVLMF-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "NPYPAHLBTDXSSS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Jones, C.P. (0000-0001-7780-5278)", - "Ferre-D'Amare, A.R. (0000-0003-4549-1619)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "34845084", - title: - "Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot.", - journal: "Rna 28: 239-249 (2022), 1469-9001", - doi: "https://doi.org/10.1261/rna.078825.121", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34845084", - pubDate: "2022", - abstract: "", - authors: ["Jones, C.P.", "Ferre-D'Amare, A.R."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lyj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lyj", - }, - }, - { - title: "X-ray Crystallographic Structure of Orf9b from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "6Z4U", - method: "X-RAY DIFFRACTION", - keywords: "orf9b, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6Z4U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6z4u_final.pdb", - externalLink: "https://pdb-redo.eu/db/6z4u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD2", - organism: "2697049", - name: "Protein 9b", - details: "", - altNames: "Accessory protein 9b,ORF-9b", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NEKPUPYOCNYQHU-UHFFFAOYSA-N"], - dbauthors: [ - "Weeks, S.D. (0000-0002-1360-0852)", - "De Graef, S. (0000-0003-2558-3890)", - "Munawar, A. (0000-0001-9617-9460)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "X-ray Crystallographic Structure of Orf9b from SARS-CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Weeks, S.D. (0000-0002-1360-0852)", - "De Graef, S. (0000-0003-2558-3890)", - "Munawar, A. (0000-0001-9617-9460)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6z4u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6z4u", - }, - }, - { - title: - "Discovery of SARS-CoV-2 3CLpro peptidomimetic inhibitors through H41-specific protein-ligand interactions", - emdb: null, - pdb: { - dbId: "7WO1", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 main protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WO1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wo1_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wo1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LOOFBLJETYWAIL-CMOCDZPBSA-N"], - dbauthors: ["Wang, Y.", "Ye, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35216507", - title: - "Discovery of SARS-CoV-2 3CL Pro Peptidomimetic Inhibitors through the Catalytic Dyad Histidine-Specific Protein-Ligand Interactions.", - journal: "Int J Mol Sci 23 (2022), 1422-0067", - doi: "https://doi.org/10.3390/ijms23042392", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35216507", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, Y.", - "Xu, B. (0000-0002-0137-3381)", - "Ma, S.", - "Wang, H.", - "Shang, L.", - "Zhu, C. (0000-0003-0260-6287)", - "Ye, S. (0000-0001-9300-6257)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7wo1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7wo1", - }, - }, - { - title: - "Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-CoV-2 RBD", - emdb: null, - pdb: { - dbId: "7RPV", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, receptor binding domain, engineered human ACE2, enhanced affinity, catalytic-null, zinc binding site, Hydrolase-Viral protein complex", - refModels: [ - { - emdbId: null, - pdbId: "7RPV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rpv_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rpv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Processed angiotensin-converting enzyme 2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Chen, Y. (0000-0001-5380-2339)", - "Pazgier, M. (0000-0003-0594-5057)", - "Tolbert, D.W. (0000-0001-7549-9596)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34845451", - title: - "Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.11.24.469776", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34845451", - pubDate: "2021", - abstract: "", - authors: [ - "Chen, Y. (0000-0001-5380-2339)", - "Sun, L. (0000-0001-8876-5099)", - "Ullah, I.", - "Beaudoin-Bussieres, G.", - "Anand, S.P.", - "Hederman, A.P.", - "Tolbert, W.D. (0000-0001-7549-9596)", - "Sherburn, R.", - "Nguyen, D.N.", - "Marchitto, L.", - "Ding, S.", - "Wu, D.", - "Luo, Y.", - "Gottumukkala, S.", - "Moran, S.", - "Kumar, P.", - "Piszczek, G. (0000-0002-5270-3678)", - "Mothes, W.", - "Ackerman, M.E.", - "Finzi, A.", - "Uchil, P.D. (0000-0002-7236-858X)", - "Gonzalez, F.J.", - "Pazgier, M. (0000-0003-0594-5057)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7rpv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7rpv", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose (P43 crystal form)", - emdb: null, - pdb: { - dbId: "7KQP", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7KQP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kqp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kqp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-ZQSHOCFMSA-N"], - dbauthors: [ - "Correy, G.J. (0000-0001-5155-7325)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Young, I.D. (0000-0003-4713-9504)", - "Thompson, M.C. (0000-0002-6099-2027)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. 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(0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kqp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kqp", - }, - }, - { - title: - "Crystal structure of synthetic nanobody (Sb45) complexes with SARS-CoV-2 receptor binding domain", - emdb: null, - pdb: { - dbId: "7KGJ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Spike Protein, RBD, Antibody, Nanobody, Sybody, VIRAL PROTEIN, epitopes, neutralization", - refModels: [ - { - emdbId: null, - pdbId: "7KGJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kgj_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kgj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "32630", - name: "Sb45, Sybody-45, Synthetic Nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: true, - }, - ], - ligands: [], - dbauthors: [ - "Jiang, J. (0000-0003-0964-5481)", - "Ahmad, J. (0000-0002-3269-1518)", - "Natarajan, K. (0000-0002-6295-2571)", - "Boyd, L.F. (0000-0002-5126-6250)", - "Margulies, D.H. (0000-0001-8530-7375)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34537245", - title: - "Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.", - journal: "J.Biol.Chem. 297: 101202-101202 (2021), 1083-351X", - doi: "https://doi.org/10.1016/j.jbc.2021.101202", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34537245", - pubDate: "2021", - abstract: "", - authors: [ - "Ahmad, J.", - "Jiang, J.", - "Boyd, L.F.", - "Zeher, A.", - "Huang, R.", - "Xia, D.", - "Natarajan, K.", - "Margulies, D.H.", - "Ahmad, J. (0000-0002-3269-1518)", - "Jiang, J. (0000-0003-0964-5481)", - "Boyd, L.F. (0000-0002-5126-6250)", - "Natarajan, K. (0000-0002-6295-2571)", - "Margulies, D.H. (0000-0001-8530-7375)", - ], - }, - { - pmID: "33532775", - title: - "Synthetic nanobody-SARS-CoV-2 receptor-binding domain structures identify distinct epitopes.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.01.27.428466", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33532775", - pubDate: "2021", - abstract: "", - authors: [ - "Ahmad, J.", - "Jiang, J.", - "Boyd, L.F.", - "Zeher, A.", - "Huang, R.", - "Xia, D.", - "Natarajan, K.", - "Margulies, D.H.", - "Ahmad, J. (0000-0002-3269-1518)", - "Jiang, J. (0000-0003-0964-5481)", - "Boyd, L.F. (0000-0002-5126-6250)", - "Natarajan, K. (0000-0002-6295-2571)", - "Margulies, D.H. (0000-0001-8530-7375)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kgj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kgj", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2027158783", - emdb: null, - pdb: { - dbId: "5SM8", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SM8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sm8_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sm8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "JJHRQXVBTBBRGJ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sm8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sm8", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW246", - emdb: null, - pdb: { - dbId: "6XBG", - method: "X-RAY DIFFRACTION", - keywords: - "COVID, COVID19, COVID-19, SARS, SARS COV2, COV, NCOV 19, CORONAVIRUS, MAIN PROTEASE, 3CL, MPRO, PRO, VIRAL PROTEIN, GC376, calpain inhibitor II, leupeptin, calpain, aldehyde, GC-376, 3cl-like, a-ketoamide, UAW41, UAW246, UAW247, UAW248, 246, 247, 248, alpheketoamide, alpha, ketoamide, PEPTIDOMIMETIC, PROTEASE, CYSTEINE, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "6XBG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xbg_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xbg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "inhibitor UAW246", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "FKNQFGJONOIPTF-UHFFFAOYSA-N"], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M.", "Ma, C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33158912", - title: - "Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L.", - journal: "Sci Adv 6 (2020), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abe0751", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33158912", - pubDate: "2020", - abstract: "", - authors: [ - "Sacco, M.D.", - "Ma, C.", - "Lagarias, P.", - "Gao, A.", - "Townsend, J.A.", - "Meng, X.", - "Dube, P.", - "Zhang, X.", - "Hu, Y.", - "Kitamura, N.", - "Hurst, B.", - "Tarbet, B.", - "Marty, M.T.", - "Kolocouris, A.", - "Xiang, Y.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xbg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xbg", - }, - }, - { - title: - "Improved Feline Drugs as SARS-CoV-2 Mpro Inhibitors: Structure-Activity Studies & Micellar Solubilization for Enhanced Bioavailability", - emdb: null, - pdb: { - dbId: "7LCS", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, 3CLpro, coronavirus, main protease, kinetics, SARS, VIRAL PROTEIN, Hydrolase-Hydrolase Inhibitor complex, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LCS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lcs_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lcs", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CAEFEWVYEZABLA-UUOKFMHZSA-J"], - dbauthors: [ - "Khan, M.B. (0000-0002-4164-9573)", - "Lemieux, M.J. (0000-0003-4745-9153)", - "Arutyunova, E.", - "Young, H.S.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli O103:H2", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34118724", - title: - "Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies.", - journal: "Eur.J.Med.Chem. 222: 113584-113584 (2021), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2021.113584", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34118724", - pubDate: "2021", - abstract: "", - authors: [ - "Vuong, W.", - "Fischer, C.", - "Khan, M.B.", - "van Belkum, M.J.", - "Lamer, T.", - "Willoughby, K.D.", - "Lu, J.", - "Arutyunova, E.", - "Joyce, M.A.", - "Saffran, H.A.", - "Shields, J.A.", - "Young, H.S.", - "Nieman, J.A.", - "Tyrrell, D.L.", - "Lemieux, M.J.", - "Vederas, J.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lcs_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lcs", - }, - }, - { - title: - "Structure of SARS-CoV-2 Alpha variant spike receptor-binding domain complexed with human ACE2", - emdb: null, - pdb: { - dbId: "7EKF", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, spike, RBD, 501Y.V1, ACE2, VIRAL PROTEIN, HYDROLASE-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7EKF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ekf_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ekf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Gao, G.F. (0000-0002-3869-615X)", - "Su, C. (0000-0002-5824-7968)", - "Qi, J.X. (0000-0002-9358-4732)", - "Han, P.C. (0000-0002-4551-6209)", - "Zhang, Y.F. (0000-0003-3026-3357)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34671049", - title: - "Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.", - journal: "Nat Commun 12: 6103-6103 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-26401-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34671049", - pubDate: "2021", - abstract: "", - authors: [ - "Han, P.", - "Su, C. (0000-0002-5824-7968)", - "Zhang, Y.", - "Bai, C.", - "Zheng, A.", - "Qiao, C.", - "Wang, Q.", - "Niu, S.", - "Chen, Q.", - "Li, W.", - "Liao, H.", - "Li, J.", - "Zhang, Z.", - "Cho, H.", - "Yang, M.", - "Rong, X.", - "Hu, Y.", - "Huang, N. (0000-0002-6912-033X)", - "Yan, J. (0000-0003-0502-3829)", - "Wang, Q. (0000-0003-3768-0401)", - "Zhao, X. (0000-0002-2001-1343)", - "Gao, G.F. (0000-0002-3869-615X)", - "Qi, J. (0000-0002-9358-4732)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ekf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ekf", - }, - }, - { - title: "SARS-CoV-2 main proteinase complex with microbial metabolite leupeptin", - emdb: null, - pdb: { - dbId: "7EIN", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, main proteinase, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7EIN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ein_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ein", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "leupeptin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Feng, Y.", "Qi, J.X.", "Gao, G.F.", "Fu, L.F."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34579576", - title: - "Mechanism of Microbial Metabolite Leupeptin in the Treatment of COVID-19 by Traditional Chinese Medicine Herbs.", - journal: "Mbio 12: e0222021-e0222021 (2021), 2150-7511", - doi: "https://doi.org/10.1128/mBio.02220-21", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34579576", - pubDate: "2021", - abstract: "", - authors: [ - "Fu, L.", - "Shao, S.", - "Feng, Y.", - "Ye, F.", - "Sun, X.", - "Wang, Q.", - "Yu, F.", - "Huang, B.", - "Niu, P.", - "Li, X.", - "Wong, C.C.L.", - "Qi, J. (0000-0002-9358-4732)", - "Tan, W.", - "Gao, G.F. (0000-0002-3869-615X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ein_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ein", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1430613393", - emdb: null, - pdb: { - dbId: "5SLJ", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slj_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "HSWJYBWHEHPWSP-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slj", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000896845531 - (R) isomer", - emdb: null, - pdb: { - dbId: "5SOQ", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5soq_final.pdb", - externalLink: "https://pdb-redo.eu/db/5soq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["AUNHHPCCLQISEV-GFCCVEGCSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5soq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5soq", - }, - }, - { - title: - "Room temperature X-ray crystallography reveals catalytic cysteine in the SARS-CoV-2 3CL Mpro is highly reactive: Insights for enzyme mechanism and drug design", - emdb: null, - pdb: { - dbId: "6XB1", - method: "X-RAY DIFFRACTION", - keywords: "Main Protease SARS-CoV-2 3CL Mpro, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6XB1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xb1_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xb1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GHAZCVNUKKZTLG-UHFFFAOYSA-N"], - dbauthors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33063790", - title: - "Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M pro : insights into enzyme mechanism and drug design.", - journal: "Iucrj 7 (2020), 2052-2525", - doi: "https://doi.org/10.1107/S2052252520012634", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33063790", - pubDate: "2020", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Phillips, G. (0000-0001-5858-3825)", - "O'Neill, H.M.", - "Tan, K. (0000-0002-4003-7903)", - "Joachimiak, A. (0000-0003-2535-6209)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xb1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xb1", - }, - }, - { - title: - "Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-F10 Fab)", - emdb: null, - pdb: { - dbId: "7KFY", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, neutralizing antibody, affinity maturation, IMMUNE SYSTEM, IMMUNE SYSTEM-Viral protein complex", - refModels: [ - { - emdbId: null, - pdbId: "7KFY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kfy_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kfy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "heavy chain of human antibody C1A-F10 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "light chain of human antibody C1A-F10 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Pan, J. (0000-0002-0070-955X)", - "Abraham, J. (0000-0002-7937-3920)", - "Clark, L. (0000-0002-6093-7597)", - "Clark, S. (0000-0001-9944-0919)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33200128", - title: - "Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.11.13.381533", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33200128", - pubDate: "2020", - abstract: "", - authors: [ - "Clark, S.A.", - "Clark, L.E.", - "Pan, J. (0000-0002-0070-955X)", - "Coscia, A.", - "McKay, L.G.A.", - "Shankar, S.", - "Johnson, R.I.", - "Griffiths, A.", - "Abraham, J. (0000-0002-7937-3920)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kfy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kfy", - }, - }, - { - title: "Complex Structure of antibody BD-503 and RBD-N501Y of COVID-19", - emdb: null, - pdb: { - dbId: "7EK0", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, Neutralization Antibody, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7EK0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ek0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ek0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Heavy Chain of BD-503", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light Chain of BD-503", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Xu, H.", "Wang, B.", "Zhao, T.N.", "Su, X.D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34480123", - title: - "Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants.", - journal: "Cell Res. 31: 1126-1129 (2021), 1001-0602", - doi: "https://doi.org/10.1038/s41422-021-00554-1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34480123", - pubDate: "2021", - abstract: "", - authors: [ - "Xu, H. (0000-0001-9283-080X)", - "Wang, B. (0000-0002-3380-4473)", - "Zhao, T.N.", - "Liang, Z.T.", - "Peng, T.B.", - "Song, X.H.", - "Wu, J.J.", - "Wang, Y.C. (0000-0001-9769-5141)", - "Su, X.D. (0000-0001-6948-2317)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ek0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ek0", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with NCL-00023824", - emdb: null, - pdb: { - dbId: "5S40", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S40", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s40_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s40", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GRVSGGNZRNHMQI-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s40_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s40", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 RBD binding to dog ACE2", - emdb: null, - pdb: { - dbId: "7E3J", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, spike, RBD, receptor binding, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7E3J", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7e3j_final.pdb", - externalLink: "https://pdb-redo.eu/db/7e3j", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9615", - name: "ACE2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Zhang, Y.", "Zhang, Z."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34234119", - title: "The molecular basis for SARS-CoV-2 binding to dog ACE2.", - journal: "Nat Commun 12: 4195-4195 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-24326-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34234119", - pubDate: "2021", - abstract: "", - authors: [ - "Zhang, Z.", - "Zhang, Y.", - "Liu, K.", - "Li, Y.", - "Lu, Q.", - "Wang, Q.", - "Wang, L.", - "Liao, H.", - "Zheng, A.", - "Ma, S.", - "Fan, Z.", - "Li, H.", - "Huang, W.", - "Bi, Y.", - "Zhao, X.", - "Gao, G.F.", - "Xiao, H.", - "Tong, Z.", - "Qi, J.", - "Sun, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7e3j_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7e3j", - }, - }, - { - title: - "Crystal structure of SARS CoV2 main protease in complex with EG009 (modelled using PanDDA event map)", - emdb: null, - pdb: { - dbId: "7NUK", - method: "X-RAY DIFFRACTION", - keywords: "Protease, Complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NUK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nuk_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nuk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "NXCZZJXJRNCFHV-UHFFFAOYSA-N"], - dbauthors: [ - "Oerlemans, R. (0000-0001-7114-3736)", - "Eris, D.", - "Wang, M. (0000-0002-5340-3036)", - "Sharpe, M.", - "Domling, A. (0000-0002-9923-8873)", - "Groves, M.R. (0000-0001-9859-5177)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34097796", - title: - "Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.", - journal: - "Angew.Chem.Int.Ed.Engl. 60: 18231-18239 (2021), 1521-3773", - doi: "https://doi.org/10.1002/anie.202105584", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34097796", - pubDate: "2021", - abstract: "", - authors: [ - "Sutanto, F.", - "Shaabani, S. (0000-0001-5546-7140)", - "Oerlemans, R.", - "Eris, D.", - "Patil, P.", - "Hadian, M.", - "Wang, M.", - "Sharpe, M.E.", - "Groves, M.R.", - "Domling, A. 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(0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. (0000-0001-9754-4503)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Mus musculus", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34016740", - title: - "Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants.", - journal: "Science 373: 818-823 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abh1139", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34016740", - pubDate: "2021", - abstract: "", - authors: [ - "Yuan, M.", - "Huang, D.", - "Lee, C.D.", - "Wu, N.C.", - "Jackson, A.M.", - "Zhu, X.", - "Liu, H.", - "Peng, L.", - "van Gils, M.J.", - "Sanders, R.W.", - "Burton, D.R.", - "Reincke, S.M.", - "Pruss, H.", - "Kreye, J.", - "Nemazee, D.", - "Ward, A.B.", - "Wilson, I.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lop_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lop", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with SF003", - emdb: null, - pdb: { - dbId: "5S4F", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S4F", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s4f_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s4f", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["FLBAYUMRQUHISI-UHFFFAOYSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-2687-0699)", - "Walsh, M.A. (0000-0001-5683-1151)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4f_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4f", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z56900771", - emdb: null, - pdb: { - dbId: "5S6Y", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5S6Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s6y_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s6y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "AUHRREWMYVOMRT-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s6y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s6y", - }, - }, - { - title: "SARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs", - emdb: null, - pdb: { - dbId: "7ZF3", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Omicron, RBD, antibody, Fab, Omi-3, EY6A, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZF3", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zf3_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zf3", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "EY6A heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-3 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-3 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "KFZMGEQAYNKOFK-UHFFFAOYSA-N"], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I.", "Huo, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35662412", - title: - "Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.", - journal: "Cell 185: 2116-2131.e18 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.05.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35662412", - pubDate: "2022", - abstract: "", - authors: [ - "Nutalai, R.", - "Zhou, D.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Supasa, P.", - "Liu, C.", - "Huo, J.", - "Mentzer, A.J.", - "Duyvesteyn, H.M.E.", - "Dijokaite-Guraliuc, A.", - "Skelly, D.", - "Ritter, T.G.", - "Amini, A.", - "Bibi, S.", - "Adele, S.", - "Johnson, S.A.", - "Constantinides, B.", - "Webster, H.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Goulder, P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Mongkolsapaya, J.", - "Fry, E.E.", - "Dejnirattisai, W.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zf3_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zf3", - }, - }, - { - title: - "2.0 Angstrom Resolution Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with S-Adenosyl-L-Homocysteine", - emdb: null, - pdb: { - dbId: "6WJT", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, VIRAL PROTEIN, S-Adenosyl-L-Homocysteine", - refModels: [ - { - emdbId: null, - pdbId: "6WJT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wjt_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wjt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32994211", - title: - "High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design.", - journal: "Sci.Signal. 13 (2020), 1937-9145", - doi: "https://doi.org/10.1126/scisignal.abe1202", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32994211", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Minasov, G. (0000-0001-5460-3462)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Kiryukhina, O. (0000-0001-5962-8423)", - "Brunzelle, J. (0000-0001-9197-0018)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.L.", - "Kiryukhina, O.", - "Wiersum, G.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Endres, M.", - "Jaroszewski, L.", - "Godzik, A.", - "Joachimiak, A.", - "Satchell, K.J.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wjt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wjt", - }, - }, - { - title: - "Crystal structure of RNA-binding domain of nucleocapsid phosphoprotein from SARS CoV-2, monoclinic crystal form", - emdb: null, - pdb: { - dbId: "6WKP", - method: "X-RAY DIFFRACTION", - keywords: - "CSGID, COVID-19, SARS COV-2, RNA-binding domain, nucleocapsid protein, nucleoprotein, Structural Genomics, Center for Structural Genomics of Infectious Diseases, VIRAL PROTEIN, RNA BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WKP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wkp_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wkp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "SXGZJKUKBWWHRA-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Godzik, A.", - "Chang, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of RNA-binding domain of nucleocapsid phosphoprotein from SARS CoV-2, monoclinic crystal form", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Chang, C.", - "Michalska, K.", - "Jedrzejczak, R.", - "Maltseva, N.", - "Endres, M.", - "Godzik, A.", - "Kim, Y.", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wkp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wkp", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Cov_HetLib030 (Mpro-x2097)", - emdb: null, - pdb: { - dbId: "5RHB", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "5RHB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rhb_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rhb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "KSQIQMUQPXONCB-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Keseru, G.M.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - "Keeley, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. (0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rhb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rhb", - }, - }, - { - title: "Crystal structure of the SARS-CoV-2 PLpro C111S mutant", - emdb: null, - pdb: { - dbId: "7CJD", - method: "X-RAY DIFFRACTION", - keywords: "Proteinase;drug target;, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7CJD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cjd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cjd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: ["Gao, X.", "Cui, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32895623", - title: "Crystal structure of SARS-CoV-2 papain-like protease.", - journal: "Acta Pharm Sin B 11: 237-245 (2021), 2211-3835", - doi: "https://doi.org/10.1016/j.apsb.2020.08.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32895623", - pubDate: "2021", - abstract: "", - authors: [ - "Gao, X.", - "Qin, B.", - "Chen, P.", - "Zhu, K.", - "Hou, P.", - "Wojdyla, J.A.", - "Wang, M.", - "Cui, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cjd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cjd", - }, - }, - { - title: "SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1", - emdb: null, - pdb: { - dbId: "7ZFE", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Omicron, BA.1, BA.2, RBD, antibody, Fab, Omi-32, VIRALPROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZFE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zfe_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zfe", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9844", - name: "Nanobody C1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-32 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-32 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I.", "Huo, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35662412", - title: - "Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.", - journal: "Cell 185: 2116-2131.e18 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.05.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35662412", - pubDate: "2022", - abstract: "", - authors: [ - "Nutalai, R.", - "Zhou, D.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Supasa, P.", - "Liu, C.", - "Huo, J.", - "Mentzer, A.J.", - "Duyvesteyn, H.M.E.", - "Dijokaite-Guraliuc, A.", - "Skelly, D.", - "Ritter, T.G.", - "Amini, A.", - "Bibi, S.", - "Adele, S.", - "Johnson, S.A.", - "Constantinides, B.", - "Webster, H.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Goulder, P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Mongkolsapaya, J.", - "Fry, E.E.", - "Dejnirattisai, W.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zfe_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zfe", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Tofogliflozin.", - emdb: null, - pdb: { - dbId: "7APH", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-!9, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7APH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aph_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aph", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "VWVKUNOPTJGDOB-AANPDWTMSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Turk, D. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7aph_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7aph", - }, - }, - { - title: - "Structure of apo SARS-CoV-2 Main Protease with large beta angle, space group C2.", - emdb: null, - pdb: { - dbId: "7AR6", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, MPro, COVID-19, PEPTIDE BINDING PROTEIN, virus protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7AR6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ar6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ar6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Oberthuer, D. 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(0000-0002-1931-8073)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m2p_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m2p", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2217052426", - emdb: null, - pdb: { - dbId: "5REE", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5REE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5ree_final.pdb", - externalLink: "https://pdb-redo.eu/db/5ree", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "ZFJGRVQFTNBLRP-YPMHNXCESA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5ree_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5ree", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1343543528 (Mpro-x2600)", - emdb: null, - pdb: { - dbId: "5RGZ", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RGZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rgz_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rgz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["DSTLUTUEFNLBST-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgz", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibody CS23", - emdb: null, - pdb: { - dbId: "7S5P", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Coronavirus, Antibody, Fab, VOC, Beta, B.1.351, Spike, RBD, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7S5P", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s5p_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s5p", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CS23 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CS23 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: ["Wilson, I.A. (0000-0002-6469-2419)", "Yuan, M. (0000-0001-9754-4503)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35076281", - title: - "SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies.", - journal: "Science 375: 782-787 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abm5835", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35076281", - pubDate: "2022", - abstract: "", - authors: [ - "Reincke, S.M. (0000-0002-8132-3527)", - "Yuan, M. (0000-0001-9754-4503)", - "Kornau, H.C. (0000-0003-4187-7549)", - "Corman, V.M. (0000-0002-3605-0136)", - "van Hoof, S. (0000-0002-2091-0904)", - "Sanchez-Sendin, E.", - "Ramberger, M. (0000-0003-3082-6906)", - "Yu, W. (0000-0002-4025-2646)", - "Hua, Y.", - "Tien, H. (0000-0001-7584-5989)", - "Schmidt, M.L.", - "Schwarz, T. (0000-0002-6054-4750)", - "Jeworowski, L.M. (0000-0002-4159-4189)", - "Brandl, S.E.", - "Rasmussen, H.F. (0000-0002-6923-875X)", - "Homeyer, M.A. (0000-0003-0630-3857)", - "Stoffler, L. (0000-0003-4724-5112)", - "Barner, M. (0000-0003-3448-7294)", - "Kunkel, D. (0000-0002-0054-955X)", - "Huo, S. (0000-0002-0119-7517)", - "Horler, J.", - "von Wardenburg, N. (0000-0003-0476-9813)", - "Kroidl, I.", - "Eser, T.M. (0000-0003-2682-9135)", - "Wieser, A.", - "Geldmacher, C.", - "Hoelscher, M. (0000-0002-7642-1835)", - "Ganzer, H. (0000-0003-0358-3689)", - "Weiss, G. (0000-0003-0709-2158)", - "Schmitz, D.", - "Drosten, C. (0000-0001-7923-0519)", - "Pruss, H. (0000-0002-8283-7976)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Kreye, J. (0000-0003-2913-1015)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s5p_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s5p", - }, - }, - { - title: - "The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate", - emdb: null, - pdb: { - dbId: "6W01", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus, endonuclease, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6W01", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6w01_final.pdb", - externalLink: "https://pdb-redo.eu/db/6w01", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "KRKNYBCHXYNGOX-UHFFFAOYSA-N", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Godzik, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32304108", - title: - "Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2.", - journal: "Protein Sci. 29: 1596-1605 (2020), 1469-896X", - doi: "https://doi.org/10.1002/pro.3873", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32304108", - pubDate: "2020", - abstract: "", - authors: [ - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Wilamowski, M.", - "Endres, M.", - "Godzik, A.", - "Michalska, K.", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w01_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w01", - }, - }, - { - title: - "Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and COVOX-278 Fabs", - emdb: null, - pdb: { - dbId: "7OR9", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, B.1.617 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7OR9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7or9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7or9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-278 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-278 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34242578", - title: - "Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.", - journal: "Cell 184: 4220-4236.e13 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.06.020", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34242578", - pubDate: "2021", - abstract: "", - authors: [ - "Liu, C.", - "Ginn, H.M.", - "Dejnirattisai, W.", - "Supasa, P.", - "Wang, B.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Zhou, D.", - "Mentzer, A.J.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Johnson, S.A.", - "Ritter, T.G.", - "Mason, C.", - "Costa Clemens, S.A.", - "Gomes Naveca, F.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Temperton, N.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Malik, T.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Baillie, V.", - "Serafin, N.", - "Ditse, Z.", - "Da Silva, K.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Madhi, S.", - "Nunes, M.C.", - "Goulder, P.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7or9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7or9", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102353", - emdb: null, - pdb: { - dbId: "5RFI", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfi_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfi", - details: "", - }, - ], - entities: [ - 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rfi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rfi", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102615", - emdb: null, - pdb: { - dbId: "5RER", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RER", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rer_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rer", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "HUEBTMPZBSOCPP-GFCCVEGCSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rer_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rer", - }, - }, - { - title: - "Joint X-ray/neutron structure of SARS-CoV-2 main protease (3CL Mpro) in complex with BBH-1", - emdb: null, - pdb: { - dbId: "7TDU", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 main protease, homodimer, cysteine protease, covalent inhibitor, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TDU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tdu_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tdu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ARSJHDLARMCGPB-KUGIMXMOSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35477935", - title: - "Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease", - journal: "Nat Commun 13 (2022), 2041-1723", - doi: "https://doi.org/10.1038/s41467-022-29915-z", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35477935", - pubDate: "2022", - abstract: "", - authors: [ - "Kneller, D.W.", - "Li, H.", - "Phillips, G.", - "Weiss, K.L.", - "Zhang, Q.", - "Arnould, M.A.", - "Jonsson, C.B.", - "Surendranathan, S.", - "Parvathareddy, J.", - "Blakeley, M.P.", - "Coates, L.", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A.", - "Kneller, D.", - "Phillips, G. 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(0000-0003-4459-9142)", - "Adams, P.D.", - "Mustyakimov, M.", - "Afonine, P.V.", - "Langan, P.", - ], - }, - { - pmID: "35169792", - title: - "Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease: room-temperature X-ray and neutron crystallography, binding thermodynamics, and antiviral activity.", - journal: "Res Sq (2022), 2693-5015", - doi: "https://doi.org/10.21203/rs.3.rs-1318037/v1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35169792", - pubDate: "2022", - abstract: "", - authors: [ - "Kneller, D.W.", - "Li, H.", - "Phillips, G.", - "Weiss, K.L.", - "Zhang, Q.", - "Arnould, M.A.", - "Jonsson, C.B.", - "Surendranathan, S.", - "Parvathareddy, J.", - "Blakeley, M.P.", - "Coates, L.", - "Louis, J.M.", - "Bonnesen, P.V.", - "Kovalevsky, A.", - "Kneller, D.", - "Phillips, G. (0000-0001-5858-3825)", - "Weiss, K. (0000-0002-6486-8007)", - "Arnould, M. (0000-0003-0172-8311)", - "Jonsson, C.", - "Blakeley, M. (0000-0002-6412-4358)", - "Coates, L. 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(0000-0003-2342-049X)", - "Louis, J. (0000-0002-0052-1899)", - "Bonnesen, P. (0000-0002-1397-8281)", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Adams, P.D.", - "Mustyakimov, M.", - "Afonine, P.V.", - "Langan, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tdu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tdu", - }, - }, - { - title: - "Structure of the SARS-CoV-2 main protease in complex with inhibitor PF-07321332", - emdb: null, - pdb: { - dbId: "7TE0", - method: "X-RAY DIFFRACTION", - keywords: "main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TE0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7te0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7te0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Yang, K.S.", "Liu, W.R."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35731933", - title: - "Evolutionary and Structural Insights about Potential SARS-CoV-2 Evasion of Nirmatrelvir.", - journal: "J.Med.Chem. 65: 8686-8698 (2022), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.2c00404", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35731933", - pubDate: "2022", - abstract: "", - authors: [ - "Yang, K.S. (0000-0002-1890-4169)", - "Leeuwon, S.Z.", - "Xu, S. (0000-0001-6260-9290)", - "Liu, W.R. (0000-0002-7078-6534)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7te0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7te0", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102142 (Mpro-x0708)", - emdb: null, - pdb: { - dbId: "5RGM", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RGM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rgm_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rgm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "DNSKRZJUSJXMPF-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgm", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Tretazicar.", - emdb: null, - pdb: { - dbId: "7AK4", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-!9, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AK4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ak4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ak4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "WOCXQMCIOTUMJV-UHFFFAOYSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Lieske, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - { - pmID: "", - title: - "Inhibition of SARS-CoV-2 main protease by allosteric drug-binding", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.11.12.378422", - pmidLink: "", - pubDate: "2020", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0001-6078-4095)", - "Guenther, S.", - "Reinke, P.", - "Ginn, H.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Paulraj, L.X.", - "Alves Franca, B.", - "Perbandt, M.", - "Giseler, H.", - "Hakanpaeae, J.", - "Noei, H.", - "Feiler, C.", - "Weiss, M.", - "Fernandez Garcia, Y.", - "Pearson, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7aku_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7aku", - }, - }, - { - title: - "Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 10d", - emdb: null, - pdb: { - dbId: "7TQ5", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TQ5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tq5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tq5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "GJLMLKMKSRQJFM-LPKXYDHTSA-N", - "GJLMLKMKSRQJFM-HDBZVZNMSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Liu, L.", - "Madden, T.K.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - "Picard, H.R.", - "Thruman, H.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36654747", - title: - "Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.", - journal: "Acs Pharmacol Transl Sci 6: 181-194 (2023), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00206", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36654747", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Nguyen, H.N.", - "Rathnayake, A.D.", - "Kim, Y.", - "Perera, K.D.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tq5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tq5", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000274438208", - emdb: null, - pdb: { - dbId: "5RSH", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsh_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GGTHBUVHAUVHID-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsh", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to AT7519", - emdb: null, - pdb: { - dbId: "7AGA", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, MPro, COVID-19, PEPTIDE BINDING PROTEIN, virus protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7AGA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aga_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aga", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVPNQJVDAFNBDN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Oberthuer, D. 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(0000-0002-6841-0298)", - "Haouz, A. (0000-0003-1196-1635)", - "Mechaly, A. (0000-0002-5305-7495)", - "Caillet-Saguy, C. (0000-0001-5066-0435)", - "Alvarez, F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35283834", - title: - "Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins.", - journal: "Front Microbiol 13: 829094-829094 (2022), 1664-302X", - doi: "https://doi.org/10.3389/fmicb.2022.829094", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35283834", - pubDate: "2022", - abstract: "", - authors: [ - "Zhu, Y.", - "Alvarez, F.", - "Wolff, N.", - "Mechaly, A.", - "Brule, S.", - "Neitthoffer, B.", - "Etienne-Manneville, S.", - "Haouz, A.", - "Boeda, B.", - "Caillet-Saguy, C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7qct_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7qct", - }, - }, - { - title: - "SARS-CoV-2 main protease in a covalent complex with a pyridine derivative of ABT-957, compound 1", - emdb: null, - pdb: { - dbId: "7AEH", - method: "X-RAY DIFFRACTION", - keywords: "covid-19, inhibitor, protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7AEH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7aeh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7aeh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "LGWQYJCCERJRJX-MZKUHISZSA-N"], - dbauthors: [ - "Owen, C.D.", - "Stuart, D.I.", - "Brewitz, L.", - "Malla, T.R.", - "Tumber, A.", - "Lukacik, P.", - "Strain-Damerell, C.", - "Walsh, M.A.", - "Schofield, C.J.", - "Fearon, D.", - "von Delft, F.", - 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"Xu, T.", - "Wang, Q.", - "Yi, H.", - "Niu, X.", - "Zhu, J.", - "Fan, M.", - "Hou, R.", - "Shao, Y.", - "Huang, S.", - "Li, C.", - "Hu, P.", - "Zheng, P.", - "He, P.", - "Luo, J.", - "Yan, Q.", - "Xiong, X.", - "Liu, J.", - "Zhao, J.", - "Chen, L. 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(0000-0002-5416-5789)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33060199", - title: - "Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography.", - journal: "J.Biol.Chem. 295: 17365-17373 (2020), 1083-351X", - doi: "https://doi.org/10.1074/jbc.AC120.016154", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33060199", - pubDate: "2020", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Phillips, G.", - "Weiss, K.L. (0000-0002-6486-8007)", - "Pant, S.", - "Zhang, Q.", - "O'Neill, H.M.", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Kneller, D.W.", - ], - }, - { - pmID: "33755450", - title: - "Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography.", - journal: "J.Med.Chem. 64: 4991-5000 (2021), 0022-2623", - doi: "https://doi.org/10.1021/acs.jmedchem.1c00058", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33755450", - pubDate: "2021", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Phillips, G.", - "Weiss, K.L. (0000-0002-6486-8007)", - "Pant, S.", - "Zhang, Q.", - "O'Neill, H.M.", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - "Kneller, D.W.", - "Weiss, K.L.", - "Coates, L.", - "Kovalevsky, A.", - "Adams, P.D.", - "Mustyakimov, M.", - "Afonine, P.V.", - "Langan, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jun_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jun", - }, - }, - { - title: - "Complex structure of a human monoclonal antibody with SARS-CoV-2 nucleocapsid protein NTD", - emdb: null, - pdb: { - dbId: "7CR5", - method: "X-RAY DIFFRACTION", - keywords: - "Human monoclonal antibody, SARS-CoV-2, nucleocapsid protein, Complex, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7CR5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cr5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cr5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "monoclonal antibody chain H", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "monoclonal antibody chain L", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: ["Chen, S. 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(0000-0002-7634-2141)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cr5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cr5", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000374420934", - emdb: null, - pdb: { - dbId: "5RSI", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsi_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UZDOXWRWKJXTPZ-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsi", - }, - }, - { - title: - "Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 6c", - emdb: null, - pdb: { - dbId: "7TQ4", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TQ4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tq4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tq4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MMZNSFGNZLNDCE-XYYCENQHSA-N"], - dbauthors: [ - "Madden, T.K.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - "Picard, H.R.", - "Thruman, H.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36654747", - title: - "Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.", - journal: "Acs Pharmacol Transl Sci 6: 181-194 (2023), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00206", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36654747", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Nguyen, H.N.", - "Rathnayake, A.D.", - "Kim, Y.", - "Perera, K.D.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tq4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tq4", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (II)", - emdb: null, - pdb: { - dbId: "7O36", - method: "X-RAY DIFFRACTION", - keywords: "Nucleocapsid, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7O36", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7o36_final.pdb", - externalLink: "https://pdb-redo.eu/db/7o36", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XKMLYUALXHKNFT-UUOKFMHZSA-J", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Ciges-Tomas, J.R. (0000-0003-2647-3052)", - "Vilar, M. (0000-0002-9376-6544)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35842466", - title: - "Identification of a guanine-specific pocket in the protein N of SARS-CoV-2.", - journal: "Commun Biol 5: 711-711 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03647-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35842466", - pubDate: "2022", - abstract: "", - authors: [ - "Rafael Ciges-Tomas, J. (0000-0003-2647-3052)", - "Franco, M.L.", - "Vilar, M. 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(0000-0003-4946-4300)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography", - journal: "Crystals 11 (2021), 2073-4352", - doi: "https://doi.org/10.3390/cryst11121579", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Guven, O.", - "Gul, M.", - "Ayan, E.", - "Johnson, J.A.", - "Cakilkaya, B.", - "Usta, G.", - "Ertem, F.B.", - "Tokay, N.", - "Yuksel, B.", - "Gocenler, O.", - "Buyukdag, C.", - "Botha, S.", - "Ketawala, G.", - "Su, Z.", - "Hayes, B.", - "Poitevin, F.", - "Batyuk, A.", - "Yoon, C.H.", - "Kupitz, C.", - "Durdagi, S.", - "Sierra, R.G.", - "DeMirci, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7vk8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7vk8", - }, - }, - { - title: "SARS-CoV-2 frameshifting pseudoknot RNA", - emdb: null, - pdb: { - dbId: "7MKY", - method: "X-RAY DIFFRACTION", - keywords: - "Pseudoknot, tetraloop, triple, SARS, virus, COVID, coronavirus, severe acute respiratory syndrome, frameshift, RNA", - refModels: [ - { - emdbId: null, - pdbId: "7MKY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7mky_final.pdb", - externalLink: "https://pdb-redo.eu/db/7mky", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "RNA (66-MER)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "DYLMFCCYOUSRTK-UHFFFAOYSA-N", - "NPYPAHLBTDXSSS-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "SVTOYMIYCMHPIV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Jones, C.P. 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(0000-0003-4549-1619)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "34845084", - title: - "Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot.", - journal: "Rna 28: 239-249 (2022), 1469-9001", - doi: "https://doi.org/10.1261/rna.078825.121", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34845084", - pubDate: "2022", - abstract: "", - authors: ["Jones, C.P.", "Ferre-D'Amare, A.R."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7mky_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7mky", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102962 (Mpro-x0705)", - emdb: null, - pdb: { - dbId: "5RGL", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RGL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rgl_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rgl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "DRKSMECTOWRXKP-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgl", - }, - }, - { - title: - "Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530724963", - emdb: null, - pdb: { - dbId: "7S4B", - method: "X-RAY DIFFRACTION", - keywords: - "enzyme-inhibitor complex, cysteine protease, homodimer, HYDROLASE, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7S4B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s4b_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s4b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["YZVOKFXROIBJSM-GFCCVEGCSA-N"], - dbauthors: ["Coates, L.", "Kneller, D.W.", "Kovalevsky, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35434531", - title: - "Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.", - journal: "Acs Pharmacol Transl Sci 5: 255-265 (2022), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00026", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35434531", - pubDate: "2022", - abstract: "", - authors: [ - "Glaser, J. (0000-0003-1852-3849)", - "Sedova, A.", - "Galanie, S. (0000-0001-5712-2568)", - "Kneller, D.W.", - "Davidson, R.B.", - "Maradzike, E.", - "Del Galdo, S.", - "Labbe, A.", - "Hsu, D.J.", - "Agarwal, R.", - "Bykov, D.", - "Tharrington, A.", - "Parks, J.M. (0000-0002-3103-9333)", - "Smith, D.M.A.", - "Daidone, I. (0000-0001-8970-8408)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A.", - "Smith, J.C. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5res_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5res", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102277", - emdb: null, - pdb: { - dbId: "5RFH", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfh_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "KIKCPJKIAGFHCO-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rfh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rfh", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibodies CS44 and COVA1-16", - emdb: null, - pdb: { - dbId: "7S5Q", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Coronavirus, Antibody, Fab, VOC, Beta, B.1.351, Spike, RBD, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7S5Q", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s5q_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s5q", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CS44 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CS44 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA1-16 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA1-16 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: ["Wilson, I.A. (0000-0002-6469-2419)", "Yuan, M. (0000-0001-9754-4503)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35076281", - title: - "SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies.", - journal: "Science 375: 782-787 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abm5835", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35076281", - pubDate: "2022", - abstract: "", - authors: [ - "Reincke, S.M. (0000-0002-8132-3527)", - "Yuan, M. (0000-0001-9754-4503)", - "Kornau, H.C. (0000-0003-4187-7549)", - "Corman, V.M. (0000-0002-3605-0136)", - "van Hoof, S. (0000-0002-2091-0904)", - "Sanchez-Sendin, E.", - "Ramberger, M. (0000-0003-3082-6906)", - "Yu, W. (0000-0002-4025-2646)", - "Hua, Y.", - "Tien, H. (0000-0001-7584-5989)", - "Schmidt, M.L.", - "Schwarz, T. (0000-0002-6054-4750)", - "Jeworowski, L.M. (0000-0002-4159-4189)", - "Brandl, S.E.", - "Rasmussen, H.F. (0000-0002-6923-875X)", - "Homeyer, M.A. (0000-0003-0630-3857)", - "Stoffler, L. (0000-0003-4724-5112)", - "Barner, M. (0000-0003-3448-7294)", - "Kunkel, D. (0000-0002-0054-955X)", - "Huo, S. (0000-0002-0119-7517)", - "Horler, J.", - "von Wardenburg, N. (0000-0003-0476-9813)", - "Kroidl, I.", - "Eser, T.M. (0000-0003-2682-9135)", - "Wieser, A.", - "Geldmacher, C.", - "Hoelscher, M. (0000-0002-7642-1835)", - "Ganzer, H. (0000-0003-0358-3689)", - "Weiss, G. (0000-0003-0709-2158)", - "Schmitz, D.", - "Drosten, C. (0000-0001-7923-0519)", - "Pruss, H. (0000-0002-8283-7976)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Kreye, J. (0000-0003-2913-1015)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s5q_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s5q", - }, - }, - { - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder441 inhibitor", - emdb: null, - pdb: { - dbId: "7JN2", - method: "X-RAY DIFFRACTION", - keywords: - "covid-19, coronavirus, SARS, CoV-2, papain-like protease, IDP51000, IDP52003, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "7JN2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jn2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jn2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease", - details: "3 first residues, SNA , are cloning artifacts (expression tag)", - altNames: - "Non-structural protein 3,nsp3, PL2-PRO, Papain-like proteinase, PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PZEBTCMUWPLVEX-CQSZACIVSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - ], - dbauthors: [ - "Zhang, Y.", - "Tesar, C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Osipiuk, J.", - "Endres, M.", - "Maki, S.", - "Azizi, S.A.", - "Dickinson, B.C.", - "Zhou, Z.", - "Lisnyak, V.", - "Taylor, C.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder441", - journal: "to be published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Osipiuk, J.", - "Tesar, C.", - "Endres, M.", - "Lisnyak, V.", - "Maki, S.", - "Taylor, C.", - "Zhang, Y.", - "Zhou, Z.", - "Azizi, S.A.", - "Jones, K.", - "Kathayat, R.", - "Snyder, S.A.", - "Dickinson, B.C.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7jn2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7jn2", - }, - }, - { - title: - "Crystal structure of nsp16-nsp10 heterodimer from SARS-CoV-2 in complex with SAM (with additional SAM during crystallization)", - emdb: null, - pdb: { - dbId: "7C2I", - method: "X-RAY DIFFRACTION", - keywords: "2'-O-Methylase, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7C2I", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c2i_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c2i", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MEFKEPWMEQBLKI-AIRLBKTGSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Chen, H.", - "Cao, Y.", - "Lu, G.W.", - "Lin, S.", - "Zheng, Y.", - "Ye, F.", - "Qiao, J.X.", - "Yang, S.Y.", - "Chen, Z.M.", - "Yang, F.L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32728018", - title: - "Crystal structure of SARS-CoV-2 nsp10/nsp16 2'-O-methylase and its implication on antiviral drug design.", - journal: - "Signal Transduct Target Ther 5: 131-131 (2020), 2059-3635", - doi: "https://doi.org/10.1038/s41392-020-00241-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32728018", - pubDate: "2020", - abstract: "", - authors: [ - "Lin, S.", - "Chen, H.", - "Ye, F.", - "Chen, Z.", - "Yang, F.", - "Zheng, Y.", - "Cao, Y.", - "Qiao, J.", - "Yang, S.", - "Lu, G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7c2i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7c2i", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434865", - emdb: null, - pdb: { - dbId: "5RED", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RED", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5red_final.pdb", - externalLink: "https://pdb-redo.eu/db/5red", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "QDTNFZGZGSMNCU-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - 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(0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5red_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5red", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z4439011520 (Mpro-x2694)", - emdb: null, - pdb: { - dbId: "5RH5", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RH5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rh5_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rh5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UCJCNZJAAQBBMU-HSZRJFAPSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rh5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rh5", - }, - }, - { - title: - "Crystal structure of spike protein receptor binding domain of escape mutant SARS-CoV-2 from immunocompromised patient (d146*) in complex with human receptor ACE2", - emdb: null, - pdb: { - dbId: "7SN0", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, spike protein, neutralization escape mutant, ACE2, receptor binding, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7SN0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7sn0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7sn0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "A0A7S6Y2X1", - organism: "2697049", - name: "Surface glycoprotein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - ], - dbauthors: [ - "Pan, J. (0000-0002-0070-955X)", - "Abraham, J. (0000-0002-7937-3920)", - "Clark, S. (0000-0001-9944-0919)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34855508", - title: - "Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.", - journal: "Science 375: eabl6251-eabl6251 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abl6251", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34855508", - pubDate: "2022", - abstract: "", - authors: [ - "Nabel, K.G. (0000-0002-4429-7075)", - "Clark, S.A. (0000-0001-9944-0919)", - "Shankar, S. (0000-0001-9340-9945)", - "Pan, J. (0000-0002-0070-955X)", - "Clark, L.E. (0000-0002-6093-7597)", - "Yang, P.", - "Coscia, A. (0000-0002-6836-9993)", - "McKay, L.G.A. (0000-0003-0369-9067)", - "Varnum, H.H.", - "Brusic, V.", - "Tolan, N.V.", - "Zhou, G.", - "Desjardins, M. (0000-0003-4028-8507)", - "Turbett, S.E. (0000-0002-3603-8110)", - "Kanjilal, S. (0000-0002-1221-5725)", - "Sherman, A.C. (0000-0002-6075-3990)", - "Dighe, A.", - "LaRocque, R.C. (0000-0003-4558-0339)", - "Ryan, E.T.", - "Tylek, C.", - "Cohen-Solal, J.F. (0000-0002-1385-2566)", - "Darcy, A.T.", - "Tavella, D. (0000-0002-2030-2087)", - "Clabbers, A. (0000-0002-4258-9680)", - "Fan, Y.", - "Griffiths, A. (0000-0001-5435-8364)", - "Correia, I.R. (0000-0003-2295-7199)", - "Seagal, J. (0000-0002-5959-5139)", - "Baden, L.R.", - "Charles, R.C.", - "Abraham, J. (0000-0002-7937-3920)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7sn0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7sn0", - }, - }, - { - title: "SARS-CoV-2 Omicron RBD in complex with Omi-25 Fab", - emdb: null, - pdb: { - dbId: "7ZFD", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Omicron, BA.1, BA.2, RBD, antibody, Fab, Omi-25, VIRALPROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7ZFD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7zfd_final.pdb", - externalLink: "https://pdb-redo.eu/db/7zfd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Omi-25 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Omi-25 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D.I.", "Huo, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35662412", - title: - "Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.", - journal: "Cell 185: 2116-2131.e18 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.05.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35662412", - pubDate: "2022", - abstract: "", - authors: [ - "Nutalai, R.", - "Zhou, D.", - "Tuekprakhon, A.", - "Ginn, H.M.", - "Supasa, P.", - "Liu, C.", - "Huo, J.", - "Mentzer, A.J.", - "Duyvesteyn, H.M.E.", - "Dijokaite-Guraliuc, A.", - "Skelly, D.", - "Ritter, T.G.", - "Amini, A.", - "Bibi, S.", - "Adele, S.", - "Johnson, S.A.", - "Constantinides, B.", - "Webster, H.", - "Temperton, N.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Crook, D.", - "Pollard, A.J.", - "Lambe, T.", - "Goulder, P.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Mongkolsapaya, J.", - "Fry, E.E.", - "Dejnirattisai, W.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zfd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zfd", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Cov_HetLib053 (Mpro-x2119)", - emdb: null, - pdb: { - dbId: "5RHC", - method: "X-RAY DIFFRACTION", - keywords: "HYDROLASE-HYDROLASE INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "5RHC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rhc_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rhc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CWGOCYXTOJEBFI-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Keseru, G.M.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - "Keeley, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rhc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rhc", - }, - }, - { - title: - "1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer from SARS-CoV-2 in Complex with Sinefungin", - emdb: null, - pdb: { - dbId: "6WKQ", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WKQ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wkq_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wkq", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "LMXOHSDXUQEUSF-YECHIGJVSA-N", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32994211", - title: - "High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design.", - journal: "Sci.Signal. 13 (2020), 1937-9145", - doi: "https://doi.org/10.1126/scisignal.abe1202", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32994211", - pubDate: "2020", - abstract: "", - authors: [ - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Minasov, G. (0000-0001-5460-3462)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Kiryukhina, O. (0000-0001-5962-8423)", - "Brunzelle, J. (0000-0001-9197-0018)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - "Rosas-Lemus, M.", - "Minasov, G.", - "Shuvalova, L.", - "Inniss, N.L.", - "Kiryukhina, O.", - "Wiersum, G.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Endres, M.", - "Jaroszewski, L.", - "Godzik, A.", - "Joachimiak, A.", - "Satchell, K.J.F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wkq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wkq", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2889976755", - emdb: null, - pdb: { - dbId: "5S6X", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5S6X", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s6x_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s6x", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "GEZOFSFHYQGWNK-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s6x_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s6x", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 6", - emdb: null, - pdb: { - dbId: "7B5Z", - method: "X-RAY DIFFRACTION", - keywords: "Inhibitor, complex, protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7B5Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7b5z_final.pdb", - externalLink: "https://pdb-redo.eu/db/7b5z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "WYBCNWLSBYEMQV-UHFFFAOYSA-N"], - dbauthors: ["Talibov, V.O. (0000-0002-1135-2744)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35142215", - title: - "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", - journal: "J.Am.Chem.Soc. 144: 2905-2920 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08402", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35142215", - pubDate: "2022", - abstract: "", - authors: [ - "Luttens, A. (0000-0003-2915-7901)", - "Gullberg, H.", - "Abdurakhmanov, E.", - "Vo, D.D.", - "Akaberi, D. (0000-0002-9595-9796)", - "Talibov, V.O.", - "Nekhotiaeva, N.", - "Vangeel, L.", - "De Jonghe, S. (0000-0002-3872-6558)", - "Jochmans, D.", - "Krambrich, J.", - "Tas, A.", - "Lundgren, B.", - "Gravenfors, Y. (0000-0001-6025-4908)", - "Craig, A.J.", - "Atilaw, Y.", - "Sandstrom, A.", - "Moodie, L.W.K. (0000-0002-9500-4535)", - "Lundkvist, A.", - "van Hemert, M.J.", - "Neyts, J.", - "Lennerstrand, J.", - "Kihlberg, J. (0000-0002-4205-6040)", - "Sandberg, K.", - "Danielson, U.H. (0000-0003-2728-0340)", - "Carlsson, J. (0000-0003-4623-2977)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7b5z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7b5z", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with SF005", - emdb: null, - pdb: { - dbId: "5S4G", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S4G", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s4g_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s4g", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["NCZQAIFOXJOCFI-UHFFFAOYSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - { - pmID: "34045440", - title: - "Exploring protein hotspots by optimized fragment pharmacophores.", - journal: "Nat Commun 12: 3201-3201 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23443-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34045440", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. 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(0000-0003-2687-0699)", - "Walsh, M.A. (0000-0001-5683-1151)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4g", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with two cross-neutralizing antibodies CV38-142 and COVA1-16 Fabs isolated from COVID-19 patients", - emdb: null, - pdb: { - dbId: "7LM8", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, SARS-CoV, Antibody, Spike, Coronavirus, COVID-19, SARS, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex, Cross-Neutralization, Synergy, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7LM8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lm8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lm8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA1-16 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA1-16 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV38-142 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV38-142 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: ["Liu, H. (0000-0002-2412-7853)", "Wilson, I.A. (0000-0002-6469-2419)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33594361", - title: - "A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.02.11.430866", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33594361", - pubDate: "2021", - abstract: "", - authors: [ - "Liu, H.", - "Yuan, M.", - "Huang, D.", - "Bangaru, S.", - "Zhao, F.", - "Lee, C.D.", - "Peng, L.", - "Barman, S.", - "Zhu, X.", - "Nemazee, D.", - "Burton, D.R.", - "van Gils, M.J.", - "Sanders, R.W.", - "Kornau, H.C.", - "Reincke, S.M.", - "Pruss, H.", - "Kreye, J.", - "Wu, N.C.", - "Ward, A.B.", - "Wilson, I.A.", - "Liu, H. (0000-0002-2412-7853)", - "Yuan, M. (0000-0001-9754-4503)", - "Huang, D. (0000-0002-6989-639X)", - "Bangaru, S. (0000-0001-7994-4693)", - "Lee, C.D. (0000-0002-5470-2484)", - "Peng, L. (0000-0002-3600-2134)", - "Zhu, X. (0000-0002-6021-3740)", - "Nemazee, D. (0000-0002-4769-6311)", - "van Gils, M.J. (0000-0003-3422-8161)", - "Sanders, R.W. (0000-0002-2324-8573)", - "Reincke, S.M. (0000-0002-8132-3527)", - "Pruss, H. (0000-0002-8283-7976)", - "Kreye, J. (0000-0003-2913-1015)", - "Wu, N.C. (0000-0002-9078-6697)", - "Ward, A.B. (0000-0001-7153-3769)", - "Wilson, I.A. (0000-0002-6469-2419)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lm8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lm8", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with NCL-00023825", - emdb: null, - pdb: { - dbId: "5S41", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S41", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s41_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s41", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SSLMGOKTIUIZLY-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s41_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s41", - }, - }, - { - title: "The crystal structure of 3CL MainPro of SARS-CoV-2 with C145S mutation", - emdb: null, - pdb: { - dbId: "6XOA", - method: "X-RAY DIFFRACTION", - keywords: - "3CL, main protease, SARS-CoV-2, mutant, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6XOA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xoa_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xoa", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Joachimiak, A. (0000-0003-2535-6209)", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Tan, K. (0000-0002-4003-7903)", - "Maltseva, N.I.", - "Welk, L.F.", - "Jedrzejczak, R.P.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of 3CL MainPro of SARS-CoV-2 with C145S mutation", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Tan, K. (0000-0002-4003-7903)", - "Maltseva, N.I.", - "Welk, L.F.", - "Jedrzejczak, R.P.", - "Joachimiak, A. (0000-0003-2535-6209)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xoa_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xoa", - }, - }, - { - title: - "Room temperature X-ray crystallography reveals catalytic cysteine in the SARS-CoV-2 3CL Mpro is highly reactive: Insights for enzyme mechanism and drug design", - emdb: null, - pdb: { - dbId: "6XB0", - method: "X-RAY DIFFRACTION", - keywords: "Main Protease SARS-CoV-2 3CL Mpro, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6XB0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xb0_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xb0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33063790", - title: - "Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M pro : insights into enzyme mechanism and drug design.", - journal: "Iucrj 7 (2020), 2052-2525", - doi: "https://doi.org/10.1107/S2052252520012634", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33063790", - pubDate: "2020", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Phillips, G. (0000-0001-5858-3825)", - "O'Neill, H.M.", - "Tan, K. (0000-0002-4003-7903)", - "Joachimiak, A. (0000-0003-2535-6209)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xb0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xb0", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC001364194305 - (R) isomer", - emdb: null, - pdb: { - dbId: "5SOP", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sop_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sop", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["CIGPPCNTUJESTR-CQSZACIVSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sop_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sop", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1354370680", - emdb: null, - pdb: { - dbId: "5SLK", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slk_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "WBIQOAOWXPGYEU-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slk", - }, - }, - { - title: - "Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-C2 Fab)", - emdb: null, - pdb: { - dbId: "7KFX", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, SARS-CoV-2, neutralizing antibody, affinity maturation, IMMUNE SYSTEM, IMMUNE SYSTEM-Viral protein complex", - refModels: [ - { - emdbId: null, - pdbId: "7KFX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kfx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kfx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "heavy chain of human antibody C1A-C2 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "light chain of human antibody C1A-C2 Fab", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Pan, J. (0000-0002-0070-955X)", - "Abraham, J. (0000-0002-7937-3920)", - "Clark, L. (0000-0002-6093-7597)", - "Clark, S. (0000-0001-9944-0919)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33200128", - title: - "Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.11.13.381533", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33200128", - pubDate: "2020", - abstract: "", - authors: [ - "Clark, S.A.", - "Clark, L.E.", - "Pan, J. (0000-0002-0070-955X)", - "Coscia, A.", - "McKay, L.G.A.", - "Shankar, S.", - "Johnson, R.I.", - "Griffiths, A.", - "Abraham, J. (0000-0002-7937-3920)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kfx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kfx", - }, - }, - { - title: - "Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-2',3'-Vanadate", - emdb: null, - pdb: { - dbId: "7K1L", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus 2, endoribonuclease, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7K1L", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k1l_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k1l", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "KOQFIXLULDPZLM-ODQFIEKDSA-L", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Welk, L.", - "Michalska, K.", - "Chang, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33564093", - title: - "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.", - journal: "Commun Biol 4: 193-193 (2021), 2399-3642", - doi: "https://doi.org/10.1038/s42003-021-01735-9", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33564093", - pubDate: "2021", - abstract: "", - authors: [ - "Kim, Y.", - "Wower, J. (0000-0001-8096-7745)", - "Maltseva, N. (0000-0002-2871-465X)", - "Chang, C.", - "Jedrzejczak, R.", - "Wilamowski, M.", - "Kang, S.", - "Nicolaescu, V.", - "Randall, G.", - "Michalska, K.", - "Joachimiak, A. (0000-0003-2535-6209)", - "Wower, J.", - "Maltseva, N.", - "Nicolaescu,, N.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k1l_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k1l", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 1-21", - emdb: null, - pdb: { - dbId: "8CWU", - method: "X-RAY DIFFRACTION", - keywords: - "cross-neutralizing antibody; nanobody; SARS-CoV-2; Sarbecovirus; IMMUNE SYSTEM; VHH, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CWU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cwu_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cwu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "VHH 1-21", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Liu, H. (0000-0002-2412-7853)", "Wilson, I.A. (0000-0002-6469-2419)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35738279", - title: "Superimmunity by pan-sarbecovirus nanobodies.", - journal: "Cell Rep 39: 111004-111004 (2022), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2022.111004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35738279", - pubDate: "2022", - abstract: "", - authors: [ - "Xiang, Y.", - "Huang, W.", - "Liu, H.", - "Sang, Z.", - "Nambulli, S.", - "Tubiana, J.", - "Williams Jr., K.L.", - "Duprex, W.P.", - "Schneidman-Duhovny, D.", - "Wilson, I.A.", - "Taylor, D.J.", - "Shi, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cwu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cwu", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.3", - emdb: null, - pdb: { - dbId: "6XC4", - method: "X-RAY DIFFRACTION", - keywords: - "Antibody, SARS-CoV-2, Coronavirus, Spike, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "6XC4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xc4_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xc4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.3 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.3 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Liu, H. (0000-0002-2412-7853)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. (0000-0001-9754-4503)", - "Wu, N.C. (0000-0002-9078-6697)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32661058", - title: - "Structural basis of a shared antibody response to SARS-CoV-2.", - journal: "Science 369: 1119-1123 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abd2321", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32661058", - pubDate: "2020", - abstract: "", - authors: [ - "Yuan, M. (0000-0001-9754-4503)", - "Liu, H. (0000-0002-2412-7853)", - "Wu, N.C. (0000-0002-9078-6697)", - "Lee, C.D. (0000-0002-5470-2484)", - "Zhu, X. (0000-0002-6021-3740)", - "Zhao, F. (0000-0002-3172-1340)", - "Huang, D. (0000-0002-6989-639X)", - "Yu, W. (0000-0002-4025-2646)", - "Hua, Y.", - "Tien, H. (0000-0001-7584-5989)", - "Rogers, T.F. 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(0000-0002-6989-639X)", - "Yu, W. (0000-0002-4025-2646)", - "Hua, Y.", - "Tien, H. (0000-0001-7584-5989)", - "Rogers, T.F. (0000-0001-9756-327X)", - "Landais, E. (0000-0002-8183-5565)", - "Sok, D. (0000-0002-9354-1740)", - "Jardine, J.G. (0000-0001-8951-1074)", - "Burton, D.R. (0000-0001-6711-9864)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Yuan, M.", - "Liu, H.", - "Wu, N.C.", - "Lee, C.D.", - "Zhu, X.", - "Zhao, F.", - "Huang, D.", - "Yu, W.", - "Tien, H.", - "Rogers, T.F.", - "Landais, E.", - "Sok, D.", - "Jardine, J.G.", - "Burton, D.R.", - "Wilson, I.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xc4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xc4", - }, - }, - { - title: - "Structure of SARS-CoV-2 Beta variant spike receptor-binding domain complexed with human ACE2", - emdb: null, - pdb: { - dbId: "7EKG", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, spike, RBD, 501Y.V2, ACE2, VIRAL PROTEIN, HYDROLASE-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7EKG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ekg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ekg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Gao, G.F. (0000-0002-3869-615X)", - "Su, C. (0000-0002-5824-7968)", - "Qi, J.X. (0000-0002-9358-4732)", - "Han, P.C. (0000-0002-4551-6209)", - "Zhang, Y.F. (0000-0003-3026-3357)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34671049", - title: - "Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.", - journal: "Nat Commun 12: 6103-6103 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-26401-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34671049", - pubDate: "2021", - abstract: "", - authors: [ - "Han, P.", - "Su, C. (0000-0002-5824-7968)", - "Zhang, Y.", - "Bai, C.", - "Zheng, A.", - "Qiao, C.", - "Wang, Q.", - "Niu, S.", - "Chen, Q.", - "Li, W.", - "Liao, H.", - "Li, J.", - "Zhang, Z.", - "Cho, H.", - "Yang, M.", - "Rong, X.", - "Hu, Y.", - "Huang, N. (0000-0002-6912-033X)", - "Yan, J. (0000-0003-0502-3829)", - "Wang, Q. (0000-0003-3768-0401)", - "Zhao, X. (0000-0002-2001-1343)", - "Gao, G.F. (0000-0002-3869-615X)", - "Qi, J. (0000-0002-9358-4732)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ekg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ekg", - }, - }, - { - title: - "Crystallographic structure of neutralizing antibody 2-15 in complex with SARS-CoV-2 spike receptor-binding Domain (RBD).", - emdb: null, - pdb: { - dbId: "7L5B", - method: "X-RAY DIFFRACTION", - keywords: - "Spike protein S1, receptor binding protein SARS COV-2, VIRAL PROTEIN, VIRAL PROTEIN-Immune System complex", - refModels: [ - { - emdbId: null, - pdbId: "7L5B", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7l5b_final.pdb", - externalLink: "https://pdb-redo.eu/db/7l5b", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "2-15 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "2-15 Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Reddem, E.R.", "Shapiro, L."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33794145", - title: - "Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class.", - journal: "Cell Rep 35: 108950-108950 (2021), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2021.108950", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33794145", - pubDate: "2021", - abstract: "", - authors: [ - "Rapp, M.", - "Guo, Y.", - "Reddem, E.R.", - "Yu, J.", - "Liu, L.", - "Wang, P.", - "Cerutti, G.", - "Katsamba, P.", - "Bimela, J.S.", - "Bahna, F.A.", - "Mannepalli, S.M.", - "Zhang, B.", - "Kwong, P.D.", - "Huang, Y.", - "Ho, D.D.", - "Shapiro, L.", - "Sheng, Z.", - "Bimela, J.", - "Bahna, F.", - "Mannepalli, S.", - ], - }, - { - pmID: "", - title: - "Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.01.11.426218", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Rapp, M.", - "Guo, Y.", - "Reddem, E.R.", - "Yu, J.", - "Liu, L.", - "Wang, P.", - "Cerutti, G.", - "Katsamba, P.", - "Bimela, J.S.", - "Bahna, F.A.", - "Mannepalli, S.M.", - "Zhang, B.", - "Kwong, P.D.", - "Huang, Y.", - "Ho, D.D.", - "Shapiro, L.", - "Sheng, Z.", - "Bimela, J.", - "Bahna, F.", - "Mannepalli, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7l5b_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7l5b", - }, - }, - { - title: - "Crystal structure of synthetic nanobody (Sb16) complexes with SARS-CoV-2 receptor binding domain", - emdb: null, - pdb: { - dbId: "7KGK", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Spike Protein, RBD, Antibody, Nanobody, Sybody, VIRAL PROTEIN, Epitope, Neutralization", - refModels: [ - { - emdbId: null, - pdbId: "7KGK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7kgk_final.pdb", - externalLink: "https://pdb-redo.eu/db/7kgk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "32630", - name: "Sb16, Sybody-16, Synthetic Nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: true, - }, - ], - ligands: [], - dbauthors: [ - "Jiang, J. 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(0000-0002-5126-6250)", - "Natarajan, K. (0000-0002-6295-2571)", - "Margulies, D.H. (0000-0001-8530-7375)", - ], - }, - { - pmID: "33532775", - title: - "Synthetic nanobody-SARS-CoV-2 receptor-binding domain structures identify distinct epitopes.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.01.27.428466", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33532775", - pubDate: "2021", - abstract: "", - authors: [ - "Ahmad, J.", - "Jiang, J.", - "Boyd, L.F.", - "Zeher, A.", - "Huang, R.", - "Xia, D.", - "Natarajan, K.", - "Margulies, D.H.", - "Ahmad, J. (0000-0002-3269-1518)", - "Jiang, J. (0000-0003-0964-5481)", - "Boyd, L.F. (0000-0002-5126-6250)", - "Natarajan, K. (0000-0002-6295-2571)", - "Margulies, D.H. 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(0000-0003-4459-9142)", - "Kneller, D.W.", - "Weiss, K.L.", - "Coates, L.", - "Kovalevsky, A.", - "Adams, P.D.", - "Mustyakimov, M.", - "Afonine, P.V.", - "Langan, P.", - ], - }, - { - pmID: "19465771", - title: - "Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.", - journal: "Acta Crystallogr.,Sect.D 65: 567-573 (2009), 1399-0047", - doi: "https://doi.org/10.1107/S0907444909011548", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/19465771", - pubDate: "2009", - abstract: "", - authors: [ - "Kneller, D.W.", - "Phillips, G.", - "Weiss, K.L.", - "Zhang, Q.", - "Coates, L.", - "Kovalevsky, A.", - "Adams, P.D.", - "Mustyakimov, M.", - "Afonine, P.V.", - "Langan, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lb7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lb7", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2234920345", - 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genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sm9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sm9", - }, - }, - { - title: "MHC I A02 Allele presenting YLQPRTFLL", - emdb: null, - pdb: { - dbId: "7P3D", - method: "X-RAY DIFFRACTION", - keywords: - "Viral Epitope, IMMUNE SYSTEM, Wuhan virus, S protein epitope, MHC presentation", - refModels: [ - { - emdbId: null, - pdbId: "7P3D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7p3d_final.pdb", - externalLink: "https://pdb-redo.eu/db/7p3d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "BHPQYMZQTOCNFJ-UHFFFAOYSA-N", - ], - dbauthors: ["Rizkallah, P.J.", "Sewell, A.K.", "Wall, A.", "Fuller, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35931021", - title: - "Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope.", - journal: "Cell 185 (2022), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2022.07.002", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35931021", - pubDate: "2022", - abstract: "", - authors: [ - "Dolton, G.", - "Rius, C.", - "Hasan, M.S.", - "Wall, A.", - "Szomolay, B.", - "Behiry, E.", - "Whalley, T.", - "Southgate, J.", - "Fuller, A.", - "Morin, T.", - "Topley, K.", - "Tan, L.R.", - "Goulder, P.J.R.", - "Spiller, O.B.", - "Rizkallah, P.J.", - "Jones, L.C.", - "Connor, T.R.", - "Sewell, A.K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7p3d_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7p3d", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid", - emdb: null, - pdb: { - dbId: "7UXZ", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, CTD, nucleocapsid, Chicoric acid, N protein, RNA BINDING PROTEIN, RNA BINDING PROTEIN-Viral Protein complex", - refModels: [ - { - emdbId: null, - pdbId: "7UXZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uxz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uxz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "YDDGKXBLOXEEMN-IABMMNSOSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Bezerra, E.H.S. (0000-0002-0421-3543)", - "Soprano, A.S. (0000-0001-7117-927X)", - "Franchini, K.G. (0000-0002-0190-6635)", - "Trivella, D.B.B. (0000-0002-7505-2345)", - "Benedetti, C.E. (0000-0002-4602-0256)", - "Tonoli, C.C.C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36323732", - title: - "Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.", - journal: "Sci Rep 12: 18500-18500 (2022), 2045-2322", - doi: "https://doi.org/10.1038/s41598-022-22576-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36323732", - pubDate: "2022", - abstract: "", - authors: [ - "Mercaldi, G.F.", - "Bezerra, E.H.S.", - "Batista, F.A.H.", - "Tonoli, C.C.C.", - "Soprano, A.S.", - "Shimizu, J.F.", - "Nagai, A.", - "da Silva, J.C.", - "Filho, H.V.R.", - "do Nascimento Faria, J.", - "da Cunha, M.G.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "Proenca-Modena, J.L.", - "Bajgelman, M.C.", - "Rocco, S.A.", - "Lopes-de-Oliveira, P.S.", - "Cordeiro, A.T.", - "Bruder, M.", - "Marques, R.E.", - "Sforca, M.L.", - "Franchini, K.G.", - "Benedetti, C.E.", - "Figueira, A.C.M.", - "Trivella, D.B.B.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uxz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uxz", - }, - }, - { - title: "GSQASS segment from the Nucleoprotein of SARS-CoV-2, residues 179-184", - emdb: null, - pdb: { - dbId: "7LV2", - method: "X-RAY DIFFRACTION", - keywords: "amyloid fibril, PROTEIN FIBRIL", - refModels: [ - { - emdbId: null, - pdbId: "7LV2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lv2_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lv2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein GSQASS", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Sawaya, M.R. (0000-0003-0874-9043)", - "Eisenberg, D.S. (0000-0003-2432-5419)", - "Cascio, D. (0000-0002-3877-6803)", - "Hou, K. (0000-0003-3869-2076)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "33688654", - title: - "Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.05.434000", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33688654", - pubDate: "2021", - abstract: "", - authors: [ - "Tayeb-Fligelman, E.", - "Cheng, X.", - "Tai, C.", - "Bowler, J.T.", - "Griner, S.", - "Sawaya, M.R.", - "Seidler, P.M.", - "Jiang, Y.X.", - "Lu, J.", - "Rosenberg, G.M.", - "Salwinski, L.", - "Abskharon, R.", - "Zee, C.T.", - "Hou, K.", - "Li, Y.", - "Boyer, D.R.", - "Murray, K.A.", - "Falcon, G.", - "Anderson, D.H.", - "Cascio, D.", - "Saelices, L.", - "Damoiseaux, R.", - "Guo, F.", - "Eisenberg, D.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lv2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lv2", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 21", - emdb: null, - pdb: { - dbId: "7NBT", - method: "X-RAY DIFFRACTION", - keywords: "Inhibitor, complex, protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7NBT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nbt_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nbt", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "IIZZXFYIZNJNIS-NSHDSACASA-N"], - dbauthors: ["Talibov, V.O. (0000-0002-1135-2744)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35142215", - title: - "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", - journal: "J.Am.Chem.Soc. 144: 2905-2920 (2022), 1520-5126", - doi: "https://doi.org/10.1021/jacs.1c08402", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35142215", - pubDate: "2022", - abstract: "", - authors: [ - "Luttens, A. (0000-0003-2915-7901)", - "Gullberg, H.", - "Abdurakhmanov, E.", - "Vo, D.D.", - "Akaberi, D. (0000-0002-9595-9796)", - "Talibov, V.O.", - "Nekhotiaeva, N.", - "Vangeel, L.", - "De Jonghe, S. (0000-0002-3872-6558)", - "Jochmans, D.", - "Krambrich, J.", - "Tas, A.", - "Lundgren, B.", - "Gravenfors, Y. (0000-0001-6025-4908)", - "Craig, A.J.", - "Atilaw, Y.", - "Sandstrom, A.", - "Moodie, L.W.K. (0000-0002-9500-4535)", - "Lundkvist, A.", - "van Hemert, M.J.", - "Neyts, J.", - "Lennerstrand, J.", - "Kihlberg, J. (0000-0002-4205-6040)", - "Sandberg, K.", - "Danielson, U.H. (0000-0003-2728-0340)", - "Carlsson, J. (0000-0003-4623-2977)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nbt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nbt", - }, - }, - { - title: "SARS-CoV-2 3CLpro", - emdb: null, - pdb: { - dbId: "7WOF", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 3CLpro, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7WOF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7wof_final.pdb", - externalLink: "https://pdb-redo.eu/db/7wof", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LLWUOBUNLOPRDK-VXUGWXBBSA-N"], - dbauthors: ["Wang, Y.", "Ye, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35216507", - title: - "Discovery of SARS-CoV-2 3CL Pro Peptidomimetic Inhibitors through the Catalytic Dyad Histidine-Specific Protein-Ligand Interactions.", - journal: "Int J Mol Sci 23 (2022), 1422-0067", - doi: "https://doi.org/10.3390/ijms23042392", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35216507", - pubDate: "2022", - abstract: "", - authors: [ - "Wang, Y.", - "Xu, B. 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(0000-0002-9446-3756)", - "Zorzini, V. (0000-0002-8727-309X)", - "Rack, J. (0000-0001-8341-6439)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33202171", - title: - "Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential.", - journal: "Open Biology 10: 200237-200237 (2020), 2046-2441", - doi: "https://doi.org/10.1098/rsob.200237", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33202171", - pubDate: "2020", - abstract: "", - authors: [ - "Rack, J.G.M.", - "Zorzini, V.", - "Zhu, Z.", - "Schuller, M.", - "Ahel, D.", - "Ahel, I.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6z6i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6z6i", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAWJ9-36-3", - emdb: null, - pdb: { - dbId: "7LYI", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, inhibitor, main protease, 3cl, SARS, SARS-CoV-2, COVID, COVID-19, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LYI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lyi_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lyi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "KXNVRILCTPCDNL-VMXHOPILSA-N", - ], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34414360", - title: - "Rational Design of Hybrid SARS-CoV-2 Main Protease Inhibitors Guided by the Superimposed Cocrystal Structures with the Peptidomimetic Inhibitors GC-376, Telaprevir, and Boceprevir.", - journal: "Acs Pharmacol Transl Sci 4: 1408-1421 (2021), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.1c00099", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34414360", - pubDate: "2021", - abstract: "", - authors: [ - "Xia, Z.", - "Sacco, M.", - "Hu, Y.", - "Ma, C.", - "Meng, X.", - "Zhang, F.", - "Szeto, T.", - "Xiang, Y.", - "Chen, Y.", - "Wang, J. (0000-0002-4845-4621)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lyi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lyi", - }, - }, - { - title: - "SARS-CoV-2 Main protease C145S mutant in complex with N and C-terminal residues", - emdb: null, - pdb: { - dbId: "7N6N", - method: "X-RAY DIFFRACTION", - keywords: "mPro, main protease, COVID-19, SARS-CoV-2, 3CL, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7N6N", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n6n_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n6n", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Lima, G.M.A.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34174328", - title: - "A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.", - journal: "J.Mol.Biol. 433: 167118-167118 (2021), 1089-8638", - doi: "https://doi.org/10.1016/j.jmb.2021.167118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34174328", - pubDate: "2021", - abstract: "", - authors: [ - "Noske, G.D.", - "Nakamura, A.M.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Lima, G.M.A.", - "Rosa, H.V.D.", - "Pereira, H.D.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "Freire, M.C.L.C.", - "Fearon, D.", - "Douangamath, A.", - "von Delft, F.", - "Oliva, G.", - "Godoy, A.S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n6n_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n6n", - }, - }, - { - title: - "Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of S-adenosyl-L-homocysteine (SAH)", - emdb: null, - pdb: { - dbId: "7LW4", - method: "X-RAY DIFFRACTION", - keywords: "product complex, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7LW4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lw4_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lw4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "SXGZJKUKBWWHRA-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Qi, S.", - "Gupta, Y.K. (0000-0001-6372-5007)", - "Viswanathan, T.", - "Misra, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34078893", - title: - "A metal ion orients SARS-CoV-2 mRNA to ensure accurate 2'-O methylation of its first nucleotide.", - journal: "Nat Commun 12: 3287-3287 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-23594-y", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34078893", - pubDate: "2021", - abstract: "", - authors: [ - "Viswanathan, T. (0000-0001-9817-6730)", - "Misra, A.", - "Chan, S.H. (0000-0002-9554-7273)", - "Qi, S. (0000-0003-0175-6267)", - "Dai, N. (0000-0003-3268-1835)", - "Arya, S. (0000-0002-7689-7411)", - "Martinez-Sobrido, L. (0000-0001-7084-0804)", - "Gupta, Y.K. (0000-0001-6372-5007)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lw4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lw4", - }, - }, - { - title: "Crystal structure of Mpro in complex with inhibitor CDD-1713", - emdb: null, - pdb: { - dbId: "7LTN", - method: "X-RAY DIFFRACTION", - keywords: - "Sars-Cov-2 main protease, nanomolar potency inhibitor, DNA-encoded library, HYDROLASE-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LTN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ltn_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ltn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LDHIKLLVVUEYPE-UHFFFAOYSA-N"], - dbauthors: [ - "Lu, S.", - "Palzkill, T.", - "Chamakuri, S.", - "Matzuk, M.", - "Young, D.", - "Melek, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34426525", - title: - "DNA-encoded chemistry technology yields expedient access to SARS-CoV-2 M pro inhibitors.", - journal: "Proc.Natl.Acad.Sci.USA 118 (2021), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2111172118", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34426525", - pubDate: "2021", - abstract: "", - authors: [ - "Chamakuri, S.", - "Lu, S.", - "Ucisik, M.N.", - "Bohren, K.M. (0000-0002-3183-4118)", - "Chen, Y.C.", - "Du, H.C.", - "Faver, J.C. (0000-0002-0181-9283)", - "Jimmidi, R.", - "Li, F. (0000-0002-9680-4614)", - "Li, J.Y.", - "Nyshadham, P.", - "Palmer, S.S.", - "Pollet, J. (0000-0003-1420-4015)", - "Qin, X.", - "Ronca, S.E.", - "Sankaran, B.", - "Sharma, K.L. (0000-0002-1988-389X)", - "Tan, Z.", - "Versteeg, L.", - "Yu, Z. (0000-0001-7278-8253)", - "Matzuk, M.M. (0000-0002-1445-8632)", - "Palzkill, T.", - "Young, D.W.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ltn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ltn", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain", - emdb: null, - pdb: { - dbId: "7UXX", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, CTD, nucleocapsid, RNA BINDING PROTEIN, Viral protein", - refModels: [ - { - emdbId: null, - pdbId: "7UXX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7uxx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7uxx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N", "QTBSBXVTEAMEQO-UHFFFAOYSA-M"], - dbauthors: [ - "Bezerra, E.H.S. (0000-0002-0421-3543)", - "Soprano, A.S. (0000-0001-7117-927X)", - "Franchini, K.G. (0000-0002-0190-6635)", - "Trivella, D.B.B. (0000-0002-7505-2345)", - "Benedetti, C.E. (0000-0002-4602-0256)", - "Tonoli, C.C.C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36323732", - title: - "Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.", - journal: "Sci Rep 12: 18500-18500 (2022), 2045-2322", - doi: "https://doi.org/10.1038/s41598-022-22576-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36323732", - pubDate: "2022", - abstract: "", - authors: [ - "Mercaldi, G.F.", - "Bezerra, E.H.S.", - "Batista, F.A.H.", - "Tonoli, C.C.C.", - "Soprano, A.S.", - "Shimizu, J.F.", - "Nagai, A.", - "da Silva, J.C.", - "Filho, H.V.R.", - "do Nascimento Faria, J.", - "da Cunha, M.G.", - "Zeri, A.C.M.", - "Nascimento, A.F.Z.", - "Proenca-Modena, J.L.", - "Bajgelman, M.C.", - "Rocco, S.A.", - "Lopes-de-Oliveira, P.S.", - "Cordeiro, A.T.", - "Bruder, M.", - "Marques, R.E.", - "Sforca, M.L.", - "Franchini, K.G.", - "Benedetti, C.E.", - "Figueira, A.C.M.", - "Trivella, D.B.B.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uxx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uxx", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) H164N Mutant in Complex with Inhibitor GC376", - emdb: null, - pdb: { - dbId: "8DD1", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, Mutation, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DD1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dd1_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dd1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - "Butler, S.G. (0000-0003-1142-0695)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36119652", - title: - "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.28.497978", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36119652", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, Y.", - "Lewandowski, E.M.", - "Tan, H.", - "Zhang, X.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Butler, S.G.", - "Gongora, M.V.", - "Choy, J.", - "Deng, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dd1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dd1", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 NendoU in complex with Z2443429438", - emdb: null, - pdb: { - dbId: "7N83", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7N83", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7n83_final.pdb", - externalLink: "https://pdb-redo.eu/db/7n83", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "ABNRKDROCBKFEH-VIFPVBQESA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7n83_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7n83", - }, - }, - { - title: - "Structure of SARS-CoV-2 spike receptor-binding domain F486L mutation complexed with human ACE2", - emdb: null, - pdb: { - dbId: "7EKE", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, spike, RBD, F486L, ACE2, VIRAL PROTEIN, HYDROLASE-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "7EKE", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7eke_final.pdb", - externalLink: "https://pdb-redo.eu/db/7eke", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - "Angiotensin-converting enzyme homolog,ACEH,Angiotensin-converting enzyme-related carboxypeptidase,ACE-related carboxypeptidase,Metalloprotease MPROT15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Gao, G.F. (0000-0002-3869-615X)", - "Su, C. (0000-0002-5824-7968)", - "Qi, J.X. (0000-0002-9358-4732)", - "Han, P.C. (0000-0002-4551-6209)", - "Zhang, Y.F. (0000-0003-3026-3357)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34671049", - title: - "Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.", - journal: "Nat Commun 12: 6103-6103 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-26401-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34671049", - pubDate: "2021", - abstract: "", - authors: [ - "Han, P.", - "Su, C. (0000-0002-5824-7968)", - "Zhang, Y.", - "Bai, C.", - "Zheng, A.", - "Qiao, C.", - "Wang, Q.", - "Niu, S.", - "Chen, Q.", - "Li, W.", - "Liao, H.", - "Li, J.", - "Zhang, Z.", - "Cho, H.", - "Yang, M.", - "Rong, X.", - "Hu, Y.", - "Huang, N. (0000-0002-6912-033X)", - "Yan, J. (0000-0003-0502-3829)", - "Wang, Q. (0000-0003-3768-0401)", - "Zhao, X. (0000-0002-2001-1343)", - "Gao, G.F. (0000-0002-3869-615X)", - "Qi, J. (0000-0002-9358-4732)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7eke_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7eke", - }, - }, - { - title: - "SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE)", - emdb: null, - pdb: { - dbId: "6X45", - method: "X-RAY DIFFRACTION", - keywords: "Coronavirus, COVID-19, SARS-CoV-2, spike, antiviral, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6X45", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6x45_final.pdb", - externalLink: "https://pdb-redo.eu/db/6x45", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S2'", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Kreitler, D.F. (0000-0003-4758-7913)", - "Outlaw, V.K. (0000-0001-7054-4204)", - "Gellman, S.H. (0000-0001-5617-0058)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Engineered peptides potently block entry of SARS-CoV-2 into human airway cells", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Outlaw, V.K. (0000-0001-7054-4204)", - "Yu, Z.", - "Kreitler, D.F.", - "Bovier, F.", - "Porotto, M.", - "Moscona, A.", - "Gellman, S.H. (0000-0001-5617-0058)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6x45_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6x45", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1003146540", - emdb: null, - pdb: { - dbId: "5SLI", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sli_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sli", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "XDODAVQVIOWLPT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sli_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sli", - }, - }, - { - title: - "Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs", - emdb: null, - pdb: { - dbId: "7NX9", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7NX9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nx9_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nx9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33852911", - title: "Antibody evasion by the P.1 strain of SARS-CoV-2.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.03.055", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33852911", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - { - pmID: "", - title: "Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.12.435194", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nx9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nx9", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000110510893", - emdb: null, - pdb: { - dbId: "5SOR", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOR", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sor_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sor", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OMFPELJWXYTVAE-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sor_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sor", - }, - }, - { - title: - "Room temperature X-ray crystallography reveals catalytic cysteine in the SARS-CoV-2 3CL Mpro is highly reactive: Insights for enzyme mechanism and drug design", - emdb: null, - pdb: { - dbId: "6XB2", - method: "X-RAY DIFFRACTION", - keywords: "Main Protease SARS-CoV-2 3CL Mpro, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6XB2", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xb2_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xb2", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["GHAZCVNUKKZTLG-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33063790", - title: - "Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M pro : insights into enzyme mechanism and drug design.", - journal: "Iucrj 7 (2020), 2052-2525", - doi: "https://doi.org/10.1107/S2052252520012634", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33063790", - pubDate: "2020", - abstract: "", - authors: [ - "Kneller, D.W. (0000-0002-5416-5789)", - "Phillips, G. (0000-0001-5858-3825)", - "O'Neill, H.M.", - "Tan, K. (0000-0002-4003-7903)", - "Joachimiak, A. (0000-0003-2535-6209)", - "Coates, L. (0000-0003-2342-049X)", - "Kovalevsky, A. (0000-0003-4459-9142)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xb2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xb2", - }, - }, - { - title: "SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-65", - emdb: null, - pdb: { - dbId: "7LOS", - method: "X-RAY DIFFRACTION", - keywords: - "papain-like protease, coronavirus inhibitor, SARS-CoV-2, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LOS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7los_final.pdb", - externalLink: "https://pdb-redo.eu/db/7los", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "JZRRCGQQCZGHEA-AUSIDOKSSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Ratia, K.M. (0000-0002-4834-9207)", - "Xiong, R. (0000-0002-6350-9037)", - "Thatcher, G.R. (0000-0002-7757-1739)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33594371", - title: - "Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.02.13.431008", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33594371", - pubDate: "2021", - abstract: "", - authors: [ - "Shen, Z.", - "Ratia, K.", - "Cooper, L.", - "Kong, D.", - "Lee, H.", - "Kwon, Y.", - "Li, Y.", - "Alqarni, S.", - "Huang, F.", - "Dubrovskyi, O.", - "Rong, L.", - "Thatcher, G.R.", - "Xiong, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7los_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7los", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z68299550", - emdb: null, - pdb: { - dbId: "5SA8", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SA8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sa8_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sa8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["XZDXDRPMHCVWBK-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sa8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sa8", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with NCL-00024661", - emdb: null, - pdb: { - dbId: "5S43", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S43", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s43_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s43", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PVCONXMDUZOPJH-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s43_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s43", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with PB2255187532", - emdb: null, - pdb: { - dbId: "5S6Z", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5S6Z", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s6z_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s6z", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["KRKNYBCHXYNGOX-UHFFFAOYSA-N", "HYQAPLLDHDEUSD-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s6z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s6z", - }, - }, - { - title: - "1.70 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 7j", - emdb: null, - pdb: { - dbId: "6XMK", - method: "X-RAY DIFFRACTION", - keywords: - "PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, COVID-19, VIRAL PROTEIN, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "6XMK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xmk_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xmk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BHZBRFONZANPNK-FPXQBCRKSA-N", "UWHCKJMYHZGTIT-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Kashipathy, M.M.", - "Zheng, J.", - "Rathnayake, A.D.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32747425", - title: - "3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice.", - journal: "Sci Transl Med 12 (2020), 1946-6242", - doi: "https://doi.org/10.1126/scitranslmed.abc5332", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32747425", - pubDate: "2020", - abstract: "", - authors: [ - "Rathnayake, A.D. (0000-0003-2588-7624)", - "Zheng, J. (0000-0003-0909-128X)", - "Kim, Y. (0000-0002-2977-4400)", - "Perera, K.D. (0000-0002-3778-4975)", - "Mackin, S.", - "Meyerholz, D.K. (0000-0003-1552-3253)", - "Kashipathy, M.M. (0000-0003-0435-989X)", - "Battaile, K.P. (0000-0003-0833-3259)", - "Lovell, S. (0000-0002-3215-4472)", - "Perlman, S. (0000-0003-4213-2354)", - "Groutas, W.C. (0000-0001-5248-7912)", - "Chang, K.O. (0000-0002-4435-3751)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xmk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xmk", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z2301685688", - emdb: null, - pdb: { - dbId: "5S4E", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S4E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s4e_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s4e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "NWVGXXPWOYZODV-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4e", - }, - }, - { - title: "Nanobody H11-H4 Q98R H100E bound to RBD", - emdb: null, - pdb: { - dbId: "7Z1E", - method: "X-RAY DIFFRACTION", - keywords: "spike, nanobody, high affinity, antiviral protein", - refModels: [ - { - emdbId: null, - pdbId: "7Z1E", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7z1e_final.pdb", - externalLink: "https://pdb-redo.eu/db/7z1e", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "H11-H4 Q98R H100E", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "NHNBFGGVMKEFGY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Naismith, J.H. (0000-0001-6744-5061)", - "Mikolajek, H. (0000-0003-0776-9974)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35858383", - title: - "Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2205412119-e2205412119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2205412119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35858383", - pubDate: "2022", - abstract: "", - authors: [ - "Mikolajek, H. (0000-0003-0776-9974)", - "Weckener, M. (0000-0002-1419-9378)", - "Brotzakis, Z.F.", - "Huo, J.", - "Dalietou, E.V.", - "Le Bas, A.", - "Sormanni, P. (0000-0002-6228-2221)", - "Harrison, P.J.", - "Ward, P.N. (0000-0003-2546-3426)", - "Truong, S. (0000-0001-9624-4461)", - "Moynie, L. (0000-0002-4097-4331)", - "Clare, D.K.", - "Dumoux, M.", - "Dormon, J.", - "Norman, C.", - "Hussain, N. (0000-0002-5170-0061)", - "Vogirala, V. (0000-0002-8534-3736)", - "Owens, R.J. (0000-0002-3705-2993)", - "Vendruscolo, M. (0000-0002-3616-1610)", - "Naismith, J.H. (0000-0001-6744-5061)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z1e_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z1e", - }, - }, - { - title: - "Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analogue (m7GpppA) and S-adenosylmethionine", - emdb: null, - pdb: { - dbId: "6WKS", - method: "X-RAY DIFFRACTION", - keywords: - "Enzyme, Transferase, hydrolase, Protein assembly, RNA BINDING PROTEIN, Methyltransferase", - refModels: [ - { - emdbId: null, - pdbId: "6WKS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wks_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wks", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "OIRDTQYFTABQOQ-KQYNXXCUSA-N", - "QQOHNVHGNZYSBP-XPWFQUROSA-O", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - ], - dbauthors: [ - "Qi, S.", - "Gupta, Y.K. (0000-0001-6372-5007)", - "Viswanathan, T.", - "Misra, A.", - "Arya, S.", - "Chan, S.-H.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32709886", - title: "Structural basis of RNA cap modification by SARS-CoV-2.", - journal: "Nat Commun 11: 3718-3718 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-17496-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32709886", - pubDate: "2020", - abstract: "", - authors: [ - "Viswanathan, T. (0000-0001-9817-6730)", - "Arya, S. (0000-0002-7689-7411)", - "Chan, S.H. (0000-0002-9554-7273)", - "Qi, S. (0000-0003-0175-6267)", - "Dai, N. (0000-0003-3268-1835)", - "Misra, A.", - "Park, J.G. (0000-0001-7163-3591)", - "Oladunni, F. (0000-0001-5050-0183)", - "Kovalskyy, D.", - "Hromas, R.A.", - "Martinez-Sobrido, L. (0000-0001-7084-0804)", - "Gupta, Y.K. (0000-0001-6372-5007)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wks_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wks", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z147647874 (Mpro-x2779)", - emdb: null, - pdb: { - dbId: "5RHA", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RHA", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rha_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rha", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEHVQKQLQOREKN-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rha_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rha", - }, - }, - { - title: - "Structure of apo SARS-CoV-2 Main Protease with small beta angle, space group C2.", - emdb: null, - pdb: { - dbId: "7AR5", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, MPro, COVID-19, PEPTIDE BINDING PROTEIN, virus protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "7AR5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ar5_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ar5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Oberthuer, D. 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(0000-0001-9366-1470)", - "Chan, J.F. (0000-0001-6336-6657)", - "Cheng, L.", - "Wang, R. (0000-0002-8040-7913)", - "Huang, W. (0000-0002-4246-8889)", - "Fang, M.", - "Chen, P. (0000-0002-9041-8392)", - "Zhou, B.", - "Song, S.", - "Shan, S. (0000-0002-7184-6818)", - "Yan, B.", - "Zhang, S. (0000-0003-1703-3848)", - "Ge, X.", - "Yu, J.", - "Zhao, J.", - "Wang, H.", - "Liu, L. (0000-0003-2566-7357)", - "Lv, Q.", - "Fu, L.", - "Shi, X.", - "Yuen, K.Y. (0000-0002-2083-1552)", - "Liu, L.", - "Wang, Y. (0000-0001-9769-5141)", - "Chen, Z. (0000-0002-4511-2888)", - "Zhang, L. (0000-0003-4931-509X)", - "Wang, X. (0000-0003-3136-8070)", - "Zhang, Z. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgn", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0103067", - emdb: null, - pdb: { - dbId: "5RFJ", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFJ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfj_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfj", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "AQDZPXNDPBKKSZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. (0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rfj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rfj", - }, - }, - { - title: - "Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose", - emdb: null, - pdb: { - dbId: "6W02", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus, macro domain, ADP-ribose, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6W02", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6w02_final.pdb", - externalLink: "https://pdb-redo.eu/db/6w02", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-KEOHHSTQSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Michalska, K.", - "Mesecar, A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32939273", - title: - "Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes.", - journal: "Iucrj 7: 814-824 (2020), 2052-2525", - doi: "https://doi.org/10.1107/S2052252520009653", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32939273", - pubDate: "2020", - abstract: "", - authors: [ - "Michalska, K.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Stols, L.", - "Endres, M.", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6w02_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6w02", - }, - }, - { - title: "SARS-COV2 Main Protease in complex with inhibitor MG78", - emdb: null, - pdb: { - dbId: "7QL8", - method: "X-RAY DIFFRACTION", - keywords: "Inhibitor complex, SARS-COV2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7QL8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ql8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ql8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PGHPGMLPXLZINT-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - ], - dbauthors: [ - "Hilgenfeld, R. (0000-0001-8850-2977)", - "El Kilani, H. (0000-0003-4084-3582)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35807537", - title: - "From Repurposing to Redesign: Optimization of Boceprevir to Highly Potent Inhibitors of the SARS-CoV-2 Main Protease.", - journal: "Molecules 27 (2022), 1420-3049", - doi: "https://doi.org/10.3390/molecules27134292", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35807537", - pubDate: "2022", - abstract: "", - authors: [ - "Gohl, M.", - "Zhang, L.", - "El Kilani, H.", - "Sun, X.", - "Zhang, K.", - "Bronstrup, M. (0000-0002-8971-7045)", - "Hilgenfeld, R. (0000-0001-8850-2977)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ql8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ql8", - }, - }, - { - title: "SARS-CoV-2 Mpro mutant (H41A) in complex with nsp6|7 peptidyl substrate", - emdb: null, - pdb: { - dbId: "7DVX", - method: "X-RAY DIFFRACTION", - keywords: "protease, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7DVX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7dvx_final.pdb", - externalLink: "https://pdb-redo.eu/db/7dvx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "nsp6/7 peptidyl substrate", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Liu, X.", "Yang, H.", "Rao, Z.", "Zhao, Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35380892", - title: - "Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2117142119-e2117142119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2117142119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35380892", - pubDate: "2022", - abstract: "", - authors: [ - "Zhao, Y. (0000-0002-2932-2164)", - "Zhu, Y. (0000-0002-7045-4847)", - "Liu, X. (0000-0001-5498-6942)", - "Jin, Z. (0000-0001-6448-820X)", - "Duan, Y.", - "Zhang, Q. (0000-0002-6271-9163)", - "Wu, C. (0000-0001-9178-7467)", - "Feng, L. (0000-0003-1060-6391)", - "Du, X.", - "Zhao, J. (0000-0002-5119-359X)", - "Shao, M. (0000-0002-9762-8608)", - "Zhang, B. (0000-0001-8556-8049)", - "Yang, X. (0000-0003-3443-9815)", - "Wu, L. (0000-0002-2253-0497)", - "Ji, X. (0000-0002-0801-8825)", - "Guddat, L.W. (0000-0002-8204-8408)", - "Yang, K.", - "Rao, Z. (0000-0001-9866-2384)", - "Yang, H. (0000-0002-1875-3268)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dvx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dvx", - }, - }, - { - title: - "Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 13d", - emdb: null, - pdb: { - dbId: "7TQ6", - method: "X-RAY DIFFRACTION", - keywords: - "COVID-19, PROTEASE, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 3CL protease Inhhibitors, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7TQ6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7tq6_final.pdb", - externalLink: "https://pdb-redo.eu/db/7tq6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ZYXQADHLOGEXOL-VRCAPQLRSA-N", - "ZYXQADHLOGEXOL-KAPKYQHQSA-N", - "UWHCKJMYHZGTIT-UHFFFAOYSA-N", - ], - dbauthors: [ - "Liu, L.", - "Madden, T.K.", - "Kim, Y.", - "Nguyen, H.N.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - "Chamandi, S.D.", - "Picard, H.R.", - "Thruman, H.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36654747", - title: - "Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.", - journal: "Acs Pharmacol Transl Sci 6: 181-194 (2023), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.2c00206", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36654747", - pubDate: "2023", - abstract: "", - authors: [ - "Dampalla, C.S.", - "Nguyen, H.N.", - "Rathnayake, A.D.", - "Kim, Y.", - "Perera, K.D.", - "Madden, T.K.", - "Thurman, H.A.", - "Machen, A.J.", - "Kashipathy, M.M.", - "Liu, L.", - "Battaile, K.P.", - "Lovell, S.", - "Chang, K.O.", - "Groutas, W.C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7tq6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7tq6", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000901381520_N3", - emdb: null, - pdb: { - dbId: "5RSK", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "5RSK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rsk_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rsk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LJWSRRLNNJPYBX-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S.", "Young, I.D.", "Thompson, M.C."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsk", - }, - }, - { - title: "Structure of SARS-CoV-2 Main Protease bound to Ipidacrine.", - emdb: null, - pdb: { - dbId: "7AF0", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, mPro, COVID-!9, PEPTIDE BINDING PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7AF0", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7af0_final.pdb", - externalLink: "https://pdb-redo.eu/db/7af0", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "YLUSMKAJIQOXPV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Zhang, L.", - "Beck, T.", - "Schubert, R.", - "Reinke, P.", - "Galchenkova, M.", - "Oberthuer, D.", - "Turk, D.", - "Schmidt, C.", - "Han, H.", - "Gelisio, L.", - "Guenther, S.", - "White, T.A.", - "Brognaro, H.", - "Knoska, J.", - "Norton-Baker, B.", - "Lorenzen, K.", - "Betzel, C.", - "Chapman, H.N.", - "Meents, A.", - "Lane, T.J.", - "Yefanov, O.", - "Seychell, B.", - "Hilgenfeld, R.", - "Kuzikov, M.", - "Gribbon, P.", - "Zaliani, A.", - "Ginn, H.", - "Domaracky, M.", - "Brehm, W.", - "Rahmani Mashour, A.", - "Pena Esperanza, G.", - "Koua, F.", - "Tolstikova, A.", - "Groessler, M.", - "Fischer, P.", - "Hennicke, V.", - "Fleckenstein, H.", - "Trost, F.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Paulraj, L.X.", - "Ullah, N.", - "Werner, N.", - "Falke, S.", - "Alves Franca, B.", - "Schwinzer, M.", - "Perbandt, M.", - "Tidow, H.", - "Meier, S.", - "Doyle, J.J.", - "Giseler, H.", - "Melo, D.", - "Dunkel, I.", - "Peck, A.", - "Saouane, S.", - "Hakanpaeae, J.", - "Meyer, J.", - "Noei, H.", - "Ellinger, B.", - "Wolf, M.", - "Ehrt, C.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.", - "Weiss, M.", - "Schulz, E.C.", - "Mehrabi, P.", - "Chari, A.", - "Fernandez Garcia, Y.", - "Rarey, M.", - "Pearson, A.", - "Lieske, J.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33811162", - title: - "X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.", - journal: "Science 372: 642-646 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf7945", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33811162", - pubDate: "2021", - abstract: "", - authors: [ - "Gunther, S.", - "Reinke, P.Y.A.", - "Fernandez-Garcia, Y.", - "Lieske, J.", - "Lane, T.J.", - "Ginn, H.M.", - "Koua, F.H.M.", - "Ehrt, C.", - "Ewert, W.", - "Oberthuer, D.", - "Yefanov, O.", - "Meier, S.", - "Lorenzen, K.", - "Krichel, B.", - "Kopicki, J.D.", - "Gelisio, L.", - "Brehm, W.", - "Dunkel, I.", - "Seychell, B.", - "Gieseler, H.", - "Norton-Baker, B.", - "Escudero-Perez, B.", - "Domaracky, M.", - "Saouane, S.", - "Tolstikova, A.", - "White, T.A.", - "Hanle, A.", - "Groessler, M.", - "Fleckenstein, H.", - "Trost, F.", - "Galchenkova, M.", - "Gevorkov, Y.", - "Li, C.", - "Awel, S.", - "Peck, A.", - "Barthelmess, M.", - "Schlunzen, F.", - "Lourdu Xavier, P.", - "Werner, N.", - "Andaleeb, H.", - "Ullah, N.", - "Falke, S.", - "Srinivasan, V.", - "Franca, B.A.", - "Schwinzer, M.", - "Brognaro, H.", - "Rogers, C.", - "Melo, D.", - "Zaitseva-Doyle, J.J.", - "Knoska, J.", - "Pena-Murillo, G.E.", - "Mashhour, A.R.", - "Hennicke, V.", - "Fischer, P.", - "Hakanpaa, J.", - "Meyer, J.", - "Gribbon, P.", - "Ellinger, B.", - "Kuzikov, M.", - "Wolf, M.", - "Beccari, A.R.", - "Bourenkov, G.", - "von Stetten, D.", - "Pompidor, G.", - "Bento, I.", - "Panneerselvam, S.", - "Karpics, I.", - "Schneider, T.R.", - "Garcia-Alai, M.M.", - "Niebling, S.", - "Gunther, C.", - "Schmidt, C.", - "Schubert, R.", - "Han, H.", - "Boger, J.", - "Monteiro, D.C.F.", - "Zhang, L.", - "Sun, X.", - "Pletzer-Zelgert, J.", - "Wollenhaupt, J.", - "Feiler, C.G.", - "Weiss, M.S.", - "Schulz, E.C.", - "Mehrabi, P.", - "Karnicar, K.", - "Usenik, A.", - "Loboda, J.", - "Tidow, H.", - "Chari, A.", - "Hilgenfeld, R.", - "Uetrecht, C.", - "Cox, R.", - "Zaliani, A.", - "Beck, T.", - "Rarey, M.", - "Turk, D.", - "Hinrichs, W.", - "Chapman, H.N.", - "Pearson, A.R.", - "Betzel, C.", - "Meents, A.", - "Guenther, S. 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(0000-0003-2647-3052)", - "Vilar, M. (0000-0002-9376-6544)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35842466", - title: - "Identification of a guanine-specific pocket in the protein N of SARS-CoV-2.", - journal: "Commun Biol 5: 711-711 (2022), 2399-3642", - doi: "https://doi.org/10.1038/s42003-022-03647-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35842466", - pubDate: "2022", - abstract: "", - authors: [ - "Rafael Ciges-Tomas, J. (0000-0003-2647-3052)", - "Franco, M.L.", - "Vilar, M. (0000-0002-9376-6544)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7o35_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7o35", - }, - }, - { - title: - "Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein", - emdb: null, - pdb: { - dbId: "7SUO", - method: "X-RAY DIFFRACTION", - keywords: "nucleocapsid protein, G3BP1, Hydrolase-Viral Protein complex", - refModels: [ - { - emdbId: null, - pdbId: "7SUO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7suo_final.pdb", - externalLink: "https://pdb-redo.eu/db/7suo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q13283", - organism: "9606", - name: "Ras GTPase-activating protein-binding protein 1", - details: "", - altNames: - "G3BP-1,ATP-dependent DNA helicase VIII,hDH VIII,GAP SH3 domain-binding protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Biswal, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rsj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rsj", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).", - emdb: null, - pdb: { - dbId: "7JYY", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, nsp16, nsp10, complex, VIRAL PROTEIN, SAM, cap-0, VIRAL PROTEIN-RNA complex", - refModels: [ - { - emdbId: null, - pdbId: "7JYY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7jyy_final.pdb", - externalLink: "https://pdb-redo.eu/db/7jyy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3')", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "MEFKEPWMEQBLKI-AIRLBKTGSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Brunzelle, J.S.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34131072", - title: - "Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16.", - journal: "Sci.Signal. 14 (2021), 1937-9145", - doi: "https://doi.org/10.1126/scisignal.abh2071", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34131072", - pubDate: "2021", - abstract: "", - authors: [ - "Minasov, G. (0000-0001-5460-3462)", - "Rosas-Lemus, M. (0000-0002-6243-0271)", - "Shuvalova, L. (0000-0003-1702-6998)", - "Inniss, N.L. (0000-0002-1510-7412)", - "Brunzelle, J.S. (0000-0001-9197-0018)", - "Daczkowski, C.M.", - "Hoover, P.", - "Mesecar, A.D. (0000-0002-1241-2577)", - "Satchell, K.J.F. 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(0000-0002-2932-2164)", - "Zhu, Y. (0000-0002-7045-4847)", - "Liu, X. (0000-0001-5498-6942)", - "Jin, Z. (0000-0001-6448-820X)", - "Duan, Y.", - "Zhang, Q. (0000-0002-6271-9163)", - "Wu, C. (0000-0001-9178-7467)", - "Feng, L. (0000-0003-1060-6391)", - "Du, X.", - "Zhao, J. (0000-0002-5119-359X)", - "Shao, M. (0000-0002-9762-8608)", - "Zhang, B. (0000-0001-8556-8049)", - "Yang, X. (0000-0003-3443-9815)", - "Wu, L. (0000-0002-2253-0497)", - "Ji, X. (0000-0002-0801-8825)", - "Guddat, L.W. (0000-0002-8204-8408)", - "Yang, K.", - "Rao, Z. (0000-0001-9866-2384)", - "Yang, H. (0000-0002-1875-3268)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7dvy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7dvy", - }, - }, - { - title: "High-resolution structure of the SARS-CoV-2 NSP3 Macro X domain", - emdb: null, - pdb: { - dbId: "6WEY", - method: "X-RAY DIFFRACTION", - keywords: "Macro domain, ADP-ribose-binding, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6WEY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wey_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wey", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Vuksanovic, N. (0000-0003-2883-6312)", - "Silvaggi, N.R. (0000-0003-0576-0714)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32578982", - title: - "Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3.", - journal: "Biochemistry 59: 2608-2615 (2020), 0006-2960", - doi: "https://doi.org/10.1021/acs.biochem.0c00309", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32578982", - pubDate: "2020", - abstract: "", - authors: [ - "Frick, D.N. (0000-0002-2434-7223)", - "Virdi, R.S.", - "Vuksanovic, N.", - "Dahal, N.", - "Silvaggi, N.R. 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(0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rep_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rep", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102575", - emdb: null, - pdb: { - dbId: "5RFK", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RFK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rfk_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rfk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "KFVWQRVNMHXHKB-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. 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(0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rfk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rfk", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102248 (Mpro-x0736)", - emdb: null, - pdb: { - dbId: "5RGO", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RGO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rgo_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rgo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "IVYZJWUTDZYPEB-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. (0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgo", - }, - }, - { - title: "Crystal structure of 2019-nCoV nucleocapsid N-terminal domain (NTD) protein", - emdb: null, - pdb: { - dbId: "7CDZ", - method: "X-RAY DIFFRACTION", - keywords: "COVID-19, RNA binding, nucleocapsid, 2019-nCoV, NTD, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CDZ", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cdz_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cdz", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Qi, J.", "Gao, G.F.", "Song, H.", "Peng, Y."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32914439", - title: - "Structures of the SARS-CoV-2 nucleocapsid and their perspectives for drug design.", - journal: "Embo J. 39: e105938-e105938 (2020), 1460-2075", - doi: "https://doi.org/10.15252/embj.2020105938", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32914439", - pubDate: "2020", - abstract: "", - authors: [ - "Peng, Y.", - "Du, N.", - "Lei, Y.", - "Dorje, S. (0000-0002-1885-3007)", - "Qi, J.", - "Luo, T.", - "Gao, G.F. (0000-0002-3869-615X)", - "Song, H. (0000-0002-2811-0370)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cdz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cdz", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1545313172", - emdb: null, - pdb: { - dbId: "5REG", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5REG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5reg_final.pdb", - externalLink: "https://pdb-redo.eu/db/5reg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "FSZYBIFIACXSAG-JTQLQIEISA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33028810", - title: - "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.", - journal: "Nat Commun 11: 5047-5047 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-18709-w", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33028810", - pubDate: "2020", - abstract: "", - authors: [ - "Douangamath, A. (0000-0002-9196-8644)", - "Fearon, D. (0000-0003-3529-7863)", - "Gehrtz, P.", - "Krojer, T. (0000-0003-0661-0814)", - "Lukacik, P.", - "Owen, C.D.", - "Resnick, E.", - "Strain-Damerell, C.", - "Aimon, A. (0000-0002-9135-129X)", - "Abranyi-Balogh, P. (0000-0002-9284-5160)", - "Brandao-Neto, J.", - "Carbery, A.", - "Davison, G.", - "Dias, A.", - "Downes, T.D. (0000-0002-6409-8831)", - "Dunnett, L.", - "Fairhead, M.", - "Firth, J.D. (0000-0003-2283-552X)", - "Jones, S.P.", - "Keeley, A.", - "Keseru, G.M.", - "Klein, H.F.", - "Martin, M.P.", - "Noble, M.E.M. (0000-0002-3595-9807)", - "O'Brien, P. (0000-0002-9966-1962)", - "Powell, A. (0000-0002-0462-2240)", - "Reddi, R.N. (0000-0001-6022-5349)", - "Skyner, R. (0000-0003-3614-6661)", - "Snee, M.", - "Waring, M.J. (0000-0002-9110-8783)", - "Wild, C.", - "London, N. (0000-0003-2687-0699)", - "von Delft, F. (0000-0003-0378-0017)", - "Walsh, M.A. (0000-0001-5683-1151)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5reg_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5reg", - }, - }, - { - title: - "Crystal Structure of ADP ribose phosphatase of NSP3 from SARS-CoV-2 in the apo form", - emdb: null, - pdb: { - dbId: "6WEN", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Coronavirus, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "6WEN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6wen_final.pdb", - externalLink: "https://pdb-redo.eu/db/6wen", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Kim, Y.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Stols, L.", - "Babnigg, G.", - "Michalska, K.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32939273", - title: - "Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes.", - journal: "Iucrj 7: 814-824 (2020), 2052-2525", - doi: "https://doi.org/10.1107/S2052252520009653", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32939273", - pubDate: "2020", - abstract: "", - authors: [ - "Michalska, K.", - "Kim, Y.", - "Jedrzejczak, R.", - "Maltseva, N.I.", - "Stols, L.", - "Endres, M.", - "Joachimiak, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6wen_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6wen", - }, - }, - { - title: - "Crystal structure of nsp16-nsp10 heterodimer from SARS-CoV-2 in complex with SAM (without additional SAM during crystallization)", - emdb: null, - pdb: { - dbId: "7C2J", - method: "X-RAY DIFFRACTION", - keywords: "2'-O-Methylase, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7C2J", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7c2j_final.pdb", - externalLink: "https://pdb-redo.eu/db/7c2j", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["MEFKEPWMEQBLKI-AIRLBKTGSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Chen, H.", - "Cao, Y.", - "Lu, G.W.", - "Lin, S.", - "Zheng, Y.", - "Ye, F.", - "Qiao, J.X.", - "Yang, S.Y.", - "Chen, Z.M.", - "Yang, F.L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32728018", - title: - "Crystal structure of SARS-CoV-2 nsp10/nsp16 2'-O-methylase and its implication on antiviral drug design.", - journal: - "Signal Transduct Target Ther 5: 131-131 (2020), 2059-3635", - doi: "https://doi.org/10.1038/s41392-020-00241-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32728018", - pubDate: "2020", - abstract: "", - authors: [ - "Lin, S.", - "Chen, H.", - "Ye, F.", - "Chen, Z.", - "Yang, F.", - "Zheng, Y.", - "Cao, Y.", - "Qiao, J.", - "Yang, S.", - "Lu, G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7c2j_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7c2j", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibodies CV07-287 and COVA1-16", - emdb: null, - pdb: { - dbId: "7S5R", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Coronavirus, Antibody, Fab, Spike, RBD, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7S5R", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7s5r_final.pdb", - externalLink: "https://pdb-redo.eu/db/7s5r", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA1-16 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVA1-16 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV07-287 Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CV07-287 Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: ["Wilson, I.A. (0000-0002-6469-2419)", "Yuan, M. (0000-0001-9754-4503)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35076281", - title: - "SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies.", - journal: "Science 375: 782-787 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.abm5835", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35076281", - pubDate: "2022", - abstract: "", - authors: [ - "Reincke, S.M. (0000-0002-8132-3527)", - "Yuan, M. (0000-0001-9754-4503)", - "Kornau, H.C. (0000-0003-4187-7549)", - "Corman, V.M. (0000-0002-3605-0136)", - "van Hoof, S. (0000-0002-2091-0904)", - "Sanchez-Sendin, E.", - "Ramberger, M. (0000-0003-3082-6906)", - "Yu, W. (0000-0002-4025-2646)", - "Hua, Y.", - "Tien, H. (0000-0001-7584-5989)", - "Schmidt, M.L.", - "Schwarz, T. (0000-0002-6054-4750)", - "Jeworowski, L.M. (0000-0002-4159-4189)", - "Brandl, S.E.", - "Rasmussen, H.F. (0000-0002-6923-875X)", - "Homeyer, M.A. (0000-0003-0630-3857)", - "Stoffler, L. (0000-0003-4724-5112)", - "Barner, M. (0000-0003-3448-7294)", - "Kunkel, D. (0000-0002-0054-955X)", - "Huo, S. (0000-0002-0119-7517)", - "Horler, J.", - "von Wardenburg, N. (0000-0003-0476-9813)", - "Kroidl, I.", - "Eser, T.M. (0000-0003-2682-9135)", - "Wieser, A.", - "Geldmacher, C.", - "Hoelscher, M. (0000-0002-7642-1835)", - "Ganzer, H. (0000-0003-0358-3689)", - "Weiss, G. (0000-0003-0709-2158)", - "Schmitz, D.", - "Drosten, C. (0000-0001-7923-0519)", - "Pruss, H. (0000-0002-8283-7976)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Kreye, J. (0000-0003-2913-1015)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7s5r_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7s5r", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1344037997 (Mpro-x2572)", - emdb: null, - pdb: { - dbId: "5RGX", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RGX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rgx_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rgx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OTFRLGRHXMKEAF-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rgx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rgx", - }, - }, - { - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z4439011588 (Mpro-x2703)", - emdb: null, - pdb: { - dbId: "5RH6", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5RH6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5rh6_final.pdb", - externalLink: "https://pdb-redo.eu/db/5rh6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "HPKVUDPRFZVZGF-AREMUKBSSA-N"], - dbauthors: [ - "Owen, C.D.", - "Lukacik, P.", - "Walsh, M.A.", - "Fearon, D.", - "Strain-Damerell, C.M.", - "von Delft, F.", - "Douangamath, A.", - "Krojer, T.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Powell, A.J.", - "Resnick, E.", - "Gehrtz, P.", - "Wild, C.", - "Carbery, A.", - "Dunnett, L.", - "Snee, M.", - "London, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Fearon, D.", - "Owen, C.D.", - "Douangamath, A.", - "Lukacik, P.", - "Powell, A.J.", - "Strain-Damerell, C.M.", - "Resnick, E.", - "Krojer, T.", - "Gehrtz, P.", - "Wild, C.", - "Aimon, A.", - "Brandao-Neto, J.", - "Carbery, A.", - "Dunnett, L.", - "Skyner, R.", - "Snee, M.", - "London, N.", - "Walsh, M.A.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5rh6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5rh6", - }, - }, - { - title: "Nanobody H11-H6 bound to RBD", - emdb: null, - pdb: { - dbId: "7Z1D", - method: "X-RAY DIFFRACTION", - keywords: "spike, nanobody, high affinity, antiviral protein", - refModels: [ - { - emdbId: null, - pdbId: "7Z1D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7z1d_final.pdb", - externalLink: "https://pdb-redo.eu/db/7z1d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "H11-H6 nanobody", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Naismith, J.H. (0000-0001-6744-5061)", - "Mikolajek, H. (0000-0003-0776-9974)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35858383", - title: - "Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2205412119-e2205412119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2205412119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35858383", - pubDate: "2022", - abstract: "", - authors: [ - "Mikolajek, H. (0000-0003-0776-9974)", - "Weckener, M. (0000-0002-1419-9378)", - "Brotzakis, Z.F.", - "Huo, J.", - "Dalietou, E.V.", - "Le Bas, A.", - "Sormanni, P. (0000-0002-6228-2221)", - "Harrison, P.J.", - "Ward, P.N. (0000-0003-2546-3426)", - "Truong, S. (0000-0001-9624-4461)", - "Moynie, L. (0000-0002-4097-4331)", - "Clare, D.K.", - "Dumoux, M.", - "Dormon, J.", - "Norman, C.", - "Hussain, N. (0000-0002-5170-0061)", - "Vogirala, V. (0000-0002-8534-3736)", - "Owens, R.J. (0000-0002-3705-2993)", - "Vendruscolo, M. (0000-0002-3616-1610)", - "Naismith, J.H. (0000-0001-6744-5061)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z1d_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z1d", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody Fab", - emdb: null, - pdb: { - dbId: "7CJF", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, RBD, antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7CJF", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7cjf_final.pdb", - externalLink: "https://pdb-redo.eu/db/7cjf", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "antibody heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "antibody light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Guo, Y.", - "Zhang, G.", - "Rao, Z.", - "Zhang, H.", - "Li, X.", - "Fu, D.", - "Schweizer, L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33976198", - title: - "A SARS-CoV-2 neutralizing antibody with extensive Spike binding coverage and modified for optimal therapeutic outcomes.", - journal: "Nat Commun 12: 2623-2623 (2021), 2041-1723", - doi: "https://doi.org/10.1038/s41467-021-22926-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33976198", - pubDate: "2021", - abstract: "", - authors: [ - "Guo, Y. (0000-0002-8109-7515)", - "Huang, L.", - "Zhang, G.", - "Yao, Y.", - "Zhou, H.", - "Shen, S. (0000-0002-0013-5365)", - "Shen, B.", - "Li, B.", - "Li, X.", - "Zhang, Q.", - "Chen, M.", - "Chen, D.", - "Wu, J.", - "Fu, D.", - "Zeng, X.", - "Feng, M.", - "Pi, C.", - "Wang, Y.", - "Zhou, X. (0000-0001-8648-8948)", - "Lu, M.", - "Li, Y.", - "Fang, Y.", - "Lu, Y.Y.", - "Hu, X.", - "Wang, S.", - "Zhang, W.", - "Gao, G.", - "Adrian, F.", - "Wang, Q. (0000-0002-0614-6903)", - "Yu, F.", - "Peng, Y.", - "Gabibov, A.G.", - "Min, J.", - "Huang, H.", - "Stepanov, A. (0000-0003-1616-4408)", - "Zhang, W. (0000-0001-8693-6747)", - "Cai, Y.", - "Liu, J.", - "Yuan, Z. (0000-0002-3234-9616)", - "Zhang, C.", - "Lou, Z. (0000-0003-2728-881X)", - "Deng, F. (0000-0002-5385-083X)", - "Zhang, H. (0000-0003-2186-5508)", - "Shan, C. (0000-0002-3953-3782)", - "Schweizer, L. (0000-0002-0903-4077)", - "Sun, K. (0000-0002-0504-7372)", - "Rao, Z. (0000-0001-9866-2384)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cjf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cjf", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z1741982441", - emdb: null, - pdb: { - dbId: "5S4D", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S4D", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s4d_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s4d", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "JVTAAEKCZFNVCJ-REOHCLBHSA-N", - "GUWSLQUAAYEZAF-UHFFFAOYSA-L", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - ], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. (0000-0002-1551-0359)", - "Correy, G.J. (0000-0001-5155-7325)", - "Gahbauer, S. (0000-0002-3115-9757)", - "Fearon, D. (0000-0003-3529-7863)", - "Wu, T. (0000-0001-6988-1414)", - "Diaz, R.E. (0000-0002-1172-9919)", - "Young, I.D. (0000-0003-4713-9504)", - "Carvalho Martins, L. (0000-0002-7747-6782)", - "Smith, D.H. (0000-0002-5136-4491)", - "Schulze-Gahmen, U. (0000-0003-3919-4474)", - "Owens, T.W. (0000-0001-7423-4879)", - "Deshpande, I. (0000-0002-8276-9635)", - "Merz, G.E. (0000-0003-0842-4935)", - "Thwin, A.C. (0000-0002-1423-8189)", - "Biel, J.T. (0000-0002-0935-8362)", - "Peters, J.K. (0000-0003-3541-7431)", - "Moritz, M. (0000-0003-3811-5623)", - "Herrera, N. (0000-0003-4157-9429)", - "Kratochvil, H.T. (0000-0001-8039-6823)", - "Aimon, A. (0000-0002-9135-129X)", - "Bennett, J.M. (0000-0003-1396-8400)", - "Brandao Neto, J. (0000-0001-6015-320X)", - "Cohen, A.E. (0000-0003-2414-9427)", - "Dias, A. (0000-0003-3609-7003)", - "Douangamath, A.", - "Dunnett, L. (0000-0001-6710-6959)", - "Fedorov, O. (0000-0002-8662-7300)", - "Ferla, M.P.", - "Fuchs, M.R. (0000-0001-9784-0927)", - "Gorrie-Stone, T.J. (0000-0002-1817-1495)", - "Holton, J.M. (0000-0002-0596-0137)", - "Johnson, M.G. (0000-0001-9213-0598)", - "Krojer, T. (0000-0003-0661-0814)", - "Meigs, G. (0000-0002-8530-661X)", - "Powell, A.J. (0000-0002-0462-2240)", - "Rack, J.G.M. (0000-0001-8341-6439)", - "Rangel, V.L. (0000-0002-7580-3452)", - "Russi, S.", - "Skyner, R.E. (0000-0003-3614-6661)", - "Smith, C.A. (0000-0002-1885-1511)", - "Soares, A.S. (0000-0002-6565-8503)", - "Wierman, J.L. (0000-0002-5206-9662)", - "Zhu, K.", - "O'Brien, P. (0000-0002-9966-1962)", - "Jura, N. (0000-0001-5129-641X)", - "Ashworth, A. (0000-0003-1446-7878)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Thompson, M.C. (0000-0002-6099-2027)", - "Gestwicki, J.E.", - "von Delft, F. (0000-0003-0378-0017)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - "Ahel, I. (0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s4d_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s4d", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2697514548", - emdb: null, - pdb: { - dbId: "5SA9", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "5SA9", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sa9_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sa9", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PVROETJHCUDAFG-UHFFFAOYSA-N"], - dbauthors: [ - "Noske, G.D.", - "Fernandes, R.S.", - "Oliva, G.", - "Godoy, A.S.", - "Fearon, D.", - "von Delft, F.", - "Douangamath, A.", - "Nakamura, A.M.", - "Dias, A.", - "Krojer, T.", - "Gawiljuk, V.O.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37115000", - title: - "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.", - journal: "Nucleic Acids Res. (2023), 1362-4962", - doi: "https://doi.org/10.1093/nar/gkad314", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37115000", - pubDate: "2023", - abstract: "", - authors: [ - "Godoy, A.S. (0000-0002-0613-9164)", - "Nakamura, A.M.", - "Douangamath, A.", - "Song, Y.", - "Noske, G.D.", - "Gawriljuk, V.O.", - "Fernandes, R.S.", - "Pereira, H.D.M.", - "Oliveira, K.I.Z.", - "Fearon, D.", - "Dias, A.", - "Krojer, T.", - "Fairhead, M.", - "Powell, A.", - "Dunnet, L.", - "Brandao-Neto, J.", - "Skyner, R.", - "Chalk, R.", - "Bajusz, D. (0000-0003-4277-9481)", - "Bege, M.", - "Borbas, A.", - "Keseru, G.M.", - "von Delft, F. (0000-0003-0378-0017)", - "Oliva, G.", - "Godoy, A.S.", - "Bajusz, D.", - "von Delft, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sa9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sa9", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with NCL-00023833", - emdb: null, - pdb: { - dbId: "5S42", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, SARS-CoV-2 Nsp3 macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5S42", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5s42_final.pdb", - externalLink: "https://pdb-redo.eu/db/5s42", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QYXNSNJTMIEAPG-UHFFFAOYSA-N", "IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Schuller, M.", - "Ahel, I.", - "Fearon, D.", - "von Delft, F.", - "Zhu, K.", - "Douangamath, A.", - "Dias, A.", - "Krojer, T.", - "Dunnet, L.", - "Aimon, A.", - "Brandao-Neto, J.", - "Skyner, R.", - "Rangel, V.L.", - "Rack, J.G.M.", - "Gorrie-Stone, T.J.", - "Powell, A.J.", - "Thompson, W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33853786", - title: - "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abf8711", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33853786", - pubDate: "2021", - abstract: "", - authors: [ - "Schuller, M. 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(0000-0002-9446-3756)", - "Bajusz, D. (0000-0003-4277-9481)", - "Wade, W.S.", - "Satala, G.", - "Bojarski, A.J.", - "Ilas, J. (0000-0002-0124-0474)", - "Ebner, J.", - "Grebien, F. (0000-0003-4289-2281)", - "Papp, H. (0000-0003-3887-5657)", - "Jakab, F.", - "Douangamath, A. (0000-0002-9196-8644)", - "Schuller, M.", - "Ahel, I.", - "Wakefield, A.", - "Vajda, S.", - "Gerencser, J. (0000-0002-1928-0650)", - "Pallai, P.", - "Keseru, G.M. (0000-0003-1039-7809)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5s42_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5s42", - }, - }, - { - title: - "Acyl-enzyme intermediate structure of SARS-CoV-2 Mpro in complex with its C-terminal autoprocessing sequence.", - emdb: null, - pdb: { - dbId: "7KHP", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7KHP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7khp_final.pdb", - externalLink: "https://pdb-redo.eu/db/7khp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Worrall, L.J. (0000-0003-4966-7175)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Lee, J.", - "Paetzel, M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33208735", - title: - "Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.", - journal: "Nat Commun 11: 5877-5877 (2020), 2041-1723", - doi: "https://doi.org/10.1038/s41467-020-19662-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33208735", - pubDate: "2020", - abstract: "", - authors: [ - "Lee, J.", - "Worrall, L.J.", - "Vuckovic, M.", - "Rosell, F.I.", - "Gentile, F.", - "Ton, A.T. (0000-0001-7418-6563)", - "Caveney, N.A. (0000-0003-4828-3479)", - "Ban, F.", - "Cherkasov, A. (0000-0002-1599-1439)", - "Paetzel, M. (0000-0002-7408-5487)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7khp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7khp", - }, - }, - { - title: "Structure of nsp14 from SARS-CoV-2 in complex with SAH", - emdb: null, - pdb: { - dbId: "7R2V", - method: "X-RAY DIFFRACTION", - keywords: "nsp14, Complex, SAH, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7R2V", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7r2v_final.pdb", - externalLink: "https://pdb-redo.eu/db/7r2v", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ZJUKTBDSGOFHSH-WFMPWKQPSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "PQYJRMFWJJONBO-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Robinson, C.", - "Matsuda, A.", - "Czarna, A.", - "Popowicz, G.M.", - "Dubin, G.", - "Pachota, M.", - "Pyrc, K.", - "Plewka, J.", - "Kresik, L.", - "Abdulkarim, K.", - "OByrne, S.", - "Cunningham, F.", - "Georgiou, I.", - "Wyatt, P.G.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35609600", - title: - "Refolding of lid subdomain of SARS-CoV-2 nsp14 upon nsp10 interaction releases exonuclease activity.", - journal: "Structure 30: 1050-1054.e2 (2022), 0969-2126", - doi: "https://doi.org/10.1016/j.str.2022.04.014", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35609600", - pubDate: "2022", - abstract: "", - authors: [ - "Czarna, A.", - "Plewka, J.", - "Kresik, L.", - "Matsuda, A.", - "Karim, A.", - "Robinson, C.", - "O'Byrne, S.", - "Cunningham, F.", - "Georgiou, I.", - "Wilk, P.", - "Pachota, M.", - "Popowicz, G.", - "Wyatt, P.G.", - "Dubin, G.", - "Pyrc, K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7r2v_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7r2v", - }, - }, - { - title: - "Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-3',5'-Diphosphate", - emdb: null, - pdb: { - dbId: "7K1O", - method: "X-RAY DIFFRACTION", - keywords: - "SARS Corona virus 2, endoribonuclease, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7K1O", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7k1o_final.pdb", - externalLink: "https://pdb-redo.eu/db/7k1o", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Uridylate-specific endoribonuclease", - details: "", - altNames: "NSP15 endoribnuclease", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["ZPVPRWPOZBXDKD-ZAKLUEHWSA-N", "LYCAIKOWRPUZTN-UHFFFAOYSA-N"], - dbauthors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Endres, M.", - "Welk, L.", - "Michalska, K.", - "Chang, C.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "hexameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-3',5'-Diphosphate", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kim, Y.", - "Maltseva, N.", - "Jedrzejczak, R.", - "Endres, M.", - "Welk, L.", - "Chang, C.", - "Michalska, K.", - "Joachimiak, A.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k1o_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k1o", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 2-31 and a human antibody CC12.1 Fab", - emdb: null, - pdb: { - dbId: "8CWV", - method: "X-RAY DIFFRACTION", - keywords: - "cross-neutralizing antibody; nanobody; SARS-CoV-2; Sarbecovirus; IMMUNE SYSTEM; VHH; CC12.1, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8CWV", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cwv_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cwv", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "VHH 2-31", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.1 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.1 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Liu, H. (0000-0002-2412-7853)", "Wilson, I.A. (0000-0002-6469-2419)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35738279", - title: "Superimmunity by pan-sarbecovirus nanobodies.", - journal: "Cell Rep 39: 111004-111004 (2022), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2022.111004", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35738279", - pubDate: "2022", - abstract: "", - authors: [ - "Xiang, Y.", - "Huang, W.", - "Liu, H.", - "Sang, Z.", - "Nambulli, S.", - "Tubiana, J.", - "Williams Jr., K.L.", - "Duprex, W.P.", - "Schneidman-Duhovny, D.", - "Wilson, I.A.", - "Taylor, D.J.", - "Shi, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8cwv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8cwv", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CC12.3 and CR3022", - emdb: null, - pdb: { - dbId: "6XC7", - method: "X-RAY DIFFRACTION", - keywords: - "Antibody, SARS-CoV-2, Coronavirus, Spike, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: null, - pdbId: "6XC7", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6xc7_final.pdb", - externalLink: "https://pdb-redo.eu/db/6xc7", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CR3022 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CR3022 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.3 heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "CC12.3 light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Liu, H. (0000-0002-2412-7853)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Zhu, X. (0000-0002-6021-3740)", - "Yuan, M. (0000-0001-9754-4503)", - "Wu, N.C. (0000-0002-9078-6697)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32661058", - title: - "Structural basis of a shared antibody response to SARS-CoV-2.", - journal: "Science 369: 1119-1123 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abd2321", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32661058", - pubDate: "2020", - abstract: "", - authors: [ - "Yuan, M. (0000-0001-9754-4503)", - "Liu, H. (0000-0002-2412-7853)", - "Wu, N.C. (0000-0002-9078-6697)", - "Lee, C.D. (0000-0002-5470-2484)", - "Zhu, X. (0000-0002-6021-3740)", - "Zhao, F. (0000-0002-3172-1340)", - "Huang, D. (0000-0002-6989-639X)", - "Yu, W. (0000-0002-4025-2646)", - "Hua, Y.", - "Tien, H. (0000-0001-7584-5989)", - "Rogers, T.F. (0000-0001-9756-327X)", - "Landais, E. (0000-0002-8183-5565)", - "Sok, D. (0000-0002-9354-1740)", - "Jardine, J.G. (0000-0001-8951-1074)", - "Burton, D.R. (0000-0001-6711-9864)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Yuan, M.", - "Liu, H.", - "Wu, N.C.", - "Lee, C.D.", - "Zhu, X.", - "Zhao, F.", - "Huang, D.", - "Yu, W.", - "Tien, H.", - "Rogers, T.F.", - "Landais, E.", - "Sok, D.", - "Jardine, J.G.", - "Burton, D.R.", - "Wilson, I.A.", - ], - }, - { - pmID: "32577642", - title: - "Structural basis of a public antibody response to SARS-CoV-2.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.06.08.141267", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32577642", - pubDate: "2020", - abstract: "", - authors: [ - "Yuan, M. (0000-0001-9754-4503)", - "Liu, H. (0000-0002-2412-7853)", - "Wu, N.C. (0000-0002-9078-6697)", - "Lee, C.D. (0000-0002-5470-2484)", - "Zhu, X. (0000-0002-6021-3740)", - "Zhao, F. (0000-0002-3172-1340)", - "Huang, D. (0000-0002-6989-639X)", - "Yu, W. (0000-0002-4025-2646)", - "Hua, Y.", - "Tien, H. (0000-0001-7584-5989)", - "Rogers, T.F. (0000-0001-9756-327X)", - "Landais, E. (0000-0002-8183-5565)", - "Sok, D. (0000-0002-9354-1740)", - "Jardine, J.G. (0000-0001-8951-1074)", - "Burton, D.R. (0000-0001-6711-9864)", - "Wilson, I.A. (0000-0002-6469-2419)", - "Yuan, M.", - "Liu, H.", - "Wu, N.C.", - "Lee, C.D.", - "Zhu, X.", - "Zhao, F.", - "Huang, D.", - "Yu, W.", - "Tien, H.", - "Rogers, T.F.", - "Landais, E.", - "Sok, D.", - "Jardine, J.G.", - "Burton, D.R.", - "Wilson, I.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xc7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xc7", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000559260078", - emdb: null, - pdb: { - dbId: "5SOS", - method: "X-RAY DIFFRACTION", - keywords: "Macrodomain, ADP-ribose, SARS-CoV-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "5SOS", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5sos_final.pdb", - externalLink: "https://pdb-redo.eu/db/5sos", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["UQCJOVCQACAKGD-UHFFFAOYSA-N"], - dbauthors: ["Correy, G.J.", "Fraser, J.S."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "35794891", - title: - "Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.27.497816", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35794891", - pubDate: "2022", - abstract: "", - authors: [ - "Gahbauer, S. (0000-0002-3115-9757)", - "Correy, G.J. (0000-0001-5155-7325)", - "Schuller, M. (0000-0002-1551-0359)", - "Ferla, M.P. (0000-0002-5508-4673)", - "Doruk, Y.U. (0000-0002-3388-7803)", - "Rachman, M. (0000-0003-3671-8885)", - "Wu, T. (0000-0001-6988-1414)", - "Diolaiti, M. (0000-0001-5900-3060)", - "Wang, S. (0000-0003-2946-1647)", - "Neitz, R.J. (0000-0002-2247-9345)", - "Fearon, D. (0000-0003-3529-7863)", - "Radchenko, D. (0000-0001-5444-7754)", - "Moroz, Y. (0000-0001-6073-002X)", - "Irwin, J.J. (0000-0002-1195-6417)", - "Renslo, A.R. (0000-0002-1240-2846)", - "Taylor, J.C. (0000-0003-3602-5704)", - "Gestwicki, J.E. (0000-0002-6125-3154)", - "von Delft, F. (0000-0003-0378-0017)", - "Ashworth, A. (0000-0003-1446-7878)", - "Ahel, I. (0000-0002-9446-3756)", - "Shoichet, B.K. (0000-0002-6098-7367)", - "Fraser, J.S. (0000-0002-5080-2859)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5sos_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5sos", - }, - }, - { - title: - "Crystal structure of the K417T mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs", - emdb: null, - pdb: { - dbId: "7NX8", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2 B.1.1.7 variant, B.1.351 variant, P.1 variant, antibody, receptor-binding-domain, spike, neutralisation, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7NX8", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7nx8_final.pdb", - externalLink: "https://pdb-redo.eu/db/7nx8", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "EY6A Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "COVOX-222 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - "MTHSVFCYNBDYFN-UHFFFAOYSA-N", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - "KRKNYBCHXYNGOX-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: ["Zhou, D.", "Ren, J.", "Stuart, D."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33852911", - title: "Antibody evasion by the P.1 strain of SARS-CoV-2.", - journal: "Cell 184 (2021), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2021.03.055", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33852911", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - { - pmID: "", - title: "Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2021.03.12.435194", - pmidLink: "", - pubDate: "2021", - abstract: "", - authors: [ - "Dejnirattisai, W.", - "Zhou, D.", - "Supasa, P.", - "Liu, C.", - "Mentzer, A.J.", - "Ginn, H.M.", - "Zhao, Y.", - "Duyvesteyn, H.M.E.", - "Tuekprakhon, A.", - "Nutalai, R.", - "Wang, B.", - "Lopez-Camacho, C.", - "Slon-Campos, J.", - "Walter, T.S.", - "Skelly, D.", - "Costa Clemens, S.A.", - "Naveca, F.G.", - "Nascimento, V.", - "Nascimento, F.", - "Fernandes da Costa, C.", - "Resende, P.C.", - "Pauvolid-Correa, A.", - "Siqueira, M.M.", - "Dold, C.", - "Levin, R.", - "Dong, T.", - "Pollard, A.J.", - "Knight, J.C.", - "Crook, D.", - "Lambe, T.", - "Clutterbuck, E.", - "Bibi, S.", - "Flaxman, A.", - "Bittaye, M.", - "Belij-Rammerstorfer, S.", - "Gilbert, S.C.", - "Carroll, M.W.", - "Klenerman, P.", - "Barnes, E.", - "Dunachie, S.J.", - "Paterson, N.G.", - "Williams, M.A.", - "Hall, D.R.", - "Hulswit, R.J.G.", - "Bowden, T.A.", - "Fry, E.E.", - "Mongkolsapaya, J.", - "Ren, J.", - "Stuart, D.I.", - "Screaton, G.R.", - "Duyvesteyn, H.M.", - "Paesen, G.C.", - "Clemens, S.A.C.", - "Gilbert, S.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nx8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nx8", - }, - }, - { - title: - "PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z65532537", - emdb: null, - pdb: { - dbId: "5SLH", - method: "X-RAY DIFFRACTION", - keywords: - "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "5SLH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "5slh_final.pdb", - externalLink: "https://pdb-redo.eu/db/5slh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Proofreading exoribonuclease nsp14", - details: "", - altNames: - "ExoN,Guanine-N7 methyltransferase,Non-structural protein 14,nsp14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "NBIIXXVUZAFLBC-UHFFFAOYSA-K", - "MMWXPDDADHYFFS-LURJTMIESA-N", - ], - dbauthors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "PanDDA analysis group deposition", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Imprachim, N.", - "Yosaatmadja, Y.", - "von-Delft, F.", - "Bountra, C.", - "Gileadi, O.", - "Newman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/5slh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/5slh", - }, - }, - { - title: - "SARS-CoV-2 Envelope Protein Transmembrane Domain: Pentameric Structure Determined by Solid-State NMR", - emdb: null, - pdb: { - dbId: "7K3G", - method: "SOLID-STATE NMR", - keywords: "Viroporin, Pentameric Ion Channel, Transmembrane Domain, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC4", - organism: "2697049", - name: "Envelope small membrane protein", - details: "", - altNames: "E,sM protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Mandala, V.S. (0000-0002-6358-0642)", - "Hong, M. (0000-0001-5255-5858)", - "McKay, M.J. (0000-0002-3079-9189)", - "Shcherbakov, A.S. (0000-0002-5728-7175)", - "Dregni, A.J. (0000-0003-3422-4734)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33177698", - title: - "Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers.", - journal: "Nat.Struct.Mol.Biol. 27: 1202-1208 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-00536-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33177698", - pubDate: "2020", - abstract: "", - authors: [ - "Mandala, V.S.", - "McKay, M.J.", - "Shcherbakov, A.A.", - "Dregni, A.J.", - "Kolocouris, A.", - "Hong, M.", - "Hong, M. (0000-0001-5255-5858)", - "Mandala, V. (0000-0002-6358-0642)", - "McKay, M.", - "Shcherbakov, A. (0000-0002-5728-7175)", - "Dregni, A.", - ], - }, - { - pmID: "32995764", - title: - "Structure and Drug Binding of the SARS-CoV-2 Envelope Protein in Phospholipid Bilayers.", - journal: "Res Sq (2020), 2693-5015", - doi: "https://doi.org/10.21203/rs.3.rs-77124/v1", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32995764", - pubDate: "2020", - abstract: "", - authors: [ - "Mandala, V.S.", - "McKay, M.J.", - "Shcherbakov, A.A.", - "Dregni, A.J.", - "Kolocouris, A.", - "Hong, M.", - "Hong, M. (0000-0001-5255-5858)", - "Mandala, V. (0000-0002-6358-0642)", - "McKay, M.", - "Shcherbakov, A. (0000-0002-5728-7175)", - "Dregni, A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k3g_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k3g", - }, - }, - { - title: "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164N Mutant", - emdb: null, - pdb: { - dbId: "8DFN", - method: "X-RAY DIFFRACTION", - keywords: "Protease, SARS-CoV-2, Mpro, Mutation, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8DFN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dfn_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dfn", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Lewandowski, E.M. (0000-0001-6235-6502)", - "Chen, Y. (0000-0002-5115-3600)", - "Hu, Y. (0000-0003-0525-7342)", - "Tan, H. (0000-0002-6640-8354)", - "Wang, J. (0000-0002-4845-4621)", - "Butler, S.G. (0000-0003-1142-0695)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "36119652", - title: - "Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.06.28.497978", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36119652", - pubDate: "2022", - abstract: "", - authors: [ - "Hu, Y.", - "Lewandowski, E.M.", - "Tan, H.", - "Zhang, X.", - "Morgan, R.T.", - "Jacobs, L.M.C.", - "Butler, S.G.", - "Gongora, M.V.", - "Choy, J.", - "Deng, X.", - "Chen, Y.", - "Wang, J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dfn_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dfn", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2", - emdb: null, - pdb: { - dbId: "7P19", - method: "X-RAY DIFFRACTION", - keywords: - "Viral spike; angiotensin converting enzyme-II; SARS-COV-2; ACE-2, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7P19", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7p19_final.pdb", - externalLink: "https://pdb-redo.eu/db/7p19", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Processed angiotensin-converting enzyme 2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "LYCAIKOWRPUZTN-UHFFFAOYSA-N", - "VEXZGXHMUGYJMC-UHFFFAOYSA-M", - ], - dbauthors: [ - "Erausquin, E. (0000-0003-1560-9671)", - "Lopez-Sagaseta, J. (0000-0002-7774-4361)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36048155", - title: - "Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution.", - journal: - "Acta Crystallogr D Struct Biol 78: 1156-1170 (2022), 2059-7983", - doi: "https://doi.org/10.1107/S2059798322007677", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36048155", - pubDate: "2022", - abstract: "", - authors: [ - "Erausquin, E. (0000-0003-1560-9671)", - "Glaser, F.", - "Fernandez-Recio, J. (0000-0002-3986-7686)", - "Lopez-Sagaseta, J. 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(0000-0002-0137-3381)", - "Ma, S.", - "Wang, H.", - "Shang, L.", - "Zhu, C. (0000-0003-0260-6287)", - "Ye, S. 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(0000-0001-8287-0269)", - "Christensen, S.", - "Lindvall, T.", - "Rasmussen, A.A.", - "Andre, I.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33036230", - title: - "Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2.", - journal: "Int J Mol Sci 21 (2020), 1422-0067", - doi: "https://doi.org/10.3390/ijms21197375", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33036230", - pubDate: "2020", - abstract: "", - authors: [ - "Rogstam, A.", - "Nyblom, M.", - "Christensen, S.", - "Sele, C.", - "Talibov, V.O.", - "Lindvall, T.", - "Rasmussen, A.A.", - "Andre, I.", - "Fisher, Z.", - "Knecht, W.", - "Kozielski, F.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zct_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zct", - }, - }, - { - title: "H11-H4 complex with SARS-CoV-2", - emdb: null, - pdb: { - dbId: "6ZBP", - method: "X-RAY DIFFRACTION", - keywords: "Complex, llama, nanobody, antibody, SARS-CoV-2, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "6ZBP", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "6zbp_final.pdb", - externalLink: "https://pdb-redo.eu/db/6zbp", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9844", - name: "H11-H4", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Huo, J. (0000-0002-7899-1815)", - "Owens, R.J. (0000-0002-3705-2993)", - "Naismith, J.H. (0000-0001-6744-5061)", - "Dumoux, M. (0000-0002-1732-1041)", - "Mikolajek, H. (0000-0003-0776-9974)", - "Ward, P. (0000-0003-2546-3426)", - "LeBas, A. (0000-0002-1100-6833)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "H11-D4 complex with SARS-CoV-2 RBD", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Naismith, J.H. (0000-0001-6744-5061)"], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zbp_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zbp", - }, - }, - { - title: "Crystal structure of the Nsp3 Y3 domain from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "7RQG", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, COVID-19, non-structural protein 3, nsp3, Y3 domain, unknown function, structural genomics, CSGID, center for structural genomics of infectious diseases, NIAID, national institute of allergy and infectious diseases, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "7RQG", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7rqg_final.pdb", - externalLink: "https://pdb-redo.eu/db/7rqg", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 3", - details: "", - altNames: "nsp3,PL2-PRO,Papain-like protease,Papain-like proteinase,PL-PRO", - 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abstract: "", - authors: ["Yan, L.M.", "Ge, J.", "Lou, Z.Y.", "Rao, Z.H."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6m5i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6m5i", - }, - }, - { - title: - "Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAWJ9-36-1", - emdb: null, - pdb: { - dbId: "7LYH", - method: "X-RAY DIFFRACTION", - keywords: - "Mpro, inhibitor, main protease, 3cl, SARS, SARS-CoV-2, COVID, COVID-19, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "7LYH", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7lyh_final.pdb", - externalLink: "https://pdb-redo.eu/db/7lyh", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["BQHAUUUZCGWWEE-HVTWWXFQSA-N", "PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Wang, J.", "Chen, Y.", "Sacco, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "34414360", - title: - "Rational Design of Hybrid SARS-CoV-2 Main Protease Inhibitors Guided by the Superimposed Cocrystal Structures with the Peptidomimetic Inhibitors GC-376, Telaprevir, and Boceprevir.", - journal: "Acs Pharmacol Transl Sci 4: 1408-1421 (2021), 2575-910", - doi: "https://doi.org/10.1021/acsptsci.1c00099", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34414360", - pubDate: "2021", - abstract: "", - authors: [ - "Xia, Z.", - "Sacco, M.", - "Hu, Y.", - "Ma, C.", - "Meng, X.", - "Zhang, F.", - "Szeto, T.", - "Xiang, Y.", - "Chen, Y.", - "Wang, J. (0000-0002-4845-4621)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7lyh_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7lyh", - }, - }, - { - title: "Crystal structure of SARS-CoV-2 Mpro with compound C5", - emdb: null, - pdb: { - dbId: "8CYU", - method: "X-RAY DIFFRACTION", - keywords: "COVID-19, SARS-CoV-2, protease, inhibitor, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8CYU", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8cyu_final.pdb", - externalLink: "https://pdb-redo.eu/db/8cyu", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "VADPVOZBGIXSAG-UHFFFAOYSA-N"], - dbauthors: ["Lee, J.", "Worrall, L.J.", "Strynadka, N.C.J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37555275", - title: - "A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants.", - journal: - "Emerg Microbes Infect 12: 2246594-2246594 (2023), 2222-1751", - doi: "https://doi.org/10.1080/22221751.2023.2246594", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37555275", - pubDate: "2023", - abstract: "", - authors: [ - "Perez-Vargas, J. (0000-0002-4337-7903)", - "Worrall, L.J. (0000-0003-4966-7175)", - "Olmstead, A.D. (0000-0002-1110-1291)", - "Ton, A.T. (0000-0001-7418-6563)", - "Lee, J.", - "Villanueva, I. (0000-0002-9325-731X)", - "Thompson, C.A.H.", - "Dudek, S.", - "Ennis, S. (0000-0002-0105-8269)", - "Smith, J.R. (0000-0001-7380-2192)", - "Shapira, T.", - "De Guzman, J.", - "Gang, S.", - "Ban, F.", - "Vuckovic, M. (0000-0002-0452-8270)", - "Bielecki, M.", - "Kovacic, S.", - "Kenward, C. (0000-0002-3771-0044)", - "Hong, C.Y.", - "Gordon, D.G.", - "Levett, P.N. (0000-0001-6854-1776)", - "Krajden, M.", - "Leduc, R. (0000-0001-6854-8003)", - "Boudreault, P.L. (0000-0002-2032-7970)", - "Niikura, M. (0000-0001-6611-8616)", - "Paetzel, M. (0000-0002-7408-5487)", - "Young, R.N. (0000-0002-8235-6080)", - "Cherkasov, A. (0000-0002-1599-1439)", - "Strynadka, N.C.J. (0000-0002-4058-9425)", - "Jean, F. 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(0000-0003-0106-2724)", - ], - }, - { - pmID: "37446375", - title: - "High-Confidence Placement of Fragments into Electron Density Using Anomalous Diffraction-A Case Study Using Hits Targeting SARS-CoV-2 Non-Structural Protein 1.", - journal: "Int J Mol Sci 24 (2023), 1422-0067", - doi: "https://doi.org/10.3390/ijms241311197", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37446375", - pubDate: "2023", - abstract: "", - authors: [ - "Ma, S.", - "Mykhaylyk, V. (0000-0003-0106-2724)", - "Bowler, M.W. (0000-0003-0465-3351)", - "Pinotsis, N. (0000-0002-5096-257X)", - "Kozielski, F. (0000-0001-6096-9102)", - "Ma, S. (0000-0002-9560-5082)", - "Damfo, S. (0000-0002-2070-7770)", - "Lou, J.", - "Haider, S. (0000-0003-2650-2925)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8crm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8crm", - }, - }, - { - title: - "Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis", - emdb: null, - pdb: { - dbId: "7YLB", - method: "X-RAY DIFFRACTION", - keywords: - "Engineered 10Fn3, SARS-CoV-2 N, Monobody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "7YLB", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "7ylb_final.pdb", - externalLink: "https://pdb-redo.eu/db/7ylb", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "NC2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QAOWNCQODCNURD-UHFFFAOYSA-L"], - dbauthors: [ - "Hu, M. (0000-0003-2903-0708)", - "Du, Y. (0000-0002-8015-4207)", - "Sun, R. (0000-0002-8628-7019)", - "Hao, Q. (0000-0002-9642-0514)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Hu, M. (0000-0003-2903-0708)", - "Du, Y. (0000-0002-8015-4207)", - "Sun, R. (0000-0002-8628-7019)", - "Hao, Q. 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(0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli B", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. 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(0000-0003-0514-281X)", - "Lovell, S. (0000-0002-3215-4472)", - "Battaile, K.P. (0000-0003-0833-3259)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8u2x_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8u2x", - }, - }, - { - title: "SARS-CoV-2 Mpro in complex with D-4-38", - emdb: null, - pdb: { - dbId: "8GVD", - method: "X-RAY DIFFRACTION", - keywords: "Mpro, inhibitor, complex, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8GVD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8gvd_final.pdb", - externalLink: "https://pdb-redo.eu/db/8gvd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Liu, M. (0000-0002-4186-4724)", "Huang, H. (0000-0001-7836-2894)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "SARS-CoV-2 Mpro in complex with D-4-38", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Liu, M. (0000-0002-4186-4724)", - "Huang, H. (0000-0001-7836-2894)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gvd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gvd", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) H163A Mutant Reduced with 20mM TCEP", - emdb: null, - pdb: { - dbId: "8SG6", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, SARS-CoV-2, 3CL-like, disulfide bond, viral protein, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8SG6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8sg6_final.pdb", - externalLink: "https://pdb-redo.eu/db/8sg6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: [ - "Tran, N. (0000-0002-9372-9444)", - "McLeod, M.J. (0000-0001-5540-916X)", - "Kalyaanamoorthy, S. (0000-0003-0854-6449)", - "Ganesan, A. (0000-0001-8689-943X)", - "Holyoak, T. (0000-0002-7329-1115)", - "Barwell, S. (0000-0002-5703-5525)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37699927", - title: - "The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease.", - journal: "Nat Commun 14: 5625-5625 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-40023-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37699927", - pubDate: "2023", - abstract: "", - authors: [ - "Tran, N.", - "Dasari, S. (0000-0002-5554-9047)", - "Barwell, S.A.E.", - "McLeod, M.J. (0000-0001-5540-916X)", - "Kalyaanamoorthy, S.", - "Holyoak, T. (0000-0002-7329-1115)", - "Ganesan, A. (0000-0001-8689-943X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8sg6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8sg6", - }, - }, - { - title: "Structure of SARS-CoV-2 NSP3 macrodomain in the apo form", - emdb: null, - pdb: { - dbId: "8AZC", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, NSP3, Macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8AZC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8azc_final.pdb", - externalLink: "https://pdb-redo.eu/db/8azc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["VEXZGXHMUGYJMC-UHFFFAOYSA-M", "DVLFYONBTKHTER-UHFFFAOYSA-N"], - dbauthors: [ - "Sander, S. 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(0000-0001-9333-8219)", - "Aksu, M.", - "Kumar, P.", - "Guttler, T.", - "Taxer, W.", - "Gregor, K.", - "Mussil, B.", - "Rymarenko, O.", - "Stegmann, K.M.", - "Dickmanns, A.", - "Gerber, S.", - "Reineking, W.", - "Schulz, C.", - "Henneck, T.", - "Mohamed, A.", - "Pohlmann, G.", - "Ramazanoglu, M.", - "Mese, K.", - "Gross, U.", - "Ben-Yedidia, T.", - "Ovadia, O.", - "Fischer, D.W.", - "Kamensky, M.", - "Reichman, A.", - "Baumgartner, W.", - "von Kockritz-Blickwede, M.", - "Dobbelstein, M.", - "Gorlich, D.", - "Kabsch, W.", - "Emsley, P.", - "Lohkamp, B.", - "Scott, W.G.", - "Cowtan, K.", - ], - }, - { - pmID: "", - title: "Structure of SARS-CoV-2 NSP3 macrodomain in the apo form", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Sander, S. (0000-0002-7985-2526)", - "Tidow, H. 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(0000-0001-9333-8219)", - ], - }, - { - pmID: "31588918", - title: - "Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.", - journal: - "Acta Crystallogr D Struct Biol 75: 861-877 (2019), 2059-7983", - doi: "https://doi.org/10.1107/S2059798319011471", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/31588918", - pubDate: "2019", - abstract: "", - authors: [ - "Sander, S. (0000-0002-7985-2526)", - "Tidow, H. (0000-0002-4702-9332)", - "Fliegert, R.", - "Sandmann, M.", - "Afonine, P.V.", - "Grosse-Kunstleve, R.W.", - "Echols, N.", - "Headd, J.J.", - "Moriarty, N.W.", - "Mustyakimov, M.", - "Terwilliger, T.C.", - "Urzhumtsev, A.", - "Zwart, P.H.", - "Adams, P.D.", - "Liebschner, D. (0000-0003-3921-3209)", - "Afonine, P.V. (0000-0002-5052-991X)", - "Baker, M.L.", - "Bunkoczi, G.", - "Chen, V.B.", - "Croll, T.I.", - "Hintze, B. (0000-0002-4871-2096)", - "Hung, L.W. (0000-0001-6690-8458)", - "Jain, S.", - "McCoy, A.J.", - "Moriarty, N.W. (0000-0001-8857-9464)", - "Oeffner, R.D. (0000-0003-3107-2202)", - "Poon, B.K. (0000-0001-9633-6067)", - "Prisant, M.G.", - "Read, R.J. (0000-0001-8273-0047)", - "Richardson, J.S.", - "Richardson, D.C.", - "Sammito, M.D.", - "Sobolev, O.V. (0000-0002-0623-3214)", - "Stockwell, D.H.", - "Terwilliger, T.C. (0000-0001-6384-0320)", - "Urzhumtsev, A.G.", - "Videau, L.L.", - "Williams, C.J.", - "Adams, P.D. (0000-0001-9333-8219)", - "Aksu, M.", - "Kumar, P.", - "Guttler, T.", - "Taxer, W.", - "Gregor, K.", - "Mussil, B.", - "Rymarenko, O.", - "Stegmann, K.M.", - "Dickmanns, A.", - "Gerber, S.", - "Reineking, W.", - "Schulz, C.", - "Henneck, T.", - "Mohamed, A.", - "Pohlmann, G.", - "Ramazanoglu, M.", - "Mese, K.", - "Gross, U.", - "Ben-Yedidia, T.", - "Ovadia, O.", - "Fischer, D.W.", - "Kamensky, M.", - "Reichman, A.", - "Baumgartner, W.", - "von Kockritz-Blickwede, M.", - "Dobbelstein, M.", - "Gorlich, D.", - "Kabsch, W.", - "Emsley, P.", - "Lohkamp, B.", - "Scott, W.G.", - "Cowtan, K.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8azc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8azc", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) H163A Mutant in Complex with GC376", - emdb: null, - pdb: { - dbId: "8DD6", - method: "X-RAY DIFFRACTION", - keywords: - "cysteine protease, SARS-CoV-2, 3CL-like, GC376, VIRAL PROTEIN, HYDROLASE-HYDROLASE INHIBITOR complex", - refModels: [ - { - emdbId: null, - pdbId: "8DD6", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8dd6_final.pdb", - externalLink: "https://pdb-redo.eu/db/8dd6", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "A0A8B1JQ63", - organism: "2697049", - name: "ORF1a polyprotein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N", "BSPZFJDYQHDZNR-BOSXTWCSSA-N"], - dbauthors: [ - "Tran, N. (0000-0002-9372-9444)", - "McLeod, M.J. (0000-0001-5540-916X)", - "Kalyaanamoorthy, S. (0000-0003-0854-6449)", - "Ganesan, A. (0000-0001-8689-943X)", - "Holyoak, T. (0000-0002-7329-1115)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37699927", - title: - "The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease.", - journal: "Nat Commun 14: 5625-5625 (2023), 2041-1723", - doi: "https://doi.org/10.1038/s41467-023-40023-4", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37699927", - pubDate: "2023", - abstract: "", - authors: [ - "Tran, N.", - "Dasari, S. (0000-0002-5554-9047)", - "Barwell, S.A.E.", - "McLeod, M.J. (0000-0001-5540-916X)", - "Kalyaanamoorthy, S.", - "Holyoak, T. (0000-0002-7329-1115)", - "Ganesan, A. 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(0000-0002-6469-2419)", "Yuan, M. (0000-0001-9754-4503)"], - details: [ - { - sample: { - name: "", - exprSystem: "Trichoplusia ni", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Broad SARS-CoV-2 Neutralization by Monoclonal and Bispecific Antibodies Derived from a Gamma-infected Individual", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.10.14.512216", - pmidLink: "", - pubDate: "2022", - abstract: "", - authors: [ - "Guerra, D.", - "Beaumont, T.", - "Radic, L.", - "Kerster, G.", - "van der Straten, K.", - "Yuan, M.", - "Torres, J.", - "Lee, W.H.", - "Liu, H.", - "Poniman, M.", - "Bontjer, I.", - "Burger, J.A.", - "Claireaux, M.", - "Caniels, T.G.", - "Snitselaar, J.L.", - "Bijl, T.P.L.", - "Kruijer, S.", - "Ozorowski, G.", - "Gideonse, D.", - "Sliepen, K.", - "Ward, A.B.", - "Eggink, D.", - "de Bree, G.J.", - "Wilson, I.A.", - "Sanders, R.W.", - "van Gils, M.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8f0i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8f0i", - }, - }, - { - title: "The crystal structure of SARS-CoV-2 main protease in complex with 14b", - emdb: null, - pdb: { - dbId: "8GXH", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Main protease, 3CLpro, Mpro, Viral protease, 14b, HYDROLASE", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [""], - dbauthors: [ - "Yang, H. (0000-0002-1875-3268)", - "Rao, Z. (0000-0001-9866-2384)", - "Zhao, Y. (0000-0002-2932-2164)", - "Zhao, J. (0000-0002-5119-359X)", - "Shao, M. (0000-0002-9762-8608)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of SARS-CoV-2 main protease in complex with 14b", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Zhao, Y. (0000-0002-2932-2164)", - "Zhao, J. (0000-0002-5119-359X)", - "Shao, M. (0000-0002-9762-8608)", - "Yang, H. (0000-0002-1875-3268)", - "Rao, Z. 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(0000-0001-9866-2384)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gxi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gxi", - }, - }, - { - title: "SARS-CoV-2 3CLpro", - emdb: null, - pdb: { - dbId: "8GZB", - method: "X-RAY DIFFRACTION", - keywords: "Inhibitor, Complex, RECOMBINATION, VIRAL PROTEIN, HYDROLASE", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["LYCAIKOWRPUZTN-UHFFFAOYSA-N", ""], - dbauthors: ["Wang, F.", "Cen, Y.X.", "Tian, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The crystal structure of COVID-19 main protease in complex with an inhibitor N3", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Liu, X.", "Zhang, B."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8gzb_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8gzb", - }, - }, - { - title: "Structure of SARS-CoV-2 NSP3 macrodomain in complex with ADPR", - emdb: null, - pdb: { - dbId: "8AZD", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, NSP3, Macrodomain, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8AZD", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8azd_final.pdb", - externalLink: "https://pdb-redo.eu/db/8azd", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["SRNWOUGRCWSEMX-KEOHHSTQSA-N"], - dbauthors: [ - "Sander, S. 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(0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. 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(0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. 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(0000-0002-1714-4399)", - "Liu, W.R. 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(0000-0002-0544-7413)", - "Wang, H. (0000-0001-8175-5621)", - "Lin, M. (0000-0002-8072-6615)", - "Zhang, X. (0000-0001-7180-0660)", - "Zhou, H. (0000-0002-4432-5187)", - "Bian, Q. (0000-0003-3668-6078)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37696289", - title: - "Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.", - journal: "Nature (2023), 1476-4687", - doi: "https://doi.org/10.1038/s41586-023-06609-0", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37696289", - pubDate: "2023", - abstract: "", - authors: [ - "Duan, Y. (0000-0002-0544-7413)", - "Zhou, H.", - "Liu, X. (0000-0001-5498-6942)", - "Iketani, S. (0000-0002-3733-9556)", - "Lin, M. (0000-0002-8072-6615)", - "Zhang, X.", - "Bian, Q.", - "Wang, H. (0000-0001-8175-5621)", - "Sun, H.", - "Hong, S.J.", - "Culbertson, B. (0000-0002-1489-1348)", - "Mohri, H. 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(0000-0002-8072-6615)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37696289", - title: - "Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.", - journal: "Nature (2023), 1476-4687", - doi: "https://doi.org/10.1038/s41586-023-06609-0", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37696289", - pubDate: "2023", - abstract: "", - authors: [ - "Duan, Y. (0000-0002-0544-7413)", - "Zhou, H.", - "Liu, X. (0000-0001-5498-6942)", - "Iketani, S. (0000-0002-3733-9556)", - "Lin, M. (0000-0002-8072-6615)", - "Zhang, X.", - "Bian, Q.", - "Wang, H. (0000-0001-8175-5621)", - "Sun, H.", - "Hong, S.J.", - "Culbertson, B. (0000-0002-1489-1348)", - "Mohri, H. (0000-0003-3101-7625)", - "Luck, M.I.", - "Zhu, Y.", - "Liu, X.", - "Lu, Y.", - "Yang, X. (0000-0003-3443-9815)", - "Yang, K.", - "Sabo, Y. (0000-0002-4973-8247)", - "Chavez, A. 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(0000-0002-8072-6615)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37696289", - title: - "Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.", - journal: "Nature (2023), 1476-4687", - doi: "https://doi.org/10.1038/s41586-023-06609-0", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37696289", - pubDate: "2023", - abstract: "", - authors: [ - "Duan, Y. (0000-0002-0544-7413)", - "Zhou, H.", - "Liu, X. (0000-0001-5498-6942)", - "Iketani, S. (0000-0002-3733-9556)", - "Lin, M. (0000-0002-8072-6615)", - "Zhang, X.", - "Bian, Q.", - "Wang, H. (0000-0001-8175-5621)", - "Sun, H.", - "Hong, S.J.", - "Culbertson, B. (0000-0002-1489-1348)", - "Mohri, H. (0000-0003-3101-7625)", - "Luck, M.I.", - "Zhu, Y.", - "Liu, X.", - "Lu, Y.", - "Yang, X. (0000-0003-3443-9815)", - "Yang, K.", - "Sabo, Y. (0000-0002-4973-8247)", - "Chavez, A. 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(0000-0002-0492-1961)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8f2d_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8f2d", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Enstrelvir", - emdb: null, - pdb: { - dbId: "8H3K", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, Mutant, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "QMPBBNUOBOFBFS-UHFFFAOYSA-N", - "JZRWCGZRTZMZEH-UHFFFAOYSA-N", - "PEDCQBHIVMGVHV-UHFFFAOYSA-N", - ], - dbauthors: [ - "Yang, H. (0000-0002-1875-3268)", - "Rao, Z. (0000-0001-9866-2384)", - "Liu, X. (0000-0001-5498-6942)", - "Duan, Y. (0000-0002-0544-7413)", - "Wang, H. (0000-0001-8175-5621)", - "Lin, M. (0000-0002-8072-6615)", - "Zhang, X. (0000-0001-7180-0660)", - "Zhou, H. (0000-0002-4432-5187)", - "Bian, Q. (0000-0003-3668-6078)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37696289", - title: - "Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.", - journal: "Nature (2023), 1476-4687", - doi: "https://doi.org/10.1038/s41586-023-06609-0", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37696289", - pubDate: "2023", - abstract: "", - authors: [ - "Duan, Y. (0000-0002-0544-7413)", - "Zhou, H.", - "Liu, X. (0000-0001-5498-6942)", - "Iketani, S. (0000-0002-3733-9556)", - "Lin, M. (0000-0002-8072-6615)", - "Zhang, X.", - "Bian, Q.", - "Wang, H. (0000-0001-8175-5621)", - "Sun, H.", - "Hong, S.J.", - "Culbertson, B. (0000-0002-1489-1348)", - "Mohri, H. (0000-0003-3101-7625)", - "Luck, M.I.", - "Zhu, Y.", - "Liu, X.", - "Lu, Y.", - "Yang, X. (0000-0003-3443-9815)", - "Yang, K.", - "Sabo, Y. (0000-0002-4973-8247)", - "Chavez, A. (0000-0001-5626-7140)", - "Goff, S.P. (0000-0002-9679-0582)", - "Rao, Z. (0000-0001-9866-2384)", - "Ho, D.D. (0000-0003-1627-149X)", - "Yang, H. (0000-0002-1875-3268)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8h3k_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8h3k", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with ML2006a", - emdb: null, - pdb: { - dbId: "8EZV", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, SARS-CoV-2, coronavirus, Main Protease, Protease, Mpro, 3C-like proteinase, CL3pro, Inhibitor, Complex, Covalent, Adduct, M2006a, Ketoamide, Azetidine, Peptidomimetic, Viral Protein", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [""], - dbauthors: [ - "Fernandez, D. (0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ezv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ezv", - }, - }, - { - title: "SARS-CoV-2 Main Protease (Mpro) in Complex with ML3006a", - emdb: null, - pdb: { - dbId: "8F2C", - method: "X-RAY DIFFRACTION", - keywords: - "SARSCoV2, SARS-CoV-2, coronavirus, Main Protease, Protease, Mpro, 3C-like proteinase, CL3pro, Inhibitor, Complex, Covalent, Adduct, M3006a, Ketoamide, Azetidine, Peptidomimetic, Viral Protein", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "VEXZGXHMUGYJMC-UHFFFAOYSA-M"], - dbauthors: [ - "Fernandez, D. (0000-0002-6221-152X)", - "Westberg, M. (0000-0002-2312-5282)", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Westberg, M. (0000-0002-2312-5282)", - "Su, Y.", - "Zou, X.", - "Rustagi, A.", - "Beck, A.", - "Ning, L.", - "Fernandez, D. (0000-0002-6221-152X)", - "Blish, C.", - "Lin, M.Z. (0000-0002-0492-1961)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8f2c_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8f2c", - }, - }, - { - title: - "Crystal Structure of L516C/Y647C Mutant of SARS-Unique Domain (SUD) from SARS-CoV-2", - emdb: null, - pdb: { - dbId: "8UFM", - method: "X-RAY DIFFRACTION", - keywords: - "Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, SUD, Sars unique domain, Center for Structural Biology of Infectious Diseases, CSBID, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "QTBSBXVTEAMEQO-UHFFFAOYSA-M", - "QAOWNCQODCNURD-UHFFFAOYSA-L", - ], - dbauthors: [ - "Center for Structural Genomics of Infectious Diseases (CSGID)", - "Center for Structural Biology of Infectious Diseases (CSBID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Brunzelle, J.S.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of L516C/Y647C Mutant of SARS-Unique Domain (SUD) from SARS-CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Minasov, G.", - "Shuvalova, L.", - "Brunzelle, J.S.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Satchell, K.J.F.", - "Center for Structural Genomics of Infectious Diseases (CSGID)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ufm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ufm", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 2'-O-Methyltransferase in Complex with Compound 5a covalently bound to nsp16 and nsp10", - emdb: null, - pdb: { - dbId: "8F4Y", - method: "X-RAY DIFFRACTION", - keywords: - "CSBID, Structural Genomics, Center for Structural Biology of Infectious Diseases, nsp16-10, 2'-O-Methyltransferase, TRANSFERASE", - refModels: [ - { - emdbId: null, - pdbId: "8F4Y", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8f4y_final.pdb", - externalLink: "https://pdb-redo.eu/db/8f4y", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Biology of Infectious Diseases (CSBID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Brunzelle, J.S.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37728236", - title: - "Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors.", - journal: "Acs Infect Dis. (2023), 2373-8227", - doi: "https://doi.org/10.1021/acsinfecdis.3c00203", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37728236", - pubDate: "2023", - abstract: "", - authors: [ - "Inniss, N.L.", - "Kozic, J.", - "Li, F.", - "Rosas-Lemus, M.", - "Minasov, G.", - "Rybacek, J.", - "Zhu, Y.", - "Pohl, R.", - "Shuvalova, L.", - "Rulisek, L.", - "Brunzelle, J.S.", - "Bednarova, L.", - "Stefek, M.", - "Kormanik, J.M.", - "Andris, E. (0000-0002-9336-0157)", - "Sebestik, J.", - "Li, A.S.M. (0000-0003-1093-9698)", - "Brown, P.J. (0000-0002-8454-0367)", - "Schmitz, U.", - "Saikatendu, K.", - "Chang, E. (0000-0001-9534-0291)", - "Nencka, R.", - "Vedadi, M. (0000-0002-0574-0169)", - "Satchell, K.J.F. (0000-0003-3274-7611)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8f4y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8f4y", - }, - }, - { - title: - "SARS-CoV-2 3CL protease (3CLpro) in complex with compound 9 (simnotrelvir, SIM0417, SSD8432)", - emdb: null, - pdb: { - dbId: "8IGX", - method: "X-RAY DIFFRACTION", - keywords: "Mpro, Viral protein-inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8IGX", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8igx_final.pdb", - externalLink: "https://pdb-redo.eu/db/8igx", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [""], - dbauthors: [ - "Li, M.J.", - "Xie, H.", - "Su, H.X.", - "Zhao, W.F.", - "Xu, Y.C.", - "Nie, T.Q.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Discovery of oral simnotrelvir, an approved SARS-CoV-2 3C-like protease inhibitor for the treatment of COVID-19", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Jiang, X.", "Su, H."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8igx_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8igx", - }, - }, - { - title: "SARS-CoV-2 3CL protease (3CLpro) in complex with nirmatrelvir", - emdb: null, - pdb: { - dbId: "8IGY", - method: "X-RAY DIFFRACTION", - keywords: "Mpro, Viral protein-inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8IGY", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8igy_final.pdb", - externalLink: "https://pdb-redo.eu/db/8igy", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: [ - "Li, M.J.", - "Xie, H.", - "Su, H.X.", - "Zhao, W.F.", - "Xu, Y.C.", - "Nie, T.Q.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Discovery of oral simnotrelvir, an approved SARS-CoV-2 3C-like protease inhibitor for the treatment of COVID-19", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Jiang, X.", "Su, H."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8igy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8igy", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-015", - emdb: null, - pdb: { - dbId: "8H5T", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8H5T", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8h5t_final.pdb", - externalLink: "https://pdb-redo.eu/db/8h5t", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "Nanobody Nb-015", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Yang, J.", "Lu, G.W.", "Lin, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Development of a bispecific nanobody conjugate broadly neutralizes circulating SARS-CoV-2 variants and structural basis for its broad neutralization", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Yang, J.", "Lin, S.", "Lu, G.W."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8h5t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8h5t", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-021", - emdb: null, - pdb: { - dbId: "8H5U", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8H5U", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8h5u_final.pdb", - externalLink: "https://pdb-redo.eu/db/8h5u", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "Nanobody Nb-021", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Yang, J.", "Lu, G.W.", "Lin, S."], - details: [ - { - sample: { - name: "", - exprSystem: "Spodoptera frugiperda", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Development of a bispecific nanobody conjugate broadly neutralizes circulating SARS-CoV-2 variants and structural basis for its broad neutralization", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Yang, J.", "Lin, S.", "Lu, G.W."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8h5u_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8h5u", - }, - }, - { - title: - "Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with Compound 5a bound to the Cryptic Pocket of nsp16", - emdb: null, - pdb: { - dbId: "8F4S", - method: "X-RAY DIFFRACTION", - keywords: - "CSBID, Center for Structural Biology of Infectious Diseases, Methyl transferase, Structural Genomics, TRANSFERASE", - refModels: [ - { - emdbId: null, - pdbId: "8F4S", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8f4s_final.pdb", - externalLink: "https://pdb-redo.eu/db/8f4s", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "2'-O-methyltransferase", - details: "", - altNames: "Non-structural protein 16, nsp16", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Non-structural protein 10", - details: "", - altNames: "nsp10, Growth factor-like peptide, GFL", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "FKNQFGJONOIPTF-UHFFFAOYSA-N", - "", - "BDAGIHXWWSANSR-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Center for Structural Biology of Infectious Diseases (CSBID)", - "Minasov, G.", - "Shuvalova, L.", - "Rosas-Lemus, M.", - "Kiryukhina, O.", - "Brunzelle, J.S.", - "Satchell, K.J.F.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37728236", - title: - "Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors.", - journal: "Acs Infect Dis. 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emdb: null, - pdb: { - dbId: "8IFT", - method: "X-RAY DIFFRACTION", - keywords: "Mpro, Viral protein-inhibitor complex", - refModels: [ - { - emdbId: null, - pdbId: "8IFT", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ift_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ift", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [""], - dbauthors: [ - "Li, M.J.", - "Xie, H.", - "Su, H.X.", - "Zhao, W.F.", - "Xu, Y.C.", - "Nie, T.Q.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Discovery of oral simnotrelvir, an approved SARS-CoV-2 3C-like protease inhibitor for the treatment of COVID-19", - 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(0000-0001-5255-5858)", - "Dregni, A.J. (0000-0003-3422-4734)", - "Medeiros-Silva, J. (0000-0003-3532-4390)", - "Somberg, N.H. (0000-0002-5222-0334)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "pentameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37831764", - title: "Atomic structure of the open SARS-CoV-2 E viroporin.", - journal: "Sci Adv 9: eadi9007-eadi9007 (2023), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.adi9007", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37831764", - pubDate: "2023", - abstract: "", - authors: [ - "Medeiros-Silva, J. (0000-0003-3532-4390)", - "Dregni, A.J. (0000-0003-3422-4734)", - "Somberg, N.H. (0000-0002-5222-0334)", - "Duan, P. (0000-0002-7395-4353)", - "Hong, M. 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(0000-0003-0378-0017)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7gkf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7gkf", - }, - }, - { - title: - "SARS-CoV-2 Envelope Protein Transmembrane Domain: Dimeric Structure Determined by Solid-State NMR", - emdb: null, - pdb: { - dbId: "8U1T", - method: "SOLID-STATE NMR", - keywords: - "SARS-CoV-2, Envelope protein, E protein, Transmembrane domain, Membrane protein, PISEMA, PISA wheel, DARR, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC4", - organism: "2697049", - name: "Envelope small membrane protein", - details: "", - altNames: "E,sM protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhang, R. (0000-0002-2496-6913)", - "Qin, H. (0009-0007-4187-7553)", - "Prasad, R. (0000-0001-9184-779X)", - "Fu, R. (0000-0003-0075-0410)", - "Zhou, H.X. (0000-0001-9020-0302)", - "Cross, T. (0000-0002-9413-0505)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37214926", - title: - "Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein.", - journal: "Biorxiv (2023), 2692-8205", - doi: "https://doi.org/10.1101/2023.05.07.539752", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37214926", - pubDate: "2023", - abstract: "", - authors: [ - "Zhang, R.", - "Qin, H.", - "Prasad, R. (0000-0001-9184-779X)", - "Fu, R. (0000-0003-0075-0410)", - "Zhou, H.X. (0000-0001-9020-0302)", - "Cross, T.A. (0000-0002-9413-0505)", - "Prasad, R.", - "Fu, R.", - "Zhou, H.X.", - "Cross, T.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8u1t_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8u1t", - }, - }, - { - title: "Crystal structure of N-terminal domain of Nucleocapsid protein of SARS-CoV-2", - emdb: null, - pdb: { - dbId: "8X1H", - method: "X-RAY DIFFRACTION", - keywords: "Nucleocapsid, SARS-CoV-2, Coronavirus, RNA BINDING PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC9", - organism: null, - name: "Nucleoprotein", - details: "", - altNames: "N,Nucleocapsid protein,NC,Protein N", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Kumari, S.", "Gupta, G.D. (0000-0003-2549-3190)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of N-terminal domain of Nucleocapsid protein of SARS-CoV-2", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Kumari, S. (0000-0002-5244-8873)", - "Gupta, G.D. 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(0000-0001-8738-987X)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli 'BL21-Gold(DE3)pLysS AG'", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "37257212", - title: - "Discovery of quinazolin-4-one-based non-covalent inhibitors targeting the severe acute respiratory syndrome coronavirus 2 main protease (SARS-CoV-2 M pro ).", - journal: "Eur.J.Med.Chem. 257: 115487-115487 (2023), 0223-5234", - doi: "https://doi.org/10.1016/j.ejmech.2023.115487", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37257212", - pubDate: "2023", - abstract: "", - authors: [ - "Zhang, K.", - "Wang, T.", - "Li, M.", - "Liu, M.", - "Tang, H.", - "Wang, L.", - "Ye, K.", - "Yang, J.", - "Jiang, S.", - "Xiao, Y.", - "Xie, Y.", - "Lu, M.", - "Zhang, X.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8i4s_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8i4s", - }, - }, - { - title: "SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain", - emdb: null, - pdb: { - dbId: "8T5P", - method: "X-RAY DIFFRACTION", - keywords: "signaling protein-viral protein complex", - refModels: [ - { - emdbId: null, - pdbId: "8T5P", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8t5p_final.pdb", - externalLink: "https://pdb-redo.eu/db/8t5p", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q13114", - organism: "9606", - name: "TNF receptor-associated factor 3", - details: "", - altNames: - "CD40 receptor-associated factor 1,CRAF1,CD40-binding protein,CD40BP,LMP1-associated protein 1,LAP1,RING-type E3 ubiquitin transferase TRAF3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC3", - organism: null, - name: "ORF3a protein", - details: "", - altNames: "ORF3a,Accessory protein 3a,Protein 3a,Protein U274,Protein X1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Busscher, B.M. 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(0000-0002-1431-9755)", - "Hilgenfeld, R. (0000-0001-8850-2977)", - "Sun, X. (0000-0002-2761-2862)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "monomeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "SARS-CoV-2 Omicron (P132H) complex with alpha-ketoamide 13b-K at pH 6.5", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Ibrahim, M. (0000-0002-1431-9755)", - "Hilgenfeld, R. (0000-0001-8850-2977)", - "Sun, X. 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(0000-0002-7354-0839)", - "Lieske, J. (0000-0002-5439-5082)", - "Rahmani Mashhour, A. (0000-0001-9177-5589)", - "Guenther, S. (0000-0002-7329-6653)", - "Meents, A. (0000-0001-6078-4095)", - "Saouane, S. (0000-0002-7260-9021)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "High-pressure macromolecular crystallography to explore the conformational space of proteins", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lieske, J. (0000-0002-5439-5082)", - "Saouane, S. (0000-0002-7260-9021)", - "Guenther, S. (0000-0002-7329-6653)", - "Reinke, P.Y.A. (0000-0002-7354-0839)", - "Falke, S. (0000-0003-3409-1791)", - "Ewert, W. (0000-0001-8626-4864)", - "Meyer, J.", - "Pakendorf, T.", - "Reime, B.", - "Burkhardt, A.", - "Crosas, E.", - "Hakanpaeae, J.", - "Stachnik, K.", - "Sieg, J. (0000-0001-5343-7255)", - "Rarey, M.", - "Assmann, M. (0000-0002-1660-5253)", - "Zaun, H. (0000-0002-1839-068X)", - "Kuballa, J. (0000-0001-6336-9452)", - "Chapman, H.N. (0000-0002-4655-1743)", - "Meents, A. (0000-0001-6078-4095)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8bs2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8bs2", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-272", - emdb: null, - pdb: { - dbId: "8UH5", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2 main protease, 3C-like proteinase, VIRAL PROTEIN, SARS-CoV-2", - refModels: [ - { - emdbId: null, - pdbId: "8UH5", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8uh5_final.pdb", - externalLink: "https://pdb-redo.eu/db/8uh5", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["", "MTHSVFCYNBDYFN-UHFFFAOYSA-N"], - dbauthors: [ - "Bulut, H. (0000-0003-0262-6296)", - "Hayashi, H.", - "Tsuji, K.", - "Kuwata, N.", - "Das, D.", - "Tamamura, H.", - "Mitsuya, H. (0000-0001-9274-3853)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Higashi-Kuwata, N.", - "Bulut, H.", - "Hayashi, H.", - "Tsuji, K.", - "Ogata-Aoki, H.", - "Kiso, M.", - "Takamune, N.", - "Kishimoto, N.", - "Hattori, S.", - "Ishii, T.", - "Kobayakawa, T.", - "Nakano, K.", - "Das, D.", - "Saruwatari, J.", - "Hasegawa, K.", - "Murayama, K.", - "Sukenaga, Y.", - "Takamatsu, Y.", - "Yoshimura, K.", - "Aoki, M.", - "Okamura, T.", - "Yamayoshi, S.", - "Kawaoka, Y.", - "Misumi, S.", - "Tamamura, H.", - "Mitsuya, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8uh5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8uh5", - }, - }, - { - title: "Room-temperature structure of SARS-CoV-2 Main protease at atmospheric pressure", - emdb: null, - pdb: { - dbId: "8BS1", - method: "X-RAY DIFFRACTION", - keywords: - "HPMX, high-pressure macromolecular crystallography, sapphire capillary, room temperature, SARS-CoV-2, Mpro, COVID-19, PEPTIDE BINDING PROTEIN, virus protease, HYDROLASE", - refModels: [ - { - emdbId: null, - pdbId: "8BS1", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8bs1_final.pdb", - externalLink: "https://pdb-redo.eu/db/8bs1", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "3C-like proteinase", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["IAZDPXIOMUYVGZ-UHFFFAOYSA-N"], - dbauthors: [ - "Reinke, P.Y.A. (0000-0002-7354-0839)", - "Lieske, J. (0000-0002-5439-5082)", - "Rahmani Mashhour, A. (0000-0001-9177-5589)", - "Guenther, S. (0000-0002-7329-6653)", - "Meents, A. (0000-0001-6078-4095)", - "Saouane, S. (0000-0002-7260-9021)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "High-pressure macromolecular crystallography to explore the conformational space of proteins", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Lieske, J. (0000-0002-5439-5082)", - "Saouane, S. (0000-0002-7260-9021)", - "Guenther, S. (0000-0002-7329-6653)", - "Reinke, P.Y.A. (0000-0002-7354-0839)", - "Falke, S. (0000-0003-3409-1791)", - "Ewert, W. (0000-0001-8626-4864)", - "Meyer, J.", - "Pakendorf, T.", - "Reime, B.", - "Burkhardt, A.", - "Crosas, E.", - "Hakanpaeae, J.", - "Stachnik, K.", - "Sieg, J. (0000-0001-5343-7255)", - "Rarey, M.", - "Assmann, M. (0000-0002-1660-5253)", - "Zaun, H. (0000-0002-1839-068X)", - "Kuballa, J. (0000-0001-6336-9452)", - "Chapman, H.N. (0000-0002-4655-1743)", - "Meents, A. (0000-0001-6078-4095)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8bs1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8bs1", - }, - }, - { - title: - "Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain", - emdb: null, - pdb: { - dbId: "8F2J", - method: "X-RAY DIFFRACTION", - keywords: - "Neutralizing antibody, SARS-CoV-2, WRAIR-2134, receptor binding domain, ANTIVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2134 Fab Heavy Chain", - details: "Antibody Heavy Chain Fab fragment", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2134 Fab Light Chain", - details: "Antibody Light Chain", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Sankhala, R.S. (0000-0001-8639-5290)", - "Joyce, M.G. (0000-0002-6808-7232)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain.", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Sankhala, R.S. (0000-0001-8639-5290)", - "Dussupt, V.", - "Modjarrad, K.", - "Joyce, M.G. (0000-0002-6808-7232)", - "Jensen, J. (0000-0002-8818-7513)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8f2j_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8f2j", - }, - }, - { - title: - "Crystal structure of antibody WRAIR-2123 in complex with SARS-CoV-2 receptor binding domain", - emdb: null, - pdb: { - dbId: "8SMI", - method: "X-RAY DIFFRACTION", - keywords: - "sars-cov-2, antibody, immune system, viral protein, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: null, - pdbId: "8SMI", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8smi_final.pdb", - externalLink: "https://pdb-redo.eu/db/8smi", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2123 Fab heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "WRAIR-2123 Fab light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: ["Sankhala, R.S.", "Jensen, J.L.", "Joyce, M.G."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of antibody WRAIR-2123 in complex with SARS-CoV-2 receptor binding domain", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Sankhala, R.S.", "Jensen, J.L.", "Joyce, M.G."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8smi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8smi", - }, - }, - { - title: "Crystal structure of main protease of SARS-CoV-2 complexed with inhibitor", - emdb: null, - pdb: { - dbId: "8FTC", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, Main protease, inhibitor, inhibitory activity, VIRAL PROTEIN", - refModels: [ - { - emdbId: null, - pdbId: "8FTC", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8ftc_final.pdb", - externalLink: "https://pdb-redo.eu/db/8ftc", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [""], - dbauthors: [ - "Lu, J. (0000-0002-4090-5176)", - "Khan, M.B. (0000-0002-4164-9573)", - "Young, H.S. (0000-0002-5990-8422)", - "Lemieux, M.J. (0000-0003-4745-9153)", - "Chen, P. (0000-0002-0434-6346)", - "Arutyunova, E. (0000-0003-4119-3622)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "The Effect of Deuteration and Homologation of the Lactam Ring of Nirmatrelvir on Its Biochemical Properties and Oxidative Metabolism", - journal: "Acs Bio Med Chem Au (2023), 2694-2437", - doi: "https://doi.org/10.1021/acsbiomedchemau.3c00039", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Arutyunova, E.", - "Belovodskiy, A.", - "Chen, P.", - "Khan, M.B.", - "Joyce, M.", - "Saffran, H.", - "Lu, J.", - "Turner, Z.", - "Bai, B.", - "Lamer, T.", - "Young, H.S.", - "Vederas, J.C.", - "Tyrrell, D.L.", - "Lemieux, M.J.", - "Nieman, J.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8ftc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8ftc", - }, - }, - { - title: - "Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir", - emdb: null, - pdb: { - dbId: "8HOM", - method: "X-RAY DIFFRACTION", - keywords: "SARS-COV-2, Omicron, main protease, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["QMPBBNUOBOFBFS-UHFFFAOYSA-N"], - dbauthors: ["Liu, X.", "Lin, M."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) in Complex with Ensitrelvir", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - 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uniprotAcc: null, - organism: "2697049", - name: "PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wang, S.Q. 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(0000-0002-1779-8675)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hso_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hso", - }, - }, - { - title: "Crystal structure of Ubl1 domain of nonstructural protein 3 of SARS-CoV-2", - emdb: null, - pdb: { - dbId: "8XAB", - method: "X-RAY DIFFRACTION", - keywords: "Ubl1, Nonstructural protein 3, SARS-CoV-2, VIRUS", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "Papain-like protease nsp3", - details: "", - altNames: - "Non-structural protein 3,nsp3,PL2-PRO,Papain-like proteinase,PL-PRO", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PEDCQBHIVMGVHV-UHFFFAOYSA-N"], - dbauthors: ["Li, Y. (0000-0003-1963-839X)", "Ke, Z. 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(0000-0003-1963-839X)", - "Zhang, H.", - "Wang, Y.", - "Wang, J.N.", - "Peng, F.", - "Wang, J.", - "Liu, X.", - "Hu, H.", - "Li, Y.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8xab_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8xab", - }, - }, - { - title: "CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67", - emdb: null, - pdb: { - dbId: "8HSM", - method: "X-RAY DIFFRACTION", - keywords: "MHC, IMMUNOLIGY, IMMUNE SYSTEM TRANSFERASE COMPLEX., IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8HSM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hsm_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hsm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "G1PNR4", - organism: "59463", - name: "Ig-like domain-containing protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "2697049", - name: "PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Wang, S.Q. 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(0000-0002-5794-0349)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "octameric (author_and_software_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37425880", - title: - "Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication.", - journal: "Biorxiv (2023), 2692-8205", - doi: "https://doi.org/10.1101/2023.06.29.546885", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37425880", - pubDate: "2023", - abstract: "", - authors: [ - "Yang, Z.", - "Johnson, B.A.", - "Meliopoulos, V.A.", - "Ju, X.", - "Zhang, P.", - "Hughes, M.P.", - "Wu, J.", - "Koreski, K.P.", - "Chang, T.C.", - "Wu, G.", - "Hixon, J.", - "Duffner, J.", - "Wong, K.", - "Lemieux, R.", - "Lokugamage, K.G.", - "Alvardo, R.E.", - "Crocquet-Valdes, P.A.", - "Walker, D.H.", - "Plante, K.S.", - "Plante, J.A.", - "Weaver, S.C.", - "Kim, H.J.", - "Meyers, R.", - "Schultz-Cherry, S.", - "Ding, Q.", - "Menachery, V.D.", - "Taylor, J.P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8th1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8th1", - }, - }, - { - title: "Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope QYIKWPWYI", - emdb: null, - pdb: { - dbId: "8HN4", - method: "X-RAY DIFFRACTION", - keywords: "SARS-CoV-2, MHC, Complex, epitope, IMMUNE SYSTEM", - refModels: [ - { - emdbId: null, - pdbId: "8HN4", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hn4_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hn4", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "F6IR24", - organism: "9606", - name: "MHC class I antigen", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61769", - organism: "9606", - name: "Beta-2-microglobulin", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "SARS-CoV-2 T-cell epitope QYIKWPWYI", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Jin, T.C. 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(0000-0002-1593-1962)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hn4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hn4", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with PF07321332", - emdb: null, - pdb: { - dbId: "8HVK", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "8HVK", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hvk_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hvk", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Zhang, J.", "Li, J.", "Zeng, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 main protease\nG15S mutant in complex with PF07321332", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zeng, P.", "Zhang, J.", "Li, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hvk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hvk", - }, - }, - { - title: - "Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody BIOLS56", - emdb: null, - pdb: { - dbId: "7Y3O", - method: "X-RAY DIFFRACTION", - keywords: - "SARS-CoV-2, antibody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: "9606", - name: "Heavy chain of BIOLS56", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "Light chain of BIOLS56", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Wu, Y. (0000-0003-2734-0673)", - "Gao, F. (0000-0002-0670-010X)", - "Rao, X. (0000-0001-6531-181X)", - "Gao, F. (0000-0002-3869-615X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "38109549", - title: - "Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.", - journal: - "Proc.Natl.Acad.Sci.USA 120: e2314193120-e2314193120 (2023), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2314193120", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/38109549", - pubDate: "2023", - abstract: "", - authors: [ - "Rao, X.", - "Zhao, R.", - "Tong, Z. (0000-0002-9867-2838)", - "Guo, S.", - "Peng, W.", - "Liu, K.", - "Li, S.", - "Wu, L.", - "Tong, J.", - "Chai, Y.", - "Han, P.", - "Wang, F.", - "Jia, P.", - "Li, Z.", - "Zhao, X.", - "Li, D.", - "Zhang, R.", - "Zhang, X.", - "Zou, W.", - "Li, W.", - "Wang, Q. (0000-0003-3768-0401)", - "Gao, G.F. (0000-0002-3869-615X)", - "Wu, Y. (0000-0003-2734-0673)", - "Dai, L.", - "Gao, F. (0000-0002-0670-010X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7y3o_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7y3o", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with PF07321332", - emdb: null, - pdb: { - dbId: "8HVO", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "8HVO", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hvo_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hvo", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Zhang, J.", "Li, J.", "Zou, X.F."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 main protease\nV186F mutant in complex with PF07321332", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zou, X.F.", "Zhang, J.", "Li, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hvo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hvo", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with PF07321332", - emdb: null, - pdb: { - dbId: "8HVN", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "8HVN", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hvn_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hvn", - 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}, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with PF07321332", - emdb: null, - pdb: { - dbId: "8HVL", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "8HVL", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hvl_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hvl", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Zhang, J.", "Li, J.", "Zou, X.F."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 main protease\nM49I mutant in complex with PF07321332", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Zou, X.F.", "Zhang, J.", "Li, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hvl_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hvl", - }, - }, - { - title: - "Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with PF07321332", - emdb: null, - pdb: { - dbId: "8HVM", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - refModels: [ - { - emdbId: null, - pdbId: "8HVM", - source: "PDB-REDO", - method: "PDB-Redo", - filename: "8hvm_final.pdb", - externalLink: "https://pdb-redo.eu/db/8hvm", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC1", - organism: "2697049", - name: "3C-like proteinase nsp5", - details: "", - altNames: - "3CL-PRO,3CLp,Main protease,Mpro,Non-structural protein 5,nsp5,SARS coronavirus main proteinase", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WDVIRQQKRMIXGS-OJFNHCPVSA-N"], - dbauthors: ["Wang, J.", "Zhang, J.", "Li, J."], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21(DE3)", - assembly: "dimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Crystal structure of SARS-Cov-2 main protease\nK90R mutant in complex with PF07321332", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Wang, J.", "Zhang, J.", "Li, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8hvm_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8hvm", - }, - }, - { - title: - "Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors", - emdb: null, - pdb: { - dbId: "8IHO", - method: "X-RAY DIFFRACTION", - keywords: "VIRAL PROTEIN-INHIBITOR COMPLEX", - 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(0000-0001-6748-9339)", - "Wrobel, A.G. (0000-0002-6680-5587)", - "Gamblin, S.J. (0000-0001-5331-639X)", - "Rosenthal, P.B. (0000-0002-0387-2862)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32647346", - title: - "SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects.", - journal: "Nat.Struct.Mol.Biol. 27: 763-767 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0468-7", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32647346", - pubDate: "2020", - abstract: "", - authors: [ - "Wrobel, A.G. (0000-0002-6680-5587)", - "Benton, D.J. (0000-0001-6748-9339)", - "Xu, P.", - "Roustan, C.", - "Martin, S.R.", - "Rosenthal, P.B. (0000-0002-0387-2862)", - "Skehel, J.J.", - "Gamblin, S.J. (0000-0001-5331-639X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zgi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zgi", - }, - }, - { - title: "H11-H4 bound to Spike", - emdb: { - dbId: "EMD-11218", - emMethod: "SINGLE PARTICLE", - resolution: "3.7", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11218/400_11218.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11218", - }, - pdb: { - dbId: "6ZHD", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-CoV-2, nanobody, llama, neutralisation, spike, ANTIVIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11218", - pdbId: "6ZHD", - source: "CERES", - method: "PHENIX", - filename: "6zhd_11218_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zhd_11218/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "10665", - name: "Spike glycoprotein,Fibritin", - details: "", - altNames: - "S glycoprotein,E2,Peplomer protein,Collar protein,Whisker antigen control protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P10104", - organism: "9844", - name: "Nanobody H11-H4", - details: "", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Naismith, J.H. (0000-0001-6744-5061)", - "Weckener, M. (0000-0002-1419-9378)", - "Vogirala, V.K. (0000-0002-8534-3736)", - "Clare, D.K. (0000-0002-3372-8378)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "hexameric (software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: "H11-H4 bound to Spike", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: ["Naismith, J.H.", "Huo, J."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zhd_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zhd", - }, - }, - { - title: "SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit", - emdb: { - dbId: "EMD-11276", - emMethod: "SINGLE PARTICLE", - resolution: "2.6", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11276/400_11276.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11276", - }, - pdb: { - dbId: "6ZLW", - method: "ELECTRON MICROSCOPY", - keywords: - "Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11276", - pdbId: "6ZLW", - source: "CERES", - method: "PHENIX", - filename: "6zlw_11276_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zlw_11276/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P15880", - organism: null, - name: "40S ribosomal protein S2", - details: "", - altNames: - "40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46782", - organism: null, - name: "40S ribosomal protein S5", - details: "", - altNames: "Small ribosomal subunit protein uS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46783", - organism: null, - name: "40S ribosomal protein S10", - details: "", - altNames: "Small ribosomal subunit protein eS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62841", - organism: null, - name: "40S ribosomal protein S15", - details: "", - altNames: "RIG protein,Small ribosomal subunit protein uS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62249", - organism: null, - name: "40S ribosomal protein S16", - details: "", - altNames: "Small ribosomal subunit protein uS9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08708", - organism: null, - name: "40S ribosomal protein S17", - details: "", - altNames: "Small ribosomal subunit protein eS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39019", - organism: null, - name: "40S ribosomal protein S19", - details: "", - altNames: "Small ribosomal subunit protein eS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60866", - organism: null, - name: "40S ribosomal protein S20", - details: "", - altNames: "Small ribosomal subunit protein uS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62857", - organism: null, - name: "40S ribosomal protein S28", - details: "", - altNames: "Small ribosomal subunit protein eS28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62273", - organism: null, - name: "40S ribosomal protein S29", - details: "", - altNames: "Small ribosomal subunit protein uS14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62979", - organism: null, - name: "Ubiquitin-40S ribosomal protein S27a", - details: "", - altNames: "Ubiquitin carboxyl extension protein 80", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62945", - organism: null, - name: "60S ribosomal protein L41", - details: "", - altNames: "HG12,Large ribosomal subunit protein eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63244", - organism: null, - name: "Receptor of activated protein C kinase 1", - details: "", - altNames: - "Cell proliferation-inducing gene 21 protein,Guanine nucleotide-binding protein subunit beta-2-like 1,Guanine nucleotide-binding protein subunit beta-like protein 12.3,Human lung cancer oncogene 7 protein,HLC-7,Receptor for activated C kinase,Small ribosomal subunit protein RACK1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "18S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "Non-structural protein 1", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,Non-structural protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Denk, T.", - "Kratzat, H.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Berninghausen, O.", - "Becker, T.", - "Beckmann, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "36-meric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32680882", - title: - "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", - journal: "Science 369: 1249-1255 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abc8665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32680882", - pubDate: "2020", - abstract: "", - authors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Koepke, L.", - "Denk, T.", - "Hirschenberger, M.", - "Kratzat, H.", - "Hayn, M.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Straub, J.H.", - "Sturzel, C.M.", - "Frohlich, T.", - "Berninghausen, O.", - "Becker, T.", - "Kirchhoff, F.", - "Sparrer, K.M.J.", - "Beckmann, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zlw_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zlw", - }, - }, - { - title: "SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex", - emdb: { - dbId: "EMD-11288", - emMethod: "SINGLE PARTICLE", - resolution: "2.7", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11288/400_11288.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11288", - }, - pdb: { - dbId: "6ZM7", - method: "ELECTRON MICROSCOPY", - keywords: - "Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "28S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5.8S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62917", - organism: null, - name: "60S ribosomal protein L8", - details: "", - altNames: "Large ribosomal subunit protein uL2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39023", - organism: null, - name: "60S ribosomal protein L3", - details: "", - altNames: - "HIV-1 TAR RNA-binding protein B,TARBP-B,Large ribosomal subunit protein uL3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P36578", - organism: null, - name: "60S ribosomal protein L4", - details: "", - altNames: "60S ribosomal protein L1,Large ribosomal subunit protein uL4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46777", - organism: null, - name: "60S ribosomal protein L5", - details: "", - altNames: "Large ribosomal subunit protein uL18", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02878", - organism: null, - name: "60S ribosomal protein L6", - details: "", - altNames: - "Large ribosomal subunit protein eL6,Neoplasm-related protein C140,Tax-responsive enhancer element-binding protein 107,TaxREB107", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18124", - organism: null, - name: "60S ribosomal protein L7", - details: "", - altNames: "Large ribosomal subunit protein uL30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62424", - organism: null, - name: "60S ribosomal protein L7a", - details: "", - altNames: - "Large ribosomal subunit protein eL8,PLA-X polypeptide,Surfeit locus protein 3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P32969", - organism: null, - name: "60S ribosomal protein L9", - details: "", - altNames: "Large ribosomal subunit protein uL6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q96L21", - organism: null, - name: "60S ribosomal protein L10-like", - details: "", - altNames: "Large ribosomal subunit protein uL16-like", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62913", - organism: null, - name: "60S ribosomal protein L11", - details: "", - altNames: - "CLL-associated antigen KW-12,Large ribosomal subunit protein uL5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P26373", - organism: null, - name: "60S ribosomal protein L13", - details: "", - altNames: - "Breast basic conserved protein 1,Large ribosomal subunit protein eL13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P50914", - organism: null, - name: "60S ribosomal protein L14", - details: "", - altNames: "CAG-ISL 7,Large ribosomal subunit protein eL14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61313", - organism: null, - name: "60S ribosomal protein L15", - details: "", - altNames: "Large ribosomal subunit protein eL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P40429", - organism: null, - name: "60S ribosomal protein L13a", - details: "", - altNames: - "23 kDa highly basic protein,Large ribosomal subunit protein uL13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18621", - organism: null, - name: "60S ribosomal protein L17", - details: "", - altNames: - "60S ribosomal protein L23,Large ribosomal subunit protein uL22,PD-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q07020", - organism: null, - name: "60S ribosomal protein L18", - details: "", - altNames: "Large ribosomal subunit protein eL18", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P84098", - organism: null, - name: "60S ribosomal protein L19", - details: "", - altNames: "Large ribosomal subunit protein eL19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02543", - organism: null, - name: "60S ribosomal protein L18a", - details: "", - altNames: "Large ribosomal subunit protein eL20", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46778", - organism: null, - name: "60S ribosomal protein L21", - details: "", - altNames: "Large ribosomal subunit protein eL21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P35268", - organism: null, - name: "60S ribosomal protein L22", - details: "", - altNames: - "EBER-associated protein,EAP,Epstein-Barr virus small RNA-associated protein,Heparin-binding protein HBp15,Large ribosomal subunit protein eL22", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62829", - organism: null, - name: "60S ribosomal protein L23", - details: "", - altNames: "60S ribosomal protein L17,Large ribosomal subunit protein uL14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P83731", - organism: null, - name: "60S ribosomal protein L24", - details: "", - altNames: "60S ribosomal protein L30,Large ribosomal subunit protein eL24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62750", - organism: null, - name: "60S ribosomal protein L23a", - details: "", - altNames: "Large ribosomal subunit protein uL23", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61254", - organism: null, - name: "60S ribosomal protein L26", - details: "", - altNames: "Large ribosomal subunit protein uL24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61353", - organism: null, - name: "60S ribosomal protein L27", - details: "", - altNames: "Large ribosomal subunit protein eL27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46776", - organism: null, - name: "60S ribosomal protein L27a", - details: "", - altNames: "Large ribosomal subunit protein uL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P47914", - organism: null, - name: "60S ribosomal protein L29", - details: "", - altNames: - "Cell surface heparin-binding protein HIP,Large ribosomal subunit protein eL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62888", - organism: null, - name: "60S ribosomal protein L30", - details: "", - altNames: "Large ribosomal subunit protein eL30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62899", - organism: null, - name: "60S ribosomal protein L31", - details: "", - altNames: "Large ribosomal subunit protein eL31", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62910", - organism: null, - name: "60S ribosomal protein L32", - details: "", - altNames: "Large ribosomal subunit protein eL32", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18077", - organism: null, - name: "60S ribosomal protein L35a", - details: "", - altNames: - "Cell growth-inhibiting gene 33 protein,Large ribosomal subunit protein eL33", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P49207", - organism: null, - name: "60S ribosomal protein L34", - details: "", - altNames: "Large ribosomal subunit protein eL34", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42766", - organism: null, - name: "60S ribosomal protein L35", - details: "", - altNames: "Large ribosomal subunit protein uL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y3U8", - organism: null, - name: "60S ribosomal protein L36", - details: "", - altNames: "Large ribosomal subunit protein eL36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61927", - organism: null, - name: "60S ribosomal protein L37", - details: "", - altNames: "G1.16,Large ribosomal subunit protein eL37", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63173", - organism: null, - name: "60S ribosomal protein L38", - details: "", - altNames: "Large ribosomal subunit protein eL38", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62891", - organism: null, - name: "60S ribosomal protein L39", - details: "", - altNames: "Large ribosomal subunit protein eL39", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62987", - organism: null, - name: "Ubiquitin-60S ribosomal protein L40", - details: "", - altNames: "CEP52,Ubiquitin A-52 residue ribosomal protein fusion product 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62945", - organism: null, - name: "60S ribosomal protein L41", - details: "", - altNames: "HG12,Large ribosomal subunit protein eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P83881", - organism: null, - name: "60S ribosomal protein L36a", - details: "", - altNames: - "60S ribosomal protein L44,Cell growth-inhibiting gene 15 protein,Cell migration-inducing gene 6 protein,Large ribosomal subunit protein eL42", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61513", - organism: null, - name: "60S ribosomal protein L37a", - details: "", - altNames: "Large ribosomal subunit protein eL43", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46779", - organism: null, - name: "60S ribosomal protein L28", - details: "", - altNames: "Large ribosomal subunit protein eL28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05388", - organism: null, - name: "60S acidic ribosomal protein P0", - details: "", - altNames: "60S ribosomal protein L10E,Large ribosomal subunit protein uL10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P30050", - organism: null, - name: "60S ribosomal protein L12", - details: "", - altNames: "Large ribosomal subunit protein uL11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62906", - organism: null, - name: "60S ribosomal protein L10a", - details: "", - altNames: - "CSA-19,Large ribosomal subunit protein uL1,Neural precursor cell expressed developmentally down-regulated protein 6,NEDD-6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "18S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46782", - organism: null, - name: "40S ribosomal protein S5", - details: "", - altNames: "Small ribosomal subunit protein uS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46783", - organism: null, - name: "40S ribosomal protein S10", - details: "", - altNames: "Small ribosomal subunit protein eS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62841", - organism: null, - name: "40S ribosomal protein S15", - details: "", - altNames: "RIG protein,Small ribosomal subunit protein uS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62249", - organism: null, - name: "40S ribosomal protein S16", - details: "", - altNames: "Small ribosomal subunit protein uS9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08708", - organism: null, - name: "40S ribosomal protein S17", - details: "", - altNames: "Small ribosomal subunit protein eS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39019", - organism: null, - name: "40S ribosomal protein S19", - details: "", - altNames: "Small ribosomal subunit protein eS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60866", - organism: null, - name: "40S ribosomal protein S20", - details: "", - altNames: "Small ribosomal subunit protein uS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62857", - organism: null, - name: "40S ribosomal protein S28", - details: "", - altNames: "Small ribosomal subunit protein eS28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62273", - organism: null, - name: "40S ribosomal protein S29", - details: "", - altNames: "Small ribosomal subunit protein uS14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63244", - organism: null, - name: "Receptor of activated protein C kinase 1", - details: "", - altNames: - "Cell proliferation-inducing gene 21 protein,Guanine nucleotide-binding protein subunit beta-2-like 1,Guanine nucleotide-binding protein subunit beta-like protein 12.3,Human lung cancer oncogene 7 protein,HLC-7,Receptor for activated C kinase,Small ribosomal subunit protein RACK1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P15880", - organism: null, - name: "40S ribosomal protein S2", - details: "", - altNames: - "40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62979", - organism: null, - name: "Ubiquitin-40S ribosomal protein S27a", - details: "", - altNames: "Ubiquitin carboxyl extension protein 80", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9UQ80", - organism: null, - name: "Proliferation-associated protein 2G4", - details: "", - altNames: - "Cell cycle protein p38-2G4 homolog,hG4-1,ErbB3-binding protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "tRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q96CT7", - organism: null, - name: "Coiled-coil domain-containing protein 124", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "Non-structural protein 1", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,Non-structural protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JLVVSXFLKOJNIY-UHFFFAOYSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Denk, T.", - "Kratzat, H.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Berninghausen, O.", - "Becker, T.", - "Beckmann, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "32680882", - title: - "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", - journal: "Science 369: 1249-1255 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abc8665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32680882", - pubDate: "2020", - abstract: "", - authors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Koepke, L.", - "Denk, T.", - "Hirschenberger, M.", - "Kratzat, H.", - "Hayn, M.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Straub, J.H.", - "Sturzel, C.M.", - "Frohlich, T.", - "Berninghausen, O.", - "Becker, T.", - "Kirchhoff, F.", - "Sparrer, K.M.J.", - "Beckmann, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zm7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zm7", - }, - }, - { - title: "SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex", - emdb: { - dbId: "EMD-11289", - emMethod: "SINGLE PARTICLE", - resolution: "3.0", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11289/400_11289.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11289", - }, - pdb: { - dbId: "6ZME", - method: "ELECTRON MICROSCOPY", - keywords: - "Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "28S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5.8S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62917", - organism: null, - name: "60S ribosomal protein L8", - details: "", - altNames: "Large ribosomal subunit protein uL2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39023", - organism: null, - name: "60S ribosomal protein L3", - details: "", - altNames: - "HIV-1 TAR RNA-binding protein B,TARBP-B,Large ribosomal subunit protein uL3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P36578", - organism: null, - name: "60S ribosomal protein L4", - details: "", - altNames: "60S ribosomal protein L1,Large ribosomal subunit protein uL4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46777", - organism: null, - name: "60S ribosomal protein L5", - details: "", - altNames: "Large ribosomal subunit protein uL18", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02878", - organism: null, - name: "60S ribosomal protein L6", - details: "", - altNames: - "Large ribosomal subunit protein eL6,Neoplasm-related protein C140,Tax-responsive enhancer element-binding protein 107,TaxREB107", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18124", - organism: null, - name: "60S ribosomal protein L7", - details: "", - altNames: "Large ribosomal subunit protein uL30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62424", - organism: null, - name: "60S ribosomal protein L7a", - details: "", - altNames: - "Large ribosomal subunit protein eL8,PLA-X polypeptide,Surfeit locus protein 3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P32969", - organism: null, - name: "60S ribosomal protein L9", - details: "", - altNames: "Large ribosomal subunit protein uL6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q96L21", - organism: null, - name: "60S ribosomal protein L10-like", - details: "", - altNames: "Large ribosomal subunit protein uL16-like", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62913", - organism: null, - name: "60S ribosomal protein L11", - details: "", - altNames: - "CLL-associated antigen KW-12,Large ribosomal subunit protein uL5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P26373", - organism: null, - name: "60S ribosomal protein L13", - details: "", - altNames: - "Breast basic conserved protein 1,Large ribosomal subunit protein eL13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P50914", - organism: null, - name: "60S ribosomal protein L14", - details: "", - altNames: "CAG-ISL 7,Large ribosomal subunit protein eL14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61313", - organism: null, - name: "60S ribosomal protein L15", - details: "", - altNames: "Large ribosomal subunit protein eL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P40429", - organism: null, - name: "60S ribosomal protein L13a", - details: "", - altNames: - "23 kDa highly basic protein,Large ribosomal subunit protein uL13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18621", - organism: null, - name: "60S ribosomal protein L17", - details: "", - altNames: - "60S ribosomal protein L23,Large ribosomal subunit protein uL22,PD-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q07020", - organism: null, - name: "60S ribosomal protein L18", - details: "", - altNames: "Large ribosomal subunit protein eL18", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P84098", - organism: null, - name: "60S ribosomal protein L19", - details: "", - altNames: "Large ribosomal subunit protein eL19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02543", - organism: null, - name: "60S ribosomal protein L18a", - details: "", - altNames: "Large ribosomal subunit protein eL20", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46778", - organism: null, - name: "60S ribosomal protein L21", - details: "", - altNames: "Large ribosomal subunit protein eL21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P35268", - organism: null, - name: "60S ribosomal protein L22", - details: "", - altNames: - "EBER-associated protein,EAP,Epstein-Barr virus small RNA-associated protein,Heparin-binding protein HBp15,Large ribosomal subunit protein eL22", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62829", - organism: null, - name: "60S ribosomal protein L23", - details: "", - altNames: "60S ribosomal protein L17,Large ribosomal subunit protein uL14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P83731", - organism: null, - name: "60S ribosomal protein L24", - details: "", - altNames: "60S ribosomal protein L30,Large ribosomal subunit protein eL24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62750", - organism: null, - name: "60S ribosomal protein L23a", - details: "", - altNames: "Large ribosomal subunit protein uL23", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61254", - organism: null, - name: "60S ribosomal protein L26", - details: "", - altNames: "Large ribosomal subunit protein uL24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61353", - organism: null, - name: "60S ribosomal protein L27", - details: "", - altNames: "Large ribosomal subunit protein eL27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46776", - organism: null, - name: "60S ribosomal protein L27a", - details: "", - altNames: "Large ribosomal subunit protein uL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P47914", - organism: null, - name: "60S ribosomal protein L29", - details: "", - altNames: - "Cell surface heparin-binding protein HIP,Large ribosomal subunit protein eL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62888", - organism: null, - name: "60S ribosomal protein L30", - details: "", - altNames: "Large ribosomal subunit protein eL30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62899", - organism: null, - name: "60S ribosomal protein L31", - details: "", - altNames: "Large ribosomal subunit protein eL31", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62910", - organism: null, - name: "60S ribosomal protein L32", - details: "", - altNames: "Large ribosomal subunit protein eL32", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18077", - organism: null, - name: "60S ribosomal protein L35a", - details: "", - altNames: - "Cell growth-inhibiting gene 33 protein,Large ribosomal subunit protein eL33", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P49207", - organism: null, - name: "60S ribosomal protein L34", - details: "", - altNames: "Large ribosomal subunit protein eL34", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42766", - organism: null, - name: "60S ribosomal protein L35", - details: "", - altNames: "Large ribosomal subunit protein uL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y3U8", - organism: null, - name: "60S ribosomal protein L36", - details: "", - altNames: "Large ribosomal subunit protein eL36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61927", - organism: null, - name: "60S ribosomal protein L37", - details: "", - altNames: "G1.16,Large ribosomal subunit protein eL37", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63173", - organism: null, - name: "60S ribosomal protein L38", - details: "", - altNames: "Large ribosomal subunit protein eL38", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62891", - organism: null, - name: "60S ribosomal protein L39", - details: "", - altNames: "Large ribosomal subunit protein eL39", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62987", - organism: null, - name: "Ubiquitin-60S ribosomal protein L40", - details: "", - altNames: "CEP52,Ubiquitin A-52 residue ribosomal protein fusion product 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62945", - organism: null, - name: "60S ribosomal protein L41", - details: "", - altNames: "HG12,Large ribosomal subunit protein eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P83881", - organism: null, - name: "60S ribosomal protein L36a", - details: "", - altNames: - "60S ribosomal protein L44,Cell growth-inhibiting gene 15 protein,Cell migration-inducing gene 6 protein,Large ribosomal subunit protein eL42", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61513", - organism: null, - name: "60S ribosomal protein L37a", - details: "", - altNames: "Large ribosomal subunit protein eL43", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46779", - organism: null, - name: "60S ribosomal protein L28", - details: "", - altNames: "Large ribosomal subunit protein eL28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05388", - organism: null, - name: "60S acidic ribosomal protein P0", - details: "", - altNames: "60S ribosomal protein L10E,Large ribosomal subunit protein uL10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P30050", - organism: null, - name: "60S ribosomal protein L12", - details: "", - altNames: "Large ribosomal subunit protein uL11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62906", - organism: null, - name: "60S ribosomal protein L10a", - details: "", - altNames: - "CSA-19,Large ribosomal subunit protein uL1,Neural precursor cell expressed developmentally down-regulated protein 6,NEDD-6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "18S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46782", - organism: null, - name: "40S ribosomal protein S5", - details: "", - altNames: "Small ribosomal subunit protein uS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46783", - organism: null, - name: "40S ribosomal protein S10", - details: "", - altNames: "Small ribosomal subunit protein eS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62841", - organism: null, - name: "40S ribosomal protein S15", - details: "", - altNames: "RIG protein,Small ribosomal subunit protein uS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62249", - organism: null, - name: "40S ribosomal protein S16", - details: "", - altNames: "Small ribosomal subunit protein uS9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08708", - organism: null, - name: "40S ribosomal protein S17", - details: "", - altNames: "Small ribosomal subunit protein eS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39019", - organism: null, - name: "40S ribosomal protein S19", - details: "", - altNames: "Small ribosomal subunit protein eS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60866", - organism: null, - name: "40S ribosomal protein S20", - details: "", - altNames: "Small ribosomal subunit protein uS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62857", - organism: null, - name: "40S ribosomal protein S28", - details: "", - altNames: "Small ribosomal subunit protein eS28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62273", - organism: null, - name: "40S ribosomal protein S29", - details: "", - altNames: "Small ribosomal subunit protein uS14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63244", - organism: null, - name: "Receptor of activated protein C kinase 1", - details: "", - altNames: - "Cell proliferation-inducing gene 21 protein,Guanine nucleotide-binding protein subunit beta-2-like 1,Guanine nucleotide-binding protein subunit beta-like protein 12.3,Human lung cancer oncogene 7 protein,HLC-7,Receptor for activated C kinase,Small ribosomal subunit protein RACK1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P15880", - organism: null, - name: "40S ribosomal protein S2", - details: "", - altNames: - "40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62979", - organism: null, - name: "Ubiquitin-40S ribosomal protein S27a", - details: "", - altNames: "Ubiquitin carboxyl extension protein 80", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9UQ80", - organism: null, - name: "Proliferation-associated protein 2G4", - details: "", - altNames: - "Cell cycle protein p38-2G4 homolog,hG4-1,ErbB3-binding protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "tRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q96CT7", - organism: null, - name: "Coiled-coil domain-containing protein 124", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "Non-structural protein 1", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,Non-structural protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61221", - organism: null, - name: "ATP-binding cassette sub-family E member 1", - details: "", - altNames: - "2'-5'-oligoadenylate-binding protein,HuHP68,RNase L inhibitor,Ribonuclease 4 inhibitor,RNS4I", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62497", - organism: "9986", - name: "Eukaryotic peptide chain release factor subunit 1", - details: "Sequence derived from GeneBank entry NP_001076236.1", - altNames: "Eukaryotic release factor 1,eRF1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "PTTXNOSMDBWCQD-UHFFFAOYSA-J", - "XTWYTFMLZFPYCI-KQYNXXCUSA-N", - ], - dbauthors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Denk, T.", - "Kratzat, H.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Berninghausen, O.", - "Becker, T.", - "Beckmann, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "32680882", - title: - "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", - journal: "Science 369: 1249-1255 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abc8665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32680882", - pubDate: "2020", - abstract: "", - authors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Koepke, L.", - "Denk, T.", - "Hirschenberger, M.", - "Kratzat, H.", - "Hayn, M.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Straub, J.H.", - "Sturzel, C.M.", - "Frohlich, T.", - "Berninghausen, O.", - "Becker, T.", - "Kirchhoff, F.", - "Sparrer, K.M.J.", - "Beckmann, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zme_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zme", - }, - }, - { - title: "SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex", - emdb: { - dbId: "EMD-11292", - emMethod: "SINGLE PARTICLE", - resolution: "2.6", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11292/400_11292.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11292", - }, - pdb: { - dbId: "6ZMI", - method: "ELECTRON MICROSCOPY", - keywords: - "Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "28S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5.8S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62917", - organism: null, - name: "60S ribosomal protein L8", - details: "", - altNames: "Large ribosomal subunit protein uL2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39023", - organism: null, - name: "60S ribosomal protein L3", - details: "", - altNames: - "HIV-1 TAR RNA-binding protein B,TARBP-B,Large ribosomal subunit protein uL3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P36578", - organism: null, - name: "60S ribosomal protein L4", - details: "", - altNames: "60S ribosomal protein L1,Large ribosomal subunit protein uL4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46777", - organism: null, - name: "60S ribosomal protein L5", - details: "", - altNames: "Large ribosomal subunit protein uL18", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02878", - organism: null, - name: "60S ribosomal protein L6", - details: "", - altNames: - "Large ribosomal subunit protein eL6,Neoplasm-related protein C140,Tax-responsive enhancer element-binding protein 107,TaxREB107", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18124", - organism: null, - name: "60S ribosomal protein L7", - details: "", - altNames: "Large ribosomal subunit protein uL30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62424", - organism: null, - name: "60S ribosomal protein L7a", - details: "", - altNames: - "Large ribosomal subunit protein eL8,PLA-X polypeptide,Surfeit locus protein 3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P32969", - organism: null, - name: "60S ribosomal protein L9", - details: "", - altNames: "Large ribosomal subunit protein uL6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q96L21", - organism: null, - name: "60S ribosomal protein L10-like", - details: "", - altNames: "Large ribosomal subunit protein uL16-like", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62913", - organism: null, - name: "60S ribosomal protein L11", - details: "", - altNames: - "CLL-associated antigen KW-12,Large ribosomal subunit protein uL5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P26373", - organism: null, - name: "60S ribosomal protein L13", - details: "", - altNames: - "Breast basic conserved protein 1,Large ribosomal subunit protein eL13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P50914", - organism: null, - name: "60S ribosomal protein L14", - details: "", - altNames: "CAG-ISL 7,Large ribosomal subunit protein eL14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61313", - organism: null, - name: "60S ribosomal protein L15", - details: "", - altNames: "Large ribosomal subunit protein eL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P40429", - organism: null, - name: "60S ribosomal protein L13a", - details: "", - altNames: - "23 kDa highly basic protein,Large ribosomal subunit protein uL13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18621", - organism: null, - name: "60S ribosomal protein L17", - details: "", - altNames: - "60S ribosomal protein L23,Large ribosomal subunit protein uL22,PD-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q07020", - organism: null, - name: "60S ribosomal protein L18", - details: "", - altNames: "Large ribosomal subunit protein eL18", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P84098", - organism: null, - name: "60S ribosomal protein L19", - details: "", - altNames: "Large ribosomal subunit protein eL19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02543", - organism: null, - name: "60S ribosomal protein L18a", - details: "", - altNames: "Large ribosomal subunit protein eL20", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46778", - organism: null, - name: "60S ribosomal protein L21", - details: "", - altNames: "Large ribosomal subunit protein eL21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P35268", - organism: null, - name: "60S ribosomal protein L22", - details: "", - altNames: - "EBER-associated protein,EAP,Epstein-Barr virus small RNA-associated protein,Heparin-binding protein HBp15,Large ribosomal subunit protein eL22", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62829", - organism: null, - name: "60S ribosomal protein L23", - details: "", - altNames: "60S ribosomal protein L17,Large ribosomal subunit protein uL14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P83731", - organism: null, - name: "60S ribosomal protein L24", - details: "", - altNames: "60S ribosomal protein L30,Large ribosomal subunit protein eL24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62750", - organism: null, - name: "60S ribosomal protein L23a", - details: "", - altNames: "Large ribosomal subunit protein uL23", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61254", - organism: null, - name: "60S ribosomal protein L26", - details: "", - altNames: "Large ribosomal subunit protein uL24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61353", - organism: null, - name: "60S ribosomal protein L27", - details: "", - altNames: "Large ribosomal subunit protein eL27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46776", - organism: null, - name: "60S ribosomal protein L27a", - details: "", - altNames: "Large ribosomal subunit protein uL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P47914", - organism: null, - name: "60S ribosomal protein L29", - details: "", - altNames: - "Cell surface heparin-binding protein HIP,Large ribosomal subunit protein eL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62888", - organism: null, - name: "60S ribosomal protein L30", - details: "", - altNames: "Large ribosomal subunit protein eL30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62899", - organism: null, - name: "60S ribosomal protein L31", - details: "", - altNames: "Large ribosomal subunit protein eL31", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62910", - organism: null, - name: "60S ribosomal protein L32", - details: "", - altNames: "Large ribosomal subunit protein eL32", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18077", - organism: null, - name: "60S ribosomal protein L35a", - details: "", - altNames: - "Cell growth-inhibiting gene 33 protein,Large ribosomal subunit protein eL33", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P49207", - organism: null, - name: "60S ribosomal protein L34", - details: "", - altNames: "Large ribosomal subunit protein eL34", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42766", - organism: null, - name: "60S ribosomal protein L35", - details: "", - altNames: "Large ribosomal subunit protein uL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y3U8", - organism: null, - name: "60S ribosomal protein L36", - details: "", - altNames: "Large ribosomal subunit protein eL36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61927", - organism: null, - name: "60S ribosomal protein L37", - details: "", - altNames: "G1.16,Large ribosomal subunit protein eL37", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63173", - organism: null, - name: "60S ribosomal protein L38", - details: "", - altNames: "Large ribosomal subunit protein eL38", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62891", - organism: null, - name: "60S ribosomal protein L39", - details: "", - altNames: "Large ribosomal subunit protein eL39", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62987", - organism: null, - name: "Ubiquitin-60S ribosomal protein L40", - details: "", - altNames: "CEP52,Ubiquitin A-52 residue ribosomal protein fusion product 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62945", - organism: null, - name: "60S ribosomal protein L41", - details: "", - altNames: "HG12,Large ribosomal subunit protein eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P83881", - organism: null, - name: "60S ribosomal protein L36a", - details: "", - altNames: - "60S ribosomal protein L44,Cell growth-inhibiting gene 15 protein,Cell migration-inducing gene 6 protein,Large ribosomal subunit protein eL42", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61513", - organism: null, - name: "60S ribosomal protein L37a", - details: "", - altNames: "Large ribosomal subunit protein eL43", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46779", - organism: null, - name: "60S ribosomal protein L28", - details: "", - altNames: "Large ribosomal subunit protein eL28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05388", - organism: null, - name: "60S acidic ribosomal protein P0", - details: "", - altNames: "60S ribosomal protein L10E,Large ribosomal subunit protein uL10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P30050", - organism: null, - name: "60S ribosomal protein L12", - details: "", - altNames: "Large ribosomal subunit protein uL11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62906", - organism: null, - name: "60S ribosomal protein L10a", - details: "", - altNames: - "CSA-19,Large ribosomal subunit protein uL1,Neural precursor cell expressed developmentally down-regulated protein 6,NEDD-6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "18S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46782", - organism: null, - name: "40S ribosomal protein S5", - details: "", - altNames: "Small ribosomal subunit protein uS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46783", - organism: null, - name: "40S ribosomal protein S10", - details: "", - altNames: "Small ribosomal subunit protein eS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62841", - organism: null, - name: "40S ribosomal protein S15", - details: "", - altNames: "RIG protein,Small ribosomal subunit protein uS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62249", - organism: null, - name: "40S ribosomal protein S16", - details: "", - altNames: "Small ribosomal subunit protein uS9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08708", - organism: null, - name: "40S ribosomal protein S17", - details: "", - altNames: "Small ribosomal subunit protein eS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39019", - organism: null, - name: "40S ribosomal protein S19", - details: "", - altNames: "Small ribosomal subunit protein eS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60866", - organism: null, - name: "40S ribosomal protein S20", - details: "", - altNames: "Small ribosomal subunit protein uS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62857", - organism: null, - name: "40S ribosomal protein S28", - details: "", - altNames: "Small ribosomal subunit protein eS28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62273", - organism: null, - name: "40S ribosomal protein S29", - details: "", - altNames: "Small ribosomal subunit protein uS14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63244", - organism: null, - name: "Receptor of activated protein C kinase 1", - details: "", - altNames: - "Cell proliferation-inducing gene 21 protein,Guanine nucleotide-binding protein subunit beta-2-like 1,Guanine nucleotide-binding protein subunit beta-like protein 12.3,Human lung cancer oncogene 7 protein,HLC-7,Receptor for activated C kinase,Small ribosomal subunit protein RACK1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P15880", - organism: null, - name: "40S ribosomal protein S2", - details: "", - altNames: - "40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62979", - organism: null, - name: "Ubiquitin-40S ribosomal protein S27a", - details: "", - altNames: "Ubiquitin carboxyl extension protein 80", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9UQ80", - organism: null, - name: "Proliferation-associated protein 2G4", - details: "", - altNames: - "Cell cycle protein p38-2G4 homolog,hG4-1,ErbB3-binding protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "tRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9NX58", - organism: null, - name: "Cell growth-regulating nucleolar protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "Non-structural protein 1", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,Non-structural protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JLVVSXFLKOJNIY-UHFFFAOYSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Denk, T.", - "Kratzat, H.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Berninghausen, O.", - "Becker, T.", - "Beckmann, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "32680882", - title: - "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", - journal: "Science 369: 1249-1255 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abc8665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32680882", - pubDate: "2020", - abstract: "", - authors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Koepke, L.", - "Denk, T.", - "Hirschenberger, M.", - "Kratzat, H.", - "Hayn, M.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Straub, J.H.", - "Sturzel, C.M.", - "Frohlich, T.", - "Berninghausen, O.", - "Becker, T.", - "Kirchhoff, F.", - "Sparrer, K.M.J.", - "Beckmann, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zmi_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zmi", - }, - }, - { - title: "SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex", - emdb: { - dbId: "EMD-11299", - emMethod: "SINGLE PARTICLE", - resolution: "3.1", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11299/400_11299.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11299", - }, - pdb: { - dbId: "6ZMO", - method: "ELECTRON MICROSCOPY", - keywords: - "Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "28S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5.8S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62917", - organism: null, - name: "60S ribosomal protein L8", - details: "", - altNames: "Large ribosomal subunit protein uL2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39023", - organism: null, - name: "60S ribosomal protein L3", - details: "", - altNames: - "HIV-1 TAR RNA-binding protein B,TARBP-B,Large ribosomal subunit protein uL3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P36578", - organism: null, - name: "60S ribosomal protein L4", - details: "", - altNames: "60S ribosomal protein L1,Large ribosomal subunit protein uL4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46777", - organism: null, - name: "60S ribosomal protein L5", - details: "", - altNames: "Large ribosomal subunit protein uL18", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02878", - organism: null, - name: "60S ribosomal protein L6", - details: "", - altNames: - "Large ribosomal subunit protein eL6,Neoplasm-related protein C140,Tax-responsive enhancer element-binding protein 107,TaxREB107", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18124", - organism: null, - name: "60S ribosomal protein L7", - details: "", - altNames: "Large ribosomal subunit protein uL30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62424", - organism: null, - name: "60S ribosomal protein L7a", - details: "", - altNames: - "Large ribosomal subunit protein eL8,PLA-X polypeptide,Surfeit locus protein 3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P32969", - organism: null, - name: "60S ribosomal protein L9", - details: "", - altNames: "Large ribosomal subunit protein uL6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q96L21", - organism: null, - name: "60S ribosomal protein L10-like", - details: "", - altNames: "Large ribosomal subunit protein uL16-like", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62913", - organism: null, - name: "60S ribosomal protein L11", - details: "", - altNames: - "CLL-associated antigen KW-12,Large ribosomal subunit protein uL5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P26373", - organism: null, - name: "60S ribosomal protein L13", - details: "", - altNames: - "Breast basic conserved protein 1,Large ribosomal subunit protein eL13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P50914", - organism: null, - name: "60S ribosomal protein L14", - details: "", - altNames: "CAG-ISL 7,Large ribosomal subunit protein eL14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61313", - organism: null, - name: "60S ribosomal protein L15", - details: "", - altNames: "Large ribosomal subunit protein eL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P40429", - organism: null, - name: "60S ribosomal protein L13a", - details: "", - altNames: - "23 kDa highly basic protein,Large ribosomal subunit protein uL13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18621", - organism: null, - name: "60S ribosomal protein L17", - details: "", - altNames: - "60S ribosomal protein L23,Large ribosomal subunit protein uL22,PD-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q07020", - organism: null, - name: "60S ribosomal protein L18", - details: "", - altNames: "Large ribosomal subunit protein eL18", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P84098", - organism: null, - name: "60S ribosomal protein L19", - details: "", - altNames: "Large ribosomal subunit protein eL19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02543", - organism: null, - name: "60S ribosomal protein L18a", - details: "", - altNames: "Large ribosomal subunit protein eL20", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46778", - organism: null, - name: "60S ribosomal protein L21", - details: "", - altNames: "Large ribosomal subunit protein eL21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P35268", - organism: null, - name: "60S ribosomal protein L22", - details: "", - altNames: - "EBER-associated protein,EAP,Epstein-Barr virus small RNA-associated protein,Heparin-binding protein HBp15,Large ribosomal subunit protein eL22", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62829", - organism: null, - name: "60S ribosomal protein L23", - details: "", - altNames: "60S ribosomal protein L17,Large ribosomal subunit protein uL14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P83731", - organism: null, - name: "60S ribosomal protein L24", - details: "", - altNames: "60S ribosomal protein L30,Large ribosomal subunit protein eL24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62750", - organism: null, - name: "60S ribosomal protein L23a", - details: "", - altNames: "Large ribosomal subunit protein uL23", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61254", - organism: null, - name: "60S ribosomal protein L26", - details: "", - altNames: "Large ribosomal subunit protein uL24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61353", - organism: null, - name: "60S ribosomal protein L27", - details: "", - altNames: "Large ribosomal subunit protein eL27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46776", - organism: null, - name: "60S ribosomal protein L27a", - details: "", - altNames: "Large ribosomal subunit protein uL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P47914", - organism: null, - name: "60S ribosomal protein L29", - details: "", - altNames: - "Cell surface heparin-binding protein HIP,Large ribosomal subunit protein eL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62888", - organism: null, - name: "60S ribosomal protein L30", - details: "", - altNames: "Large ribosomal subunit protein eL30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62899", - organism: null, - name: "60S ribosomal protein L31", - details: "", - altNames: "Large ribosomal subunit protein eL31", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62910", - organism: null, - name: "60S ribosomal protein L32", - details: "", - altNames: "Large ribosomal subunit protein eL32", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P18077", - organism: null, - name: "60S ribosomal protein L35a", - details: "", - altNames: - "Cell growth-inhibiting gene 33 protein,Large ribosomal subunit protein eL33", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P49207", - organism: null, - name: "60S ribosomal protein L34", - details: "", - altNames: "Large ribosomal subunit protein eL34", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42766", - organism: null, - name: "60S ribosomal protein L35", - details: "", - altNames: "Large ribosomal subunit protein uL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y3U8", - organism: null, - name: "60S ribosomal protein L36", - details: "", - altNames: "Large ribosomal subunit protein eL36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61927", - organism: null, - name: "60S ribosomal protein L37", - details: "", - altNames: "G1.16,Large ribosomal subunit protein eL37", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63173", - organism: null, - name: "60S ribosomal protein L38", - details: "", - altNames: "Large ribosomal subunit protein eL38", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62891", - organism: null, - name: "60S ribosomal protein L39", - details: "", - altNames: "Large ribosomal subunit protein eL39", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62987", - organism: null, - name: "Ubiquitin-60S ribosomal protein L40", - details: "", - altNames: "CEP52,Ubiquitin A-52 residue ribosomal protein fusion product 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62945", - organism: null, - name: "60S ribosomal protein L41", - details: "", - altNames: "HG12,Large ribosomal subunit protein eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P83881", - organism: null, - name: "60S ribosomal protein L36a", - details: "", - altNames: - "60S ribosomal protein L44,Cell growth-inhibiting gene 15 protein,Cell migration-inducing gene 6 protein,Large ribosomal subunit protein eL42", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61513", - organism: null, - name: "60S ribosomal protein L37a", - details: "", - altNames: "Large ribosomal subunit protein eL43", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46779", - organism: null, - name: "60S ribosomal protein L28", - details: "", - altNames: "Large ribosomal subunit protein eL28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05388", - organism: null, - name: "60S acidic ribosomal protein P0", - details: "", - altNames: "60S ribosomal protein L10E,Large ribosomal subunit protein uL10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P30050", - organism: null, - name: "60S ribosomal protein L12", - details: "", - altNames: "Large ribosomal subunit protein uL11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62906", - organism: null, - name: "60S ribosomal protein L10a", - details: "", - altNames: - "CSA-19,Large ribosomal subunit protein uL1,Neural precursor cell expressed developmentally down-regulated protein 6,NEDD-6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "18S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46782", - organism: null, - name: "40S ribosomal protein S5", - details: "", - altNames: "Small ribosomal subunit protein uS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46783", - organism: null, - name: "40S ribosomal protein S10", - details: "", - altNames: "Small ribosomal subunit protein eS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62841", - organism: null, - name: "40S ribosomal protein S15", - details: "", - altNames: "RIG protein,Small ribosomal subunit protein uS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62249", - organism: null, - name: "40S ribosomal protein S16", - details: "", - altNames: "Small ribosomal subunit protein uS9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08708", - organism: null, - name: "40S ribosomal protein S17", - details: "", - altNames: "Small ribosomal subunit protein eS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39019", - organism: null, - name: "40S ribosomal protein S19", - details: "", - altNames: "Small ribosomal subunit protein eS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60866", - organism: null, - name: "40S ribosomal protein S20", - details: "", - altNames: "Small ribosomal subunit protein uS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62857", - organism: null, - name: "40S ribosomal protein S28", - details: "", - altNames: "Small ribosomal subunit protein eS28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62273", - organism: null, - name: "40S ribosomal protein S29", - details: "", - altNames: "Small ribosomal subunit protein uS14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63244", - organism: null, - name: "Receptor of activated protein C kinase 1", - details: "", - altNames: - "Cell proliferation-inducing gene 21 protein,Guanine nucleotide-binding protein subunit beta-2-like 1,Guanine nucleotide-binding protein subunit beta-like protein 12.3,Human lung cancer oncogene 7 protein,HLC-7,Receptor for activated C kinase,Small ribosomal subunit protein RACK1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P15880", - organism: null, - name: "40S ribosomal protein S2", - details: "", - altNames: - "40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62979", - organism: null, - name: "Ubiquitin-40S ribosomal protein S27a", - details: "", - altNames: "Ubiquitin carboxyl extension protein 80", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9UQ80", - organism: null, - name: "Proliferation-associated protein 2G4", - details: "", - altNames: - "Cell cycle protein p38-2G4 homolog,hG4-1,ErbB3-binding protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "tRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P68104", - organism: null, - name: "Elongation factor 1-alpha 1", - details: "", - altNames: - "EF-1-alpha-1,Elongation factor Tu,EF-Tu,Eukaryotic elongation factor 1 A-1,eEF1A-1,Leukocyte receptor cluster member 7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9NX58", - organism: null, - name: "Cell growth-regulating nucleolar protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "Non-structural protein 1", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,Non-structural protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JLVVSXFLKOJNIY-UHFFFAOYSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Denk, T.", - "Kratzat, H.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Berninghausen, O.", - "Becker, T.", - "Beckmann, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "32680882", - title: - "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", - journal: "Science 369: 1249-1255 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abc8665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32680882", - pubDate: "2020", - abstract: "", - authors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Koepke, L.", - "Denk, T.", - "Hirschenberger, M.", - "Kratzat, H.", - "Hayn, M.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Straub, J.H.", - "Sturzel, C.M.", - "Frohlich, T.", - "Berninghausen, O.", - "Becker, T.", - "Kirchhoff, F.", - "Sparrer, K.M.J.", - "Beckmann, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zmo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zmo", - }, - }, - { - title: "SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex", - emdb: { - dbId: "EMD-11301", - emMethod: "SINGLE PARTICLE", - resolution: "3.0", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11301/400_11301.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11301", - }, - pdb: { - dbId: "6ZMT", - method: "ELECTRON MICROSCOPY", - keywords: - "Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P15880", - organism: null, - name: "40S ribosomal protein S2", - details: "", - altNames: - "40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46782", - organism: null, - name: "40S ribosomal protein S5", - details: "", - altNames: "Small ribosomal subunit protein uS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46783", - organism: null, - name: "40S ribosomal protein S10", - details: "", - altNames: "Small ribosomal subunit protein eS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62841", - organism: null, - name: "40S ribosomal protein S15", - details: "", - altNames: "RIG protein,Small ribosomal subunit protein uS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62249", - organism: null, - name: "40S ribosomal protein S16", - details: "", - altNames: "Small ribosomal subunit protein uS9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08708", - organism: null, - name: "40S ribosomal protein S17", - details: "", - altNames: "Small ribosomal subunit protein eS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - 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{ - pmID: "32680882", - title: - "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", - journal: "Science 369: 1249-1255 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abc8665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32680882", - pubDate: "2020", - abstract: "", - authors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Koepke, L.", - "Denk, T.", - "Hirschenberger, M.", - "Kratzat, H.", - "Hayn, M.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Straub, J.H.", - "Sturzel, C.M.", - "Frohlich, T.", - "Berninghausen, O.", - "Becker, T.", - "Kirchhoff, F.", - "Sparrer, K.M.J.", - "Beckmann, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zmt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zmt", - }, - }, - { - title: "SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2", - emdb: { - dbId: "EMD-11310", - emMethod: "SINGLE PARTICLE", - resolution: "3.2", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11310/400_11310.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11310", - }, - pdb: { - dbId: "6ZN5", - method: "ELECTRON MICROSCOPY", - keywords: - "Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11310", - pdbId: "6ZN5", - source: "CERES", - method: "PHENIX", - filename: "6zn5_11310_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zn5_11310/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - 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{ - pmID: "32680882", - title: - "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", - journal: "Science 369: 1249-1255 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abc8665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32680882", - pubDate: "2020", - abstract: "", - authors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Koepke, L.", - "Denk, T.", - "Hirschenberger, M.", - "Kratzat, H.", - "Hayn, M.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Straub, J.H.", - "Sturzel, C.M.", - "Frohlich, T.", - "Berninghausen, O.", - "Becker, T.", - "Kirchhoff, F.", - "Sparrer, K.M.J.", - "Beckmann, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zn5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zn5", - }, - }, - { - title: "SARS-CoV-2-Nsp1-40S complex, composite map", - emdb: { - dbId: "EMD-11320", - emMethod: "SINGLE PARTICLE", - resolution: "2.8", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11320/400_11320.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11320", - }, - pdb: { - dbId: "6ZOJ", - method: "ELECTRON MICROSCOPY", - keywords: "inhibitor, mRNA channel, 40S ribosomal subunit, TRANSLATION", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "18S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - 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details: "", - altNames: "Small ribosomal subunit protein eS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60866", - organism: null, - name: "40S ribosomal protein S20", - details: "", - altNames: "Small ribosomal subunit protein uS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62857", - organism: null, - name: "40S ribosomal protein S28", - details: "", - altNames: "Small ribosomal subunit protein eS28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62273", - organism: null, - name: "40S ribosomal protein S29", - details: "", - altNames: "Small ribosomal subunit protein uS14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q5RKT7", - organism: null, - name: "Ribosomal protein S27a", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63244", - organism: null, - name: "Receptor of activated protein C kinase 1", - details: "", - altNames: - "Cell proliferation-inducing gene 21 protein,Guanine nucleotide-binding protein subunit beta-2-like 1,Guanine nucleotide-binding protein subunit beta-like protein 12.3,Human lung cancer oncogene 7 protein,HLC-7,Receptor for activated C kinase,Small ribosomal subunit protein RACK1", - 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(0000-0003-3832-7730)", - "Karousis, E.D. (0000-0002-0390-0181)", - "Jomaa, A. (0000-0002-4786-934X)", - "Scaiola, A. (0000-0003-3233-3910)", - "Echeverria, B. (0000-0002-9096-7682)", - "Gurzeler, L.-A. (0000-0002-1463-2207)", - "Thiel, V.", - "Muehlemann, O.", - "Ban, N.", - "Leibundgut, M.L.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "36-meric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32908316", - title: - "SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.", - journal: "Nat.Struct.Mol.Biol. 27: 959-966 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0511-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32908316", - pubDate: "2020", - abstract: "", - authors: [ - "Schubert, K. (0000-0003-3832-7730)", - "Karousis, E.D.", - "Jomaa, A. (0000-0002-4786-934X)", - "Scaiola, A. (0000-0003-3233-3910)", - "Echeverria, B.", - "Gurzeler, L.A. (0000-0002-1463-2207)", - "Leibundgut, M.", - "Thiel, V. (0000-0002-5783-0887)", - "Muhlemann, O. (0000-0003-0657-1368)", - "Ban, N. (0000-0002-9527-210X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zoj_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zoj", - }, - }, - { - title: "SARS-CoV-2-Nsp1-40S complex, focused on body", - emdb: { - dbId: "EMD-11321", - emMethod: "SINGLE PARTICLE", - resolution: "2.8", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11321/400_11321.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11321", - }, - pdb: { - dbId: "6ZOK", - method: "ELECTRON MICROSCOPY", - keywords: "inhibitor, mRNA channel, 40S ribosomal subunit, TRANSLATION", - refModels: [ - { - emdbId: "EMD-11321", - pdbId: "6ZOK", - source: "CERES", - method: "PHENIX", - filename: "6zok_11321_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zok_11321/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "18S ribosomal RNA", - details: "", - 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isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08708", - organism: null, - name: "40S ribosomal protein S17", - details: "", - altNames: "Small ribosomal subunit protein eS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "Non-structural protein 1", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,Non-structural protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62945", - organism: null, - name: "60S ribosomal protein L41", - details: "", - altNames: "HG12,Large ribosomal subunit protein eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["JLVVSXFLKOJNIY-UHFFFAOYSA-N", "PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Schubert, K. (0000-0003-3832-7730)", - "Karousis, E.D. (0000-0002-0390-0181)", - "Jomaa, A. (0000-0002-4786-934X)", - "Scaiola, A. (0000-0003-3233-3910)", - "Echeverria, B. (0000-0002-9096-7682)", - "Gurzeler, L.-A. (0000-0002-1463-2207)", - "Leibundgut, M.", - "Thiel, V.", - "Muehlemann, O.", - "Ban, N.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "22-meric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32908316", - title: - "SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.", - journal: "Nat.Struct.Mol.Biol. 27: 959-966 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0511-8", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32908316", - pubDate: "2020", - abstract: "", - authors: [ - "Schubert, K. (0000-0003-3832-7730)", - "Karousis, E.D.", - "Jomaa, A. (0000-0002-4786-934X)", - "Scaiola, A. (0000-0003-3233-3910)", - "Echeverria, B.", - "Gurzeler, L.A. (0000-0002-1463-2207)", - "Leibundgut, M.", - "Thiel, V. (0000-0002-5783-0887)", - "Muhlemann, O. (0000-0003-0657-1368)", - "Ban, N. (0000-0002-9527-210X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zok_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zok", - }, - }, - { - title: "SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1", - emdb: { - dbId: "EMD-11325", - emMethod: "SINGLE PARTICLE", - resolution: "3.0", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11325/400_11325.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11325", - }, - pdb: { - dbId: "6ZON", - method: "ELECTRON MICROSCOPY", - keywords: - "Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11325", - pdbId: "6ZON", - source: "CERES", - method: "PHENIX", - filename: "6zon_11325_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zon_11325/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P15880", - organism: null, - name: "40S ribosomal protein S2", - details: "", - altNames: - "40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62945", - organism: null, - name: "60S ribosomal protein L41", - details: "", - altNames: "HG12,Large ribosomal subunit protein eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "18S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08708", - organism: null, - name: "40S ribosomal protein S17", - details: "", - altNames: "Small ribosomal subunit protein eS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62249", - organism: null, - name: "40S ribosomal protein S16", - details: "", - altNames: "Small ribosomal subunit protein uS9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46782", - organism: null, - name: "40S ribosomal protein S5", - details: "", - altNames: "Small ribosomal subunit protein uS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46783", - organism: null, - name: "40S ribosomal protein S10", - details: "", - altNames: "Small ribosomal subunit protein eS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62841", - organism: null, - name: "40S ribosomal protein S15", - details: "", - altNames: "RIG protein,Small ribosomal subunit protein uS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39019", - organism: null, - name: "40S ribosomal protein S19", - details: "", - altNames: "Small ribosomal subunit protein eS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60866", - organism: null, - name: "40S ribosomal protein S20", - details: "", - altNames: "Small ribosomal subunit protein uS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62857", - organism: null, - name: "40S ribosomal protein S28", - details: "", - altNames: "Small ribosomal subunit protein eS28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62273", - organism: null, - name: "40S ribosomal protein S29", - details: "", - altNames: "Small ribosomal subunit protein uS14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62979", - organism: null, - name: "Ubiquitin-40S ribosomal protein S27a", - details: "", - altNames: "Ubiquitin carboxyl extension protein 80", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63244", - organism: null, - name: "Receptor of activated protein C kinase 1", - details: "", - altNames: - "Cell proliferation-inducing gene 21 protein,Guanine nucleotide-binding protein subunit beta-2-like 1,Guanine nucleotide-binding protein subunit beta-like protein 12.3,Human lung cancer oncogene 7 protein,HLC-7,Receptor for activated C kinase,Small ribosomal subunit protein RACK1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q13347", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit I", - details: "", - altNames: - "eIF3i,Eukaryotic translation initiation factor 3 subunit 2,TGF-beta receptor-interacting protein 1,TRIP-1,eIF-3-beta,eIF3 p36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P55884", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit B", - details: "", - altNames: - "eIF3b,Eukaryotic translation initiation factor 3 subunit 9,Prt1 homolog,hPrt1,eIF-3-eta,eIF3 p110,eIF3 p116", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q14152", - organism: "9606", - name: - "Eukaryotic translation initiation factor 3 subunit A,Eukaryotic translation initiation factor 3 subunit A", - details: "", - altNames: - "eIF3a,Eukaryotic translation initiation factor 3 subunit 10,eIF-3-theta,eIF3 p167,eIF3 p180,eIF3 p185,eIF3a,Eukaryotic translation initiation factor 3 subunit 10,eIF-3-theta,eIF3 p167,eIF3 p180,eIF3 p185", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q99613", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit C", - details: "", - altNames: - "eIF3c,Eukaryotic translation initiation factor 3 subunit 8,eIF3 p110", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60228", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit E", - details: "", - altNames: - "eIF3e,Eukaryotic translation initiation factor 3 subunit 6,Viral integration site protein INT-6 homolog,eIF-3 p48", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "O00303", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit F", - details: "", - altNames: - "eIF3f,Deubiquitinating enzyme eIF3f,Eukaryotic translation initiation factor 3 subunit 5,eIF-3-epsilon,eIF3 p47", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "O15372", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit H", - details: "", - altNames: - "eIF3h,Eukaryotic translation initiation factor 3 subunit 3,eIF-3-gamma,eIF3 p40 subunit", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9UBQ5", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit K", - details: "", - altNames: - "eIF3k,Eukaryotic translation initiation factor 3 subunit 12,Muscle-specific gene M9 protein,PLAC-24,eIF-3 p25,eIF-3 p28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y262", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit L", - details: "", - altNames: - "eIF3l,Eukaryotic translation initiation factor 3 subunit 6-interacting protein,Eukaryotic translation initiation factor 3 subunit E-interacting protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q7L2H7", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit M", - details: "", - altNames: - "eIF3m,Fetal lung protein B5,hFL-B5,PCI domain-containing protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "O15371", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit D", - details: "", - altNames: - "eIF3d,Eukaryotic translation initiation factor 3 subunit 7,eIF-3-zeta,eIF3 p66", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Unknown factor", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "2697049", - name: "Host translation inhibitor Nsp1", - details: "Host translation inhibitor Nsp1", - altNames: "pp1ab,ORF1ab polyprotein,Host translation inhibitor Nsp1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["PTFCDOFLOPIGGS-UHFFFAOYSA-N"], - dbauthors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Denk, T.", - "Kratzat, H.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Berninghausen, O.", - "Becker, T.", - "Beckmann, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli K-12", - assembly: "48-meric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32680882", - title: - "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", - journal: "Science 369: 1249-1255 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abc8665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32680882", - pubDate: "2020", - abstract: "", - authors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Koepke, L.", - "Denk, T.", - "Hirschenberger, M.", - "Kratzat, H.", - "Hayn, M.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Straub, J.H.", - "Sturzel, C.M.", - "Frohlich, T.", - "Berninghausen, O.", - "Becker, T.", - "Kirchhoff, F.", - "Sparrer, K.M.J.", - "Beckmann, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zon_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zon", - }, - }, - { - title: "SARS-CoV-2 spike in prefusion state", - emdb: { - dbId: "EMD-11328", - emMethod: "SINGLE PARTICLE", - resolution: "3", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11328/400_11328.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11328", - }, - pdb: { - dbId: "6ZOW", - method: "ELECTRON MICROSCOPY", - keywords: "Spike, Prefusion, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11328", - pdbId: "6ZOW", - source: "CERES", - method: "PHENIX", - filename: "6zow_11328_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zow_11328/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "WQZGKKKJIJFFOK-QTVWNMPRSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - ], - dbauthors: ["Martinez, M.", "Carazo, J.M.", "Marabini, R."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "tetrameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33063791", - title: - "Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.", - journal: "Iucrj 7: 1059-1069 (2020), 2052-2525", - doi: "https://doi.org/10.1107/S2052252520012725", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33063791", - pubDate: "2020", - abstract: "", - authors: [ - "Melero, R. (0000-0001-9467-9381)", - "Sorzano, C.O.S.", - "Foster, B.", - "Vilas, J.L.", - "Martinez, M. (0000-0002-8435-5540)", - "Marabini, R. (0000-0001-7876-1684)", - "Ramirez-Aportela, E.", - "Sanchez-Garcia, R. (0000-0001-6156-3542)", - "Herreros, D.", - "Del Cano, L.", - "Losana, P.", - "Fonseca-Reyna, Y.C.", - "Conesa, P.", - "Wrapp, D.", - "Chacon, P.", - "McLellan, J.S.", - "Tagare, H.D.", - "Carazo, J.M.", - ], - }, - { - pmID: "32676604", - title: - "Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.", - journal: "Biorxiv (2020), 2692-8205", - doi: "https://doi.org/10.1101/2020.07.08.191072", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32676604", - pubDate: "2020", - abstract: "", - authors: [ - "Melero, R. (0000-0001-9467-9381)", - "Sorzano, C.O.S.", - "Foster, B.", - "Vilas, J.L.", - "Martinez, M. (0000-0002-8435-5540)", - "Marabini, R. (0000-0001-7876-1684)", - "Ramirez-Aportela, E.", - "Sanchez-Garcia, R. (0000-0001-6156-3542)", - "Herreros, D.", - "Del Cano, L.", - "Losana, P.", - "Fonseca-Reyna, Y.C.", - "Conesa, P.", - "Wrapp, D.", - "Chacon, P.", - "McLellan, J.S.", - "Tagare, H.D.", - "Carazo, J.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zow_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zow", - }, - }, - { - title: - "Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x2 disulphide-bond mutant, G413C, V987C, single Arg S1/S2 cleavage site)", - emdb: { - dbId: "EMD-11329", - emMethod: "SINGLE PARTICLE", - resolution: "3.0", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11329/400_11329.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11329", - }, - pdb: { - dbId: "6ZOX", - method: "ELECTRON MICROSCOPY", - keywords: - "coronavirus, SARS-CoV-2, Spike protein, S protein, S antigen, COVID-19, receptor binding, membrane fusion, vaccine design, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11329", - pdbId: "6ZOX", - source: "CERES", - method: "PHENIX", - filename: "6zox_11329_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zox_11329/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Briggs, J.A.G. (0000-0003-3990-6910)", - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K. (0000-0002-3152-2237)", - "Scheres, S.H.W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32737467", - title: "A thermostable, closed SARS-CoV-2 spike protein trimer.", - journal: "Nat.Struct.Mol.Biol. 27: 934-941 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0478-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32737467", - pubDate: "2020", - abstract: "", - authors: [ - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K.", - "Ciazynska, K.A.", - "Hosmillo, M.", - "Carter, A.P.", - "Ebrahimi, S.", - "Ke, Z. (0000-0002-8408-850X)", - "Scheres, S.H.W. (0000-0002-0462-6540)", - "Bergamaschi, L.", - "Grice, G.L.", - "Zhang, Y.", - "Nathan, J.A. (0000-0002-0248-1632)", - "Baker, S.", - "James, L.C.", - "Baxendale, H.E.", - "Goodfellow, I.", - "Doffinger, R. (0000-0002-9841-3617)", - "Briggs, J.A.G. (0000-0003-3990-6910)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zox_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zox", - }, - }, - { - title: - "Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Closed State", - emdb: { - dbId: "EMD-11330", - emMethod: "SINGLE PARTICLE", - resolution: "3.1", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11330/400_11330.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11330", - }, - pdb: { - dbId: "6ZOY", - method: "ELECTRON MICROSCOPY", - keywords: - "coronavirus, SARS-CoV-2, Spike protein, S protein, S antigen, COVID-19, receptor binding, membrane fusion, vaccine design, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11330", - pdbId: "6ZOY", - source: "CERES", - method: "PHENIX", - filename: "6zoy_11330_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zoy_11330/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Briggs, J.A.G. (0000-0003-3990-6910)", - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K. (0000-0002-3152-2237)", - "Scheres, S.H.W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32737467", - title: "A thermostable, closed SARS-CoV-2 spike protein trimer.", - journal: "Nat.Struct.Mol.Biol. 27: 934-941 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0478-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32737467", - pubDate: "2020", - abstract: "", - authors: [ - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K.", - "Ciazynska, K.A.", - "Hosmillo, M.", - "Carter, A.P.", - "Ebrahimi, S.", - "Ke, Z. (0000-0002-8408-850X)", - "Scheres, S.H.W. (0000-0002-0462-6540)", - "Bergamaschi, L.", - "Grice, G.L.", - "Zhang, Y.", - "Nathan, J.A. (0000-0002-0248-1632)", - "Baker, S.", - "James, L.C.", - "Baxendale, H.E.", - "Goodfellow, I.", - "Doffinger, R. (0000-0002-9841-3617)", - "Briggs, J.A.G. (0000-0003-3990-6910)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zoy_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zoy", - }, - }, - { - title: - "Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Locked State", - emdb: { - dbId: "EMD-11331", - emMethod: "SINGLE PARTICLE", - resolution: "3.5", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11331/400_11331.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11331", - }, - pdb: { - dbId: "6ZOZ", - method: "ELECTRON MICROSCOPY", - keywords: - "coronavirus, SARS-CoV-2, Spike protein, S protein, S antigen, COVID-19, receptor binding, membrane fusion, vaccine design, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11331", - pdbId: "6ZOZ", - source: "CERES", - method: "PHENIX", - filename: "6zoz_11331_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zoz_11331/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "RCNSAJSGRJSBKK-NSQVQWHSSA-N"], - dbauthors: [ - "Briggs, J.A.G. (0000-0003-3990-6910)", - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K. (0000-0002-3152-2237)", - "Scheres, S.H.W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32737467", - title: "A thermostable, closed SARS-CoV-2 spike protein trimer.", - journal: "Nat.Struct.Mol.Biol. 27: 934-941 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0478-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32737467", - pubDate: "2020", - abstract: "", - authors: [ - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K.", - "Ciazynska, K.A.", - "Hosmillo, M.", - "Carter, A.P.", - "Ebrahimi, S.", - "Ke, Z. (0000-0002-8408-850X)", - "Scheres, S.H.W. (0000-0002-0462-6540)", - "Bergamaschi, L.", - "Grice, G.L.", - "Zhang, Y.", - "Nathan, J.A. (0000-0002-0248-1632)", - "Baker, S.", - "James, L.C.", - "Baxendale, H.E.", - "Goodfellow, I.", - "Doffinger, R. (0000-0002-9841-3617)", - "Briggs, J.A.G. (0000-0003-3990-6910)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zoz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zoz", - }, - }, - { - title: - "Structure of SARS-CoV-2 Spike Protein Trimer (single Arg S1/S2 cleavage site) in Closed State", - emdb: { - dbId: "EMD-11332", - emMethod: "SINGLE PARTICLE", - resolution: "3.0", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11332/400_11332.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11332", - }, - pdb: { - dbId: "6ZP0", - method: "ELECTRON MICROSCOPY", - keywords: - "coronavirus, SARS-CoV-2, Spike protein, S protein, S antigen, COVID-19, receptor binding, membrane fusion, vaccine design, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11332", - pdbId: "6ZP0", - source: "CERES", - method: "PHENIX", - filename: "6zp0_11332_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zp0_11332/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Briggs, J.A.G. (0000-0003-3990-6910)", - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K. (0000-0002-3152-2237)", - "Scheres, S.H.W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32737467", - title: "A thermostable, closed SARS-CoV-2 spike protein trimer.", - journal: "Nat.Struct.Mol.Biol. 27: 934-941 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0478-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32737467", - pubDate: "2020", - abstract: "", - authors: [ - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K.", - "Ciazynska, K.A.", - "Hosmillo, M.", - "Carter, A.P.", - "Ebrahimi, S.", - "Ke, Z. (0000-0002-8408-850X)", - "Scheres, S.H.W. (0000-0002-0462-6540)", - "Bergamaschi, L.", - "Grice, G.L.", - "Zhang, Y.", - "Nathan, J.A. (0000-0002-0248-1632)", - "Baker, S.", - "James, L.C.", - "Baxendale, H.E.", - "Goodfellow, I.", - "Doffinger, R. (0000-0002-9841-3617)", - "Briggs, J.A.G. (0000-0003-3990-6910)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zp0_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zp0", - }, - }, - { - title: - "Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Closed State", - emdb: { - dbId: "EMD-11333", - emMethod: "SINGLE PARTICLE", - resolution: "3.3", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11333/400_11333.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11333", - }, - pdb: { - dbId: "6ZP1", - method: "ELECTRON MICROSCOPY", - keywords: - "coronavirus, SARS-CoV-2, Spike protein, S protein, S antigen, COVID-19, receptor binding, membrane fusion, vaccine design, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11333", - pdbId: "6ZP1", - source: "CERES", - method: "PHENIX", - filename: "6zp1_11333_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zp1_11333/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Briggs, J.A.G. (0000-0003-3990-6910)", - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K. (0000-0002-3152-2237)", - "Scheres, S.H.W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32737467", - title: "A thermostable, closed SARS-CoV-2 spike protein trimer.", - journal: "Nat.Struct.Mol.Biol. 27: 934-941 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0478-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32737467", - pubDate: "2020", - abstract: "", - authors: [ - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K.", - "Ciazynska, K.A.", - "Hosmillo, M.", - "Carter, A.P.", - "Ebrahimi, S.", - "Ke, Z. (0000-0002-8408-850X)", - "Scheres, S.H.W. (0000-0002-0462-6540)", - "Bergamaschi, L.", - "Grice, G.L.", - "Zhang, Y.", - "Nathan, J.A. (0000-0002-0248-1632)", - "Baker, S.", - "James, L.C.", - "Baxendale, H.E.", - "Goodfellow, I.", - "Doffinger, R. (0000-0002-9841-3617)", - "Briggs, J.A.G. (0000-0003-3990-6910)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zp1_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zp1", - }, - }, - { - title: - "Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Locked State", - emdb: { - dbId: "EMD-11334", - emMethod: "SINGLE PARTICLE", - resolution: "3.1", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11334/400_11334.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11334", - }, - pdb: { - dbId: "6ZP2", - method: "ELECTRON MICROSCOPY", - keywords: - "coronavirus, SARS-CoV-2, Spike protein, S protein, S antigen, COVID-19, receptor binding, membrane fusion, vaccine design, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11334", - pdbId: "6ZP2", - source: "CERES", - method: "PHENIX", - filename: "6zp2_11334_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zp2_11334/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "RCNSAJSGRJSBKK-NSQVQWHSSA-N", - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "OYHQOLUKZRVURQ-HZJYTTRNSA-N", - ], - dbauthors: [ - "Briggs, J.A.G. (0000-0003-3990-6910)", - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K. (0000-0002-3152-2237)", - "Scheres, S.H.W.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "32737467", - title: "A thermostable, closed SARS-CoV-2 spike protein trimer.", - journal: "Nat.Struct.Mol.Biol. 27: 934-941 (2020), 1545-9985", - doi: "https://doi.org/10.1038/s41594-020-0478-5", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32737467", - pubDate: "2020", - abstract: "", - authors: [ - "Xiong, X. (0000-0002-4632-9122)", - "Qu, K.", - "Ciazynska, K.A.", - "Hosmillo, M.", - "Carter, A.P.", - "Ebrahimi, S.", - "Ke, Z. (0000-0002-8408-850X)", - "Scheres, S.H.W. (0000-0002-0462-6540)", - "Bergamaschi, L.", - "Grice, G.L.", - "Zhang, Y.", - "Nathan, J.A. (0000-0002-0248-1632)", - "Baker, S.", - "James, L.C.", - "Baxendale, H.E.", - "Goodfellow, I.", - "Doffinger, R. (0000-0002-9841-3617)", - "Briggs, J.A.G. (0000-0003-3990-6910)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zp2_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zp2", - }, - }, - { - title: "SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2", - emdb: { - dbId: "EMD-11335", - emMethod: "SINGLE PARTICLE", - resolution: "2.9", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11335/400_11335.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11335", - }, - pdb: { - dbId: "6ZP4", - method: "ELECTRON MICROSCOPY", - keywords: - "Translational Inhibition, SARS-CoV-2, Immune Evasion, Human Ribosome, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11335", - pdbId: "6ZP4", - source: "CERES", - method: "PHENIX", - filename: "6zp4_11335_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zp4_11335/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P15880", - organism: null, - name: "40S ribosomal protein S2", - details: "", - altNames: - "40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62945", - organism: null, - name: "60S ribosomal protein L41", - details: "", - altNames: "HG12,Large ribosomal subunit protein eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "18S ribosomal RNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08708", - organism: null, - name: "40S ribosomal protein S17", - details: "", - altNames: "Small ribosomal subunit protein eS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46782", - organism: null, - name: "40S ribosomal protein S5", - details: "", - altNames: "Small ribosomal subunit protein uS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46783", - organism: null, - name: "40S ribosomal protein S10", - details: "", - altNames: "Small ribosomal subunit protein eS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62841", - organism: null, - name: "40S ribosomal protein S15", - details: "", - altNames: "RIG protein,Small ribosomal subunit protein uS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62249", - organism: null, - name: "40S ribosomal protein S16", - details: "", - altNames: "Small ribosomal subunit protein uS9", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P39019", - organism: null, - name: "40S ribosomal protein S19", - details: "", - altNames: "Small ribosomal subunit protein eS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60866", - organism: null, - name: "40S ribosomal protein S20", - details: "", - altNames: "Small ribosomal subunit protein uS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62857", - organism: null, - name: "40S ribosomal protein S28", - details: "", - altNames: "Small ribosomal subunit protein eS28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62273", - organism: null, - name: "40S ribosomal protein S29", - details: "", - altNames: "Small ribosomal subunit protein uS14", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62979", - organism: null, - name: "Ubiquitin-40S ribosomal protein S27a", - details: "", - altNames: "Ubiquitin carboxyl extension protein 80", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63244", - organism: null, - name: "Receptor of activated protein C kinase 1", - details: "", - altNames: - "Cell proliferation-inducing gene 21 protein,Guanine nucleotide-binding protein subunit beta-2-like 1,Guanine nucleotide-binding protein subunit beta-like protein 12.3,Human lung cancer oncogene 7 protein,HLC-7,Receptor for activated C kinase,Small ribosomal subunit protein RACK1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P47813", - organism: null, - name: "Eukaryotic translation initiation factor 1A, X-chromosomal", - details: "", - altNames: - "eIF-1A X isoform,Eukaryotic translation initiation factor 4C,eIF-4C", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q13347", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit I", - details: "", - altNames: - "eIF3i,Eukaryotic translation initiation factor 3 subunit 2,TGF-beta receptor-interacting protein 1,TRIP-1,eIF-3-beta,eIF3 p36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P55884", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit B", - details: "", - altNames: - "eIF3b,Eukaryotic translation initiation factor 3 subunit 9,Prt1 homolog,hPrt1,eIF-3-eta,eIF3 p110,eIF3 p116", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q14152", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit A", - details: "", - altNames: - "eIF3a,Eukaryotic translation initiation factor 3 subunit 10,eIF-3-theta,eIF3 p167,eIF3 p180,eIF3 p185", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q99613", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit C", - details: "", - altNames: - "eIF3c,Eukaryotic translation initiation factor 3 subunit 8,eIF3 p110", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P60228", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit E", - details: "", - altNames: - "eIF3e,Eukaryotic translation initiation factor 3 subunit 6,Viral integration site protein INT-6 homolog,eIF-3 p48", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "O00303", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit F", - details: "", - altNames: - "eIF3f,Deubiquitinating enzyme eIF3f,Eukaryotic translation initiation factor 3 subunit 5,eIF-3-epsilon,eIF3 p47", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "O15372", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit H", - details: "", - altNames: - "eIF3h,Eukaryotic translation initiation factor 3 subunit 3,eIF-3-gamma,eIF3 p40 subunit", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9UBQ5", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit K", - details: "", - altNames: - "eIF3k,Eukaryotic translation initiation factor 3 subunit 12,Muscle-specific gene M9 protein,PLAC-24,eIF-3 p25,eIF-3 p28", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y262", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit L", - details: "", - altNames: - "eIF3l,Eukaryotic translation initiation factor 3 subunit 6-interacting protein,Eukaryotic translation initiation factor 3 subunit E-interacting protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q7L2H7", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit M", - details: "", - altNames: - "eIF3m,Fetal lung protein B5,hFL-B5,PCI domain-containing protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "O15371", - organism: null, - name: "Eukaryotic translation initiation factor 3 subunit D", - details: "", - altNames: - "eIF3d,Eukaryotic translation initiation factor 3 subunit 7,eIF-3-zeta,eIF3 p66", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Unknown factor", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "tRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P20042", - organism: null, - name: "Eukaryotic translation initiation factor 2 subunit 2", - details: "", - altNames: - "Eukaryotic translation initiation factor 2 subunit beta,eIF-2-beta", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05198", - organism: null, - name: "Eukaryotic translation initiation factor 2 subunit 1", - details: "", - altNames: - "Eukaryotic translation initiation factor 2 subunit alpha,eIF-2alpha", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P41091", - organism: null, - name: "Eukaryotic translation initiation factor 2 subunit 3", - details: "", - altNames: - "Eukaryotic translation initiation factor 2 subunit gamma X,eIF-2gX", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P41567", - organism: null, - name: "Eukaryotic translation initiation factor 1", - details: "", - altNames: "eIF1,A121,Protein translation factor SUI1 homolog,Sui1iso1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: null, - name: "Non-structural protein 1", - details: "", - altNames: "pp1ab,ORF1ab polyprotein,Non-structural protein 1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "XKMLYUALXHKNFT-UUOKFMHZSA-J", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Denk, T.", - "Kratzat, H.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Berninghausen, O.", - "Becker, T.", - "Beckmann, R.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "32680882", - title: - "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", - journal: "Science 369: 1249-1255 (2020), 1095-9203", - doi: "https://doi.org/10.1126/science.abc8665", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32680882", - pubDate: "2020", - abstract: "", - authors: [ - "Thoms, M.", - "Buschauer, R.", - "Ameismeier, M.", - "Koepke, L.", - "Denk, T.", - "Hirschenberger, M.", - "Kratzat, H.", - "Hayn, M.", - "Mackens-Kiani, T.", - "Cheng, J.", - "Straub, J.H.", - "Sturzel, C.M.", - "Frohlich, T.", - "Berninghausen, O.", - "Becker, T.", - "Kirchhoff, F.", - "Sparrer, K.M.J.", - "Beckmann, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zp4_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zp4", - }, - }, - { - title: - "SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation)", - emdb: { - dbId: "EMD-11336", - emMethod: "SINGLE PARTICLE", - resolution: "3.1", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11336/400_11336.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11336", - }, - pdb: { - dbId: "6ZP5", - method: "ELECTRON MICROSCOPY", - keywords: "Spike, Prefusion, Flexibility, Closed, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11336", - pdbId: "6ZP5", - source: "CERES", - method: "PHENIX", - filename: "6zp5_11336_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zp5_11336/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "WQZGKKKJIJFFOK-QTVWNMPRSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - ], - dbauthors: ["Martinez, M.", "Carazo, J.M.", "Marabini, R."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - 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(0000-0001-6156-3542)", - "Herreros, D.", - "Del Cano, L.", - "Losana, P.", - "Fonseca-Reyna, Y.C.", - "Conesa, P.", - "Wrapp, D.", - "Chacon, P.", - "McLellan, J.S.", - "Tagare, H.D.", - "Carazo, J.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zp5_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zp5", - }, - }, - { - title: - "SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up open conformation)", - emdb: { - dbId: "EMD-11337", - emMethod: "SINGLE PARTICLE", - resolution: "3.3", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11337/400_11337.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11337", - }, - pdb: { - dbId: "6ZP7", - method: "ELECTRON MICROSCOPY", - keywords: "Spike, Prefusion, Flexibility, Open, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11337", - pdbId: "6ZP7", - source: "CERES", - method: "PHENIX", - filename: "6zp7_11337_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zp7_11337/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "OVRNDRQMDRJTHS-FMDGEEDCSA-N", - "WQZGKKKJIJFFOK-QTVWNMPRSA-N", - "IAZDPXIOMUYVGZ-UHFFFAOYSA-N", - ], - dbauthors: ["Martinez, M.", "Carazo, J.M.", "Marabini, R."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33063791", - title: - "Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.", - journal: "Iucrj 7: 1059-1069 (2020), 2052-2525", - doi: "https://doi.org/10.1107/S2052252520012725", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33063791", - pubDate: "2020", - abstract: "", - authors: [ - "Melero, R. 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(0000-0001-6156-3542)", - "Herreros, D.", - "Del Cano, L.", - "Losana, P.", - "Fonseca-Reyna, Y.C.", - "Conesa, P.", - "Wrapp, D.", - "Chacon, P.", - "McLellan, J.S.", - "Tagare, H.D.", - "Carazo, J.M.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zp7_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zp7", - }, - }, - { - title: - "Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: 3 Closed RBDs", - emdb: { - dbId: "EMD-11497", - emMethod: "SINGLE PARTICLE", - resolution: "3.5", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11497/400_11497.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11497", - }, - pdb: { - dbId: "6ZWV", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-CoV-2, Spike Protein, Virions, Glycoprotein, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11497", - pdbId: "6ZWV", - source: "CERES", - method: "PHENIX", - filename: "6zwv_11497_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zwv_11497/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Xiong, X.", - "Scheres, S.H.W.", - "Qu, K.", - "Ke, Z.", - "Briggs, J.A.G.", - "Nakane, T.", - "Cortese, M.", - "Zila, V.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "32805734", - title: - "Structures and distributions of SARS-CoV-2 spike proteins on intact virions.", - journal: "Nature 588: 498-502 (2020), 1476-4687", - doi: "https://doi.org/10.1038/s41586-020-2665-2", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32805734", - pubDate: "2020", - abstract: "", - authors: [ - "Ke, Z.", - "Oton, J.", - "Qu, K.", - "Cortese, M.", - "Zila, V.", - "McKeane, L.", - "Nakane, T.", - "Zivanov, J.", - "Neufeldt, C.J.", - "Cerikan, B.", - "Lu, J.M.", - "Peukes, J.", - "Xiong, X.", - "Krausslich, H.G.", - "Scheres, S.H.W.", - "Bartenschlager, R.", - "Briggs, J.A.G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6zwv_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6zwv", - }, - }, - { - title: - "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1)", - emdb: { - dbId: "EMD-11526", - emMethod: "SINGLE PARTICLE", - resolution: "2.93", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-11526/400_11526.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-11526", - }, - pdb: { - dbId: "6ZXN", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-CoV-2, spike protein, neutralising antibody, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-11526", - pdbId: "6ZXN", - source: "CERES", - method: "PHENIX", - filename: "6zxn_11526_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6zxn_11526/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "30538", - name: "Nanobody Ty1", - details: - "Nanobody Ty1 that neutralises SARS-CoV-2 by blocking the receptor bindings site on the spike glykoprotein", - altNames: "", - isAntibody: false, - isNanobody: true, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Hallberg, B.M. 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"Dos Santos, M.S.", - "Rosadas, C.", - "Susana, A.", - "Rhys, H.", - "Nans, A.", - "Masino, L.", - "Roustan, C.", - "Christodoulou, E.", - "Ulferts, R.", - "Wrobel, A.G.", - "Short, C.E.", - "Fertleman, M.", - "Sanders, R.W.", - "Heaney, J.", - "Spyer, M.", - "Kjaer, S.", - "Riddell, A.", - "Malim, M.H.", - "Beale, R.", - "MacRae, J.I.", - "Taylor, G.P.", - "Nastouli, E.", - "van Gils, M.J.", - "Rosenthal, P.B.", - "Pizzato, M.", - "McClure, M.O.", - "Tedder, R.S.", - "Kassiotis, G.", - "McCoy, L.E.", - "Doores, K.J.", - "Cherepanov, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nt9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nt9", - }, - }, - { - title: - "Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect)", - emdb: { - dbId: "EMD-12586", - emMethod: "SINGLE PARTICLE", - resolution: "3.5", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-12586/400_12586.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-12586", - }, - pdb: { - dbId: "7NTA", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-CoV-2, spike, biliverdin, COVID19, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-12586", - pdbId: "7NTA", - source: "CERES", - method: "PHENIX", - filename: "7nta_12586_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7nta_12586/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RCNSAJSGRJSBKK-NSQVQWHSSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Rosa, A.", "Pye, V.E.", "Cherepanov, P.", "Nans, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33888467", - title: - "SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abg7607", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33888467", - pubDate: "2021", - abstract: "", - authors: [ - "Rosa, A.", - "Pye, V.E.", - "Graham, C.", - "Muir, L.", - "Seow, J.", - "Ng, K.W.", - "Cook, N.J.", - "Rees-Spear, C.", - "Parker, E.", - "Dos Santos, M.S.", - "Rosadas, C.", - "Susana, A.", - "Rhys, H.", - "Nans, A.", - "Masino, L.", - "Roustan, C.", - "Christodoulou, E.", - "Ulferts, R.", - "Wrobel, A.G.", - "Short, C.E.", - "Fertleman, M.", - "Sanders, R.W.", - "Heaney, J.", - "Spyer, M.", - "Kjaer, S.", - "Riddell, A.", - "Malim, M.H.", - "Beale, R.", - "MacRae, J.I.", - "Taylor, G.P.", - "Nastouli, E.", - "van Gils, M.J.", - "Rosenthal, P.B.", - "Pizzato, M.", - "McClure, M.O.", - "Tedder, R.S.", - "Kassiotis, G.", - "McCoy, L.E.", - "Doores, K.J.", - "Cherepanov, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7nta_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7nta", - }, - }, - { - title: "Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab", - emdb: { - dbId: "EMD-12587", - emMethod: "SINGLE PARTICLE", - resolution: "3.6", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-12587/400_12587.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-12587", - }, - pdb: { - dbId: "7NTC", - method: "ELECTRON MICROSCOPY", - keywords: - "SARS-CoV-2, spike, biliverdin, COVID19, Antibody, Fab, epitope, NTD, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-12587", - pdbId: "7NTC", - source: "CERES", - method: "PHENIX", - filename: "7ntc_12587_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7ntc_12587/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P008_056 Fab Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P008_056 Fab Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["RCNSAJSGRJSBKK-NSQVQWHSSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Rosa, A.", "Pye, V.E.", "Cherepanov, P.", "Nans, A."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "pentameric (author_and_software_defined_assembly, PISA)", - genes: [], - }, - refdoc: [ - { - pmID: "33888467", - title: - "SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity.", - journal: "Sci Adv 7 (2021), 2375-2548", - doi: "https://doi.org/10.1126/sciadv.abg7607", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33888467", - pubDate: "2021", - abstract: "", - authors: [ - "Rosa, A.", - "Pye, V.E.", - "Graham, C.", - "Muir, L.", - "Seow, J.", - "Ng, K.W.", - "Cook, N.J.", - "Rees-Spear, C.", - "Parker, E.", - "Dos Santos, M.S.", - "Rosadas, C.", - "Susana, A.", - "Rhys, H.", - "Nans, A.", - "Masino, L.", - "Roustan, C.", - "Christodoulou, E.", - "Ulferts, R.", - "Wrobel, A.G.", - "Short, C.E.", - "Fertleman, M.", - "Sanders, R.W.", - "Heaney, J.", - "Spyer, M.", - "Kjaer, S.", - "Riddell, A.", - "Malim, M.H.", - "Beale, R.", - "MacRae, J.I.", - "Taylor, G.P.", - "Nastouli, E.", - "van Gils, M.J.", - "Rosenthal, P.B.", - "Pizzato, M.", - "McClure, M.O.", - "Tedder, R.S.", - "Kassiotis, G.", - "McCoy, L.E.", - "Doores, K.J.", - "Cherepanov, P.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7ntc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7ntc", - }, - }, - { - title: - "Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution)", - emdb: { - dbId: "EMD-12756", - emMethod: "SINGLE PARTICLE", - resolution: "2.2", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-12756/400_12756.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-12756", - }, - pdb: { - dbId: "7O7Y", - method: "ELECTRON MICROSCOPY", - keywords: "Frameshift, virus, pseudoknot, RIBOSOME", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "18S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TIB4", - organism: null, - name: "Ribosomal protein S28", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q5RKT7", - organism: null, - name: "Ribosomal protein S27a", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS26", - details: "Sequence from GeneBank entry XP_008254857.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SJB4", - organism: null, - name: "RACK1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U7M4", - organism: null, - name: "uS14", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "mRNA containing SARS-CoV-2 sequence", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "E-site tRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "P-site Phe-tRNA(Phe)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uS5", - details: "Sequence from GeneBank entry GBAX01005410.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS4", - details: "Sequence from GeneBank entry XP_002720153.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TFM5", - organism: null, - name: "Ribosomal protein S5", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "B7NZS8", - organism: null, - name: "Ribosomal protein S9 (Predicted)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TPV3", - organism: null, - name: "eS10", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SP51", - organism: null, - name: "uS15", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T1F0", - organism: null, - name: "40S ribosomal protein uS11", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U0Q2", - organism: null, - name: "40S ribosomal protein uS19", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SGX4", - organism: null, - name: "uS9", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TU13", - organism: null, - name: "40S ribosomal protein eS17", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS19", - details: "Sequence from GeneBank entry DN883431.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SIZ2", - organism: null, - name: "40S ribosomal protein uS10", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS21", - details: "Sequence from UniProt entry DN885342.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TG89", - organism: null, - name: "Ribosomal protein S15a", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "A0A087WNH4", - organism: null, - name: "60s ribosomal protein l41", - details: "", - altNames: "eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "28S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5.8S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uL2", - details: "Sequence from GeneBank entry XP_002723515.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TL06", - organism: null, - name: "Ribosomal protein L3", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P36578", - organism: null, - name: "60S ribosomal protein L4", - details: "", - altNames: "60S ribosomal protein L1,Large ribosomal subunit protein uL4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SYJ6", - organism: null, - name: "Ribosomal_L18_c domain-containing protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02878", - organism: null, - name: "60S ribosomal protein L6", - details: "", - altNames: - "Large ribosomal subunit protein eL6,Neoplasm-related protein C140,Tax-responsive enhancer element-binding protein 107,TaxREB107", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal Protein uL30", - details: "Sequence from GeneBank entry XP_002710681.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL8", - details: "Sequence from GeneBank entry GBCD01000651.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P32969", - organism: null, - name: "60S ribosomal protein L9", - details: "", - altNames: "Large ribosomal subunit protein uL6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "B7NZQ2", - organism: null, - name: "60S ribosomal protein L10", - details: "", - altNames: "Ribosomal protein L10 (Predicted)", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TUB8", - organism: null, - name: "Ribosomal protein L11", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL13", - details: "Sequence from GeneBank entry XP_002710580.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SZ12", - organism: null, - name: "Ribosomal protein L14", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T0C1", - organism: null, - name: "Ribosomal protein L15", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uL13", - details: "Sequence from GeneBank entry XP_002723961.2", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TVT6", - organism: null, - name: "uL22", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal Protein eL18", - details: "Sequence from GeneBank entry XP_008250645.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P84098", - organism: null, - name: "60S ribosomal protein L19", - details: "", - altNames: "Large ribosomal subunit protein eL19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL20", - details: "Sequence from GeneBank entry GBCK01009614.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SHQ2", - organism: null, - name: "eL21", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL22", - details: "Sequence from GeneBank entry CU464830.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T6D1", - organism: null, - name: "Ribosomal protein L23", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SE28", - organism: null, - name: "eL24", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SE76", - organism: null, - name: "uL23", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SQH0", - organism: null, - name: "Ribosomal protein L26", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61353", - organism: null, - name: "60S ribosomal protein L27", - details: "", - altNames: "Large ribosomal subunit protein eL27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46776", - organism: null, - name: "60S ribosomal protein L27a", - details: "", - altNames: "Large ribosomal subunit protein uL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P47914", - organism: null, - name: "60S ribosomal protein L29", - details: "", - altNames: - "Cell surface heparin-binding protein HIP,Large ribosomal subunit protein eL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TDL2", - organism: null, - name: "eL30", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SHG0", - organism: null, - name: "eL31", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U437", - organism: null, - name: "eL32", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SF08", - organism: null, - name: "eL33", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P49207", - organism: null, - name: "60S ribosomal protein L34", - details: "", - altNames: "Large ribosomal subunit protein eL34", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SIT5", - organism: null, - name: "uL29", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y3U8", - organism: null, - name: "60S ribosomal protein L36", - details: "", - altNames: "Large ribosomal subunit protein eL36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "U3KPD5", - organism: null, - name: "Ribosomal protein L37", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U001", - organism: null, - name: "eL38", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TTN1", - organism: null, - name: "eL39", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "60S ribosomal protein L40", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U344", - organism: null, - name: "eL42", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SY53", - organism: null, - name: "eL43", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL28", - details: "Sequence from GeneBank entry GBCM01003096.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05388", - organism: null, - name: "60S acidic ribosomal protein P0", - details: "", - altNames: "60S ribosomal protein L10E,Large ribosomal subunit protein uL10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SMR7", - organism: null, - name: "Ribosomal protein L12", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SKZ8", - organism: null, - name: "Ribosomal protein uL1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ATHGHQPFGPMSJY-UHFFFAOYSA-N", - "PFNFFQXMRSDOHW-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Scaiola, A. (0000-0003-3233-3910)", - "Ban, N. (0000-0002-9527-210X)", - "Bhatt, P.R. (0000-0003-1451-9105)", - "Leibundgut, M.A. (0000-0002-0902-5859)", - "Atkins, J.F. (0000-0001-7933-0165)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Oryctolagus cuniculus", - assembly: "86-meric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34029205", - title: - "Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome.", - journal: "Science 372: 1306-1313 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf3546", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34029205", - pubDate: "2021", - abstract: "", - authors: [ - "Bhatt, P.R.", - "Scaiola, A.", - "Loughran, G.", - "Leibundgut, M.", - "Kratzel, A.", - "Meurs, R.", - "Dreos, R.", - "O'Connor, K.M.", - "McMillan, A.", - "Bode, J.W.", - "Thiel, V.", - "Gatfield, D.", - "Atkins, J.F.", - "Ban, N.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7o7y_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7o7y", - }, - }, - { - title: - "Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)", - emdb: { - dbId: "EMD-12757", - emMethod: "SINGLE PARTICLE", - resolution: "2.4", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-12757/400_12757.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-12757", - }, - pdb: { - dbId: "7O7Z", - method: "ELECTRON MICROSCOPY", - keywords: "Frameshift, virus, pseudoknot, RIBOSOME", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "18S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TIB4", - organism: null, - name: "Ribosomal protein S28", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q5RKT7", - organism: null, - name: "Ribosomal protein S27a", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS26", - details: "Sequence from GeneBank entry XP_008254857.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SJB4", - organism: null, - name: "RACK1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U7M4", - organism: null, - name: "uS14", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "mRNA containing SARS-CoV-2 sequence", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "E-site tRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "P-site Phe-tRNA(Phe)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uS5", - details: "Sequence from GeneBank entry GBAX01005410.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS4", - details: "Sequence from GeneBank entry XP_002720153.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TFM5", - organism: null, - name: "Ribosomal protein S5", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "B7NZS8", - organism: null, - name: "Ribosomal protein S9 (Predicted)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TPV3", - organism: null, - name: "eS10", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SP51", - organism: null, - name: "uS15", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T1F0", - organism: null, - name: "40S ribosomal protein uS11", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U0Q2", - organism: null, - name: "40S ribosomal protein uS19", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SGX4", - organism: null, - name: "uS9", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TU13", - organism: null, - name: "40S ribosomal protein eS17", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS19", - details: "Sequence from GeneBank entry DN883431.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SIZ2", - organism: null, - name: "40S ribosomal protein uS10", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS21", - details: "Sequence from UniProt entry DN885342.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TG89", - organism: null, - name: "Ribosomal protein S15a", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "A0A087WNH4", - organism: null, - name: "60s ribosomal protein l41", - details: "", - altNames: "eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "28S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5S", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5.8S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uL2", - details: "Sequence from GeneBank entry XP_002723515.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TL06", - organism: null, - name: "Ribosomal protein L3", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P36578", - organism: null, - name: "60S ribosomal protein L4", - details: "", - altNames: "60S ribosomal protein L1,Large ribosomal subunit protein uL4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SYJ6", - organism: null, - name: "Ribosomal_L18_c domain-containing protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02878", - organism: null, - name: "60S ribosomal protein L6", - details: "", - altNames: - "Large ribosomal subunit protein eL6,Neoplasm-related protein C140,Tax-responsive enhancer element-binding protein 107,TaxREB107", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal Protein uL30", - details: "Sequence from GeneBank entry XP_002710681.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL8", - details: "Sequence from GeneBank entry GBCD01000651.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P32969", - organism: null, - name: "60S ribosomal protein L9", - details: "", - altNames: "Large ribosomal subunit protein uL6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "B7NZQ2", - organism: null, - name: "60S ribosomal protein L10", - details: "", - altNames: "Ribosomal protein L10 (Predicted)", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TUB8", - organism: null, - name: "Ribosomal protein L11", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL13", - details: "Sequence from GeneBank entry XP_002710580.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SZ12", - organism: null, - name: "Ribosomal protein L14", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T0C1", - organism: null, - name: "Ribosomal protein L15", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uL13", - details: "Sequence from GeneBank entry XP_002723961.2", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TVT6", - organism: null, - name: "uL22", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal Protein eL18", - details: "Sequence from GeneBank entry XP_008250645.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P84098", - organism: null, - name: "60S ribosomal protein L19", - details: "", - altNames: "Large ribosomal subunit protein eL19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL20", - details: "Sequence from GeneBank entry GBCK01009614.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SHQ2", - organism: null, - name: "eL21", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL22", - details: "Sequence from GeneBank entry CU464830.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T6D1", - organism: null, - name: "Ribosomal protein L23", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SE28", - organism: null, - name: "eL24", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SE76", - organism: null, - name: "uL23", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SQH0", - organism: null, - name: "Ribosomal protein L26", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61353", - organism: null, - name: "60S ribosomal protein L27", - details: "", - altNames: "Large ribosomal subunit protein eL27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46776", - organism: null, - name: "60S ribosomal protein L27a", - details: "", - altNames: "Large ribosomal subunit protein uL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P47914", - organism: null, - name: "60S ribosomal protein L29", - details: "", - altNames: - "Cell surface heparin-binding protein HIP,Large ribosomal subunit protein eL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TDL2", - organism: null, - name: "eL30", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SHG0", - organism: null, - name: "eL31", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U437", - organism: null, - name: "eL32", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SF08", - organism: null, - name: "eL33", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P49207", - organism: null, - name: "60S ribosomal protein L34", - details: "", - altNames: "Large ribosomal subunit protein eL34", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SIT5", - organism: null, - name: "uL29", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y3U8", - organism: null, - name: "60S ribosomal protein L36", - details: "", - altNames: "Large ribosomal subunit protein eL36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "U3KPD5", - organism: null, - name: "Ribosomal protein L37", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U001", - organism: null, - name: "eL38", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TTN1", - organism: null, - name: "eL39", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "60S ribosomal protein L40", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U344", - organism: null, - name: "eL42", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SY53", - organism: null, - name: "eL43", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL28", - details: "Sequence from GeneBank entry GBCM01003096.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05388", - organism: null, - name: "60S acidic ribosomal protein P0", - details: "", - altNames: "60S ribosomal protein L10E,Large ribosomal subunit protein uL10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SMR7", - organism: null, - name: "Ribosomal protein L12", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SKZ8", - organism: null, - name: "Ribosomal protein uL1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ATHGHQPFGPMSJY-UHFFFAOYSA-N", - "PFNFFQXMRSDOHW-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - ], - dbauthors: [ - "Scaiola, A. (0000-0003-3233-3910)", - "Ban, N. (0000-0002-9527-210X)", - "Bhatt, P.R. (0000-0003-1451-9105)", - "Leibundgut, M.A. (0000-0002-0902-5859)", - "Atkins, J.F. (0000-0001-7933-0165)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Oryctolagus cuniculus", - assembly: "86-meric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34029205", - title: - "Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome.", - journal: "Science 372: 1306-1313 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf3546", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34029205", - pubDate: "2021", - abstract: "", - authors: [ - "Bhatt, P.R.", - "Scaiola, A.", - "Loughran, G.", - "Leibundgut, M.", - "Kratzel, A.", - "Meurs, R.", - "Dreos, R.", - "O'Connor, K.M.", - "McMillan, A.", - "Bode, J.W.", - "Thiel, V.", - "Gatfield, D.", - "Atkins, J.F.", - "Ban, N.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7o7z_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7o7z", - }, - }, - { - title: - "Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery site", - emdb: { - dbId: "EMD-12758", - emMethod: "SINGLE PARTICLE", - resolution: "2.9", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-12758/400_12758.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-12758", - }, - pdb: { - dbId: "7O80", - method: "ELECTRON MICROSCOPY", - keywords: "Frameshift, virus, pseudoknot, RIBOSOME", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "18S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TIB4", - organism: null, - name: "Ribosomal protein S28", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q5RKT7", - organism: null, - name: "Ribosomal protein S27a", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS26", - details: "Sequence from GeneBank entry XP_008254857.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SJB4", - organism: null, - name: "RACK1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U7M4", - organism: null, - name: "uS14", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "mRNA containing SARS-CoV-2 sequence", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "E-site tRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "P-site Leu-tRNA(Leu)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uS5", - details: "Sequence from GeneBank entry GBAX01005410.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS4", - details: "Sequence from GeneBank entry XP_002720153.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TFM5", - organism: null, - name: "Ribosomal protein S5", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "B7NZS8", - organism: null, - name: "Ribosomal protein S9 (Predicted)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TPV3", - organism: null, - name: "Ribosomal protein eS10", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SP51", - organism: null, - name: "uS15", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T1F0", - organism: null, - name: "40S ribosomal protein uS11", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U0Q2", - organism: null, - name: "40S ribosomal protein uS19", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SGX4", - organism: null, - name: "Ribosomal protein S16", - details: "Sequence from GeneBank entry XP_002711497.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TU13", - organism: null, - name: "40S ribosomal protein eS17", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS19", - details: "Sequence from GeneBank entry DN883431.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SIZ2", - organism: null, - name: "40S ribosomal protein uS10", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS21", - details: "Sequence from UniProt entry DN885342.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TG89", - organism: null, - name: "Ribosomal protein S15a", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "A0A087WNH4", - organism: null, - name: "60s ribosomal protein l41", - details: "", - altNames: "eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "28S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5.8S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uL2", - details: "Sequence from GeneBank entry XP_002723515.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TL06", - organism: null, - name: "Ribosomal protein L3", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P36578", - organism: null, - name: "60S ribosomal protein L4", - details: "", - altNames: "60S ribosomal protein L1,Large ribosomal subunit protein uL4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SYJ6", - organism: null, - name: "Ribosomal_L18_c domain-containing protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02878", - organism: null, - name: "60S ribosomal protein L6", - details: "", - altNames: - "Large ribosomal subunit protein eL6,Neoplasm-related protein C140,Tax-responsive enhancer element-binding protein 107,TaxREB107", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal Protein uL30", - details: "Sequence from GeneBank entry XP_002710681.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL8", - details: "Sequence from GeneBank entry GBCD01000651.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P32969", - organism: null, - name: "60S ribosomal protein L9", - details: "", - altNames: "Large ribosomal subunit protein uL6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "B7NZQ2", - organism: null, - name: "60S ribosomal protein L10", - details: "", - altNames: "Ribosomal protein L10 (Predicted)", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TUB8", - organism: null, - name: "Ribosomal protein L11", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL13", - details: "Sequence from GeneBank entry XP_002710580.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SZ12", - organism: null, - name: "Ribosomal protein L14", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T0C1", - organism: null, - name: "Ribosomal protein L15", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein L13a", - details: "Sequence form GeneBank entry XP_002723961.2", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TVT6", - organism: null, - name: "uL22", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein L18", - details: "Sequence from GeneBank entry XP_008250645.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P84098", - organism: null, - name: "60S ribosomal protein L19", - details: "", - altNames: "Large ribosomal subunit protein eL19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein L18a", - details: "Sequence from GeneBank entry GBCK01009614.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SHQ2", - organism: null, - name: "eL21", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL22", - details: "Sequence from GeneBank entry CU464830.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T6D1", - organism: null, - name: "Ribosomal protein L23", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SE28", - organism: null, - name: "eL24", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SE76", - organism: null, - name: "uL23", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SQH0", - organism: null, - name: "Ribosomal protein L26", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61353", - organism: null, - name: "60S ribosomal protein L27", - details: "", - altNames: "Large ribosomal subunit protein eL27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46776", - organism: null, - name: "60S ribosomal protein L27a", - details: "", - altNames: "Large ribosomal subunit protein uL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P47914", - organism: null, - name: "60S ribosomal protein L29", - details: "", - altNames: - "Cell surface heparin-binding protein HIP,Large ribosomal subunit protein eL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TDL2", - organism: null, - name: "eL30", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SHG0", - organism: null, - name: "eL31", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U437", - organism: null, - name: "eL32", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SF08", - organism: null, - name: "eL33", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P49207", - organism: null, - name: "60S ribosomal protein L34", - details: "", - altNames: "Large ribosomal subunit protein eL34", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SIT5", - organism: null, - name: "uL29", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y3U8", - organism: null, - name: "60S ribosomal protein L36", - details: "", - altNames: "Large ribosomal subunit protein eL36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "U3KPD5", - organism: null, - name: "Ribosomal protein L37", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U001", - organism: null, - name: "eL38", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TTN1", - organism: null, - name: "eL39", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "60S ribosomal protein L40", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U344", - organism: null, - name: "eL42", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SY53", - organism: null, - name: "eL43", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL28", - details: "Sequence from GeneBank entry GBCM01003096.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05388", - organism: null, - name: "60S acidic ribosomal protein P0", - details: "", - altNames: "60S ribosomal protein L10E,Large ribosomal subunit protein uL10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SMR7", - organism: null, - name: "Ribosomal protein L12", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SKZ8", - organism: null, - name: "Ribosomal protein", - details: "Sequence from UniProt entry G1SKZ8", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62497", - organism: "9986", - name: "Eukaryotic peptide chain release factor subunit 1", - details: "Sequence derived from GeneBank entry NP_001076236.1", - altNames: "Eukaryotic release factor 1,eRF1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SG72", - organism: null, - name: "ATP binding cassette subfamily E member 1", - details: - "Sequence from GeneBank entry XP_008265616.1 Connection built as poly-alanine", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "ATHGHQPFGPMSJY-UHFFFAOYSA-N", - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "XKMLYUALXHKNFT-UUOKFMHZSA-J", - "PTTXNOSMDBWCQD-UHFFFAOYSA-J", - ], - dbauthors: [ - "Scaiola, A. (0000-0003-3233-3910)", - "Ban, N. (0000-0002-9527-210X)", - "Bhatt, P.R. (0000-0003-1451-9105)", - "Leibundgut, M.A. (0000-0002-0902-5859)", - "Atkins, J.F. (0000-0001-7933-0165)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Oryctolagus cuniculus", - assembly: "88-meric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34029205", - title: - "Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome.", - journal: "Science 372: 1306-1313 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abf3546", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34029205", - pubDate: "2021", - abstract: "", - authors: [ - "Bhatt, P.R.", - "Scaiola, A.", - "Loughran, G.", - "Leibundgut, M.", - "Kratzel, A.", - "Meurs, R.", - "Dreos, R.", - "O'Connor, K.M.", - "McMillan, A.", - "Bode, J.W.", - "Thiel, V.", - "Gatfield, D.", - "Atkins, J.F.", - "Ban, N.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7o80_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7o80", - }, - }, - { - title: - "Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot", - emdb: { - dbId: "EMD-12759", - emMethod: "SINGLE PARTICLE", - resolution: "3.1", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-12759/400_12759.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-12759", - }, - pdb: { - dbId: "7O81", - method: "ELECTRON MICROSCOPY", - keywords: "Frameshift, virus, pseudoknot, RIBOSOME", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "18S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TIB4", - organism: null, - name: "Ribosomal protein S28", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q5RKT7", - organism: null, - name: "Ribosomal protein S27a", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS26", - details: "Sequence from GeneBank entry XP_008254857.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SJB4", - organism: null, - name: "RACK1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U7M4", - organism: null, - name: "uS14", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "mRNA containing SARS-CoV-2 sequence", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "A-site Met-tRNA(Met)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "P-site tRNA(Pro)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "EDF1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P08865", - organism: null, - name: "40S ribosomal protein SA", - details: "", - altNames: - "37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Colon carcinoma laminin-binding protein,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40,Multidrug resistance-associated protein MGr1-Ag,NEM/1CHD4,Small ribosomal subunit protein uS2", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uS5", - details: "Sequence from GeneBank entry GBAX01005410.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P23396", - organism: null, - name: "40S ribosomal protein S3", - details: "", - altNames: "Small ribosomal subunit protein uS3", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS4", - details: "Sequence from GeneBank entry XP_002720153.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TFM5", - organism: null, - name: "Ribosomal protein S5", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "B7NZS8", - organism: null, - name: "Ribosomal protein S9 (Predicted)", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TPV3", - organism: null, - name: "Ribosomal protein eS10", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SP51", - organism: null, - name: "uS15", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T1F0", - organism: null, - name: "40S ribosomal protein uS11", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U0Q2", - organism: null, - name: "40S ribosomal protein uS19", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SGX4", - organism: null, - name: "uS9", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TU13", - organism: null, - name: "40S ribosomal protein eS17", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62269", - organism: null, - name: "40S ribosomal protein S18", - details: "", - altNames: "Ke-3,Ke3,Small ribosomal subunit protein uS13", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS19", - details: "Sequence from GeneBank entry DN883431.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SIZ2", - organism: null, - name: "40S ribosomal protein uS10", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eS21", - details: "Sequence from UniProt entry DN885342.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TG89", - organism: null, - name: "Ribosomal protein S15a", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62851", - organism: null, - name: "40S ribosomal protein S25", - details: "", - altNames: "Small ribosomal subunit protein eS25", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "A0A087WNH4", - organism: null, - name: "60s ribosomal protein l41", - details: "", - altNames: "eL41", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "28S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "5.8S rRNA", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein uL2", - details: "Sequence from GeneBank entry XP_002723515.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TL06", - organism: null, - name: "Ribosomal protein L3", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P36578", - organism: null, - name: "60S ribosomal protein L4", - details: "", - altNames: "60S ribosomal protein L1,Large ribosomal subunit protein uL4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SYJ6", - organism: null, - name: "Ribosomal_L18_c domain-containing protein", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q02878", - organism: null, - name: "60S ribosomal protein L6", - details: "", - altNames: - "Large ribosomal subunit protein eL6,Neoplasm-related protein C140,Tax-responsive enhancer element-binding protein 107,TaxREB107", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal Protein uL30", - details: "Sequence from GeneBank entry XP_002710681.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL8", - details: "Sequence from GeneBank entry GBCD01000651.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P32969", - organism: null, - name: "60S ribosomal protein L9", - details: "", - altNames: "Large ribosomal subunit protein uL6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "B7NZQ2", - organism: null, - name: "60S ribosomal protein L10", - details: "", - altNames: "Ribosomal protein L10 (Predicted)", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TUB8", - organism: null, - name: "Ribosomal protein L11", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "Replicase polyprotein 1ab", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL13", - details: "Sequence from GeneBank entry XP_002710580.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SZ12", - organism: null, - name: "Ribosomal protein L14", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T0C1", - organism: null, - name: "Ribosomal protein L15", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein L13a", - details: "Sequence form GeneBank entry XP_002723961.2", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TVT6", - organism: null, - name: "uL22", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein L18", - details: "Sequence from GeneBank entry XP_008250645.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P84098", - organism: null, - name: "60S ribosomal protein L19", - details: "", - altNames: "Large ribosomal subunit protein eL19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein L18a", - details: "Sequence from GeneBank entry GBCK01009614.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SHQ2", - organism: null, - name: "eL21", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL22", - details: "Sequence from GeneBank entry CU464830.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1T6D1", - organism: null, - name: "Ribosomal protein L23", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SE28", - organism: null, - name: "eL24", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SE76", - organism: null, - name: "uL23", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SQH0", - organism: null, - name: "Ribosomal protein L26", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61353", - organism: null, - name: "60S ribosomal protein L27", - details: "", - altNames: "Large ribosomal subunit protein eL27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46776", - organism: null, - name: "60S ribosomal protein L27a", - details: "", - altNames: "Large ribosomal subunit protein uL15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P47914", - organism: null, - name: "60S ribosomal protein L29", - details: "", - altNames: - "Cell surface heparin-binding protein HIP,Large ribosomal subunit protein eL29", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TDL2", - organism: null, - name: "eL30", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SHG0", - organism: null, - name: "eL31", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U437", - organism: null, - name: "eL32", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SF08", - organism: null, - name: "eL33", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P49207", - organism: null, - name: "60S ribosomal protein L34", - details: "", - altNames: "Large ribosomal subunit protein eL34", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SIT5", - organism: null, - name: "uL29", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9Y3U8", - organism: null, - name: "60S ribosomal protein L36", - details: "", - altNames: "Large ribosomal subunit protein eL36", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "U3KPD5", - organism: null, - name: "Ribosomal protein L37", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U001", - organism: null, - name: "eL38", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TTN1", - organism: null, - name: "eL39", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "60S ribosomal protein L40", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1U344", - organism: null, - name: "eL42", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SY53", - organism: null, - name: "eL43", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: null, - name: "Ribosomal protein eL28", - details: "Sequence from GeneBank entry GBCM01003096.1", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P05388", - organism: null, - name: "60S acidic ribosomal protein P0", - details: "", - altNames: "60S ribosomal protein L10E,Large ribosomal subunit protein uL10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SMR7", - organism: null, - name: "Ribosomal protein L12", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1SKZ8", - organism: null, - name: "Ribosomal protein uL1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [ - "JLVVSXFLKOJNIY-UHFFFAOYSA-N", - "PTFCDOFLOPIGGS-UHFFFAOYSA-N", - "ATHGHQPFGPMSJY-UHFFFAOYSA-N", - ], - dbauthors: [ - "Scaiola, A. (0000-0003-3233-3910)", - "Ban, N. (0000-0002-9527-210X)", - "Bhatt, P.R. (0000-0003-1451-9105)", - "Leibundgut, M.A. (0000-0002-0902-5859)", - "Atkins, J.F. 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(0000-0001-6744-5061)", - "Weckener, M. (0000-0002-1419-9378)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo", - assembly: "hexameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35858383", - title: - "Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.", - journal: - "Proc.Natl.Acad.Sci.USA 119: e2205412119-e2205412119 (2022), 1091-6490", - doi: "https://doi.org/10.1073/pnas.2205412119", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35858383", - pubDate: "2022", - abstract: "", - authors: [ - "Mikolajek, H. (0000-0003-0776-9974)", - "Weckener, M. (0000-0002-1419-9378)", - "Brotzakis, Z.F.", - "Huo, J.", - "Dalietou, E.V.", - "Le Bas, A.", - "Sormanni, P. (0000-0002-6228-2221)", - "Harrison, P.J.", - "Ward, P.N. (0000-0003-2546-3426)", - "Truong, S. (0000-0001-9624-4461)", - "Moynie, L. (0000-0002-4097-4331)", - "Clare, D.K.", - "Dumoux, M.", - "Dormon, J.", - "Norman, C.", - "Hussain, N. (0000-0002-5170-0061)", - "Vogirala, V. (0000-0002-8534-3736)", - "Owens, R.J. (0000-0002-3705-2993)", - "Vendruscolo, M. (0000-0002-3616-1610)", - "Naismith, J.H. 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(0000-0002-4097-4331)", - "Clare, D.K.", - "Dumoux, M.", - "Dormon, J.", - "Norman, C.", - "Hussain, N. (0000-0002-5170-0061)", - "Vogirala, V. (0000-0002-8534-3736)", - "Owens, R.J. (0000-0002-3705-2993)", - "Vendruscolo, M. (0000-0002-3616-1610)", - "Naismith, J.H. (0000-0001-6744-5061)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7z9r_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7z9r", - }, - }, - { - title: - "CryoEM structure of SARS-CoV-2 spike monomer in complex with neutralising antibody P008_60", - emdb: { - dbId: "EMD-14591", - emMethod: "SINGLE PARTICLE", - resolution: "4.31", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-14591/400_14591.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-14591", - }, - pdb: { - dbId: "7ZBU", - method: "ELECTRON MICROSCOPY", - keywords: - "covid-19, SARS-CoV-2, spike, neutralizing antibody, immunity, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-14591", - pdbId: "7ZBU", - source: "CERES", - method: "PHENIX", - filename: "7zbu_14591_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7zbu_14591/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P008_60 antibody, Heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "P008_60 antibody, Light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "SMLDYXOZVOUSFE-UHFFFAOYSA-N"], - dbauthors: ["Rosa, A.", "Pye, V.E.", "Cronin, N.", "Cherepanov, P."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35981534", - title: - "A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination.", - journal: "Cell Rep 40: 111276-111276 (2022), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2022.111276", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35981534", - pubDate: "2022", - abstract: "", - authors: [ - "Seow, J.", - "Khan, H.", - "Rosa, A.", - "Calvaresi, V.", - "Graham, C.", - "Pickering, S.", - "Pye, V.E.", - "Cronin, N.B.", - "Huettner, I.", - "Malim, M.H.", - "Politis, A.", - "Cherepanov, P.", - "Doores, K.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zbu_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zbu", - }, - }, - { - title: "SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76", - emdb: { - dbId: "EMD-14628", - emMethod: "SINGLE PARTICLE", - resolution: "3.5", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-14628/400_14628.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-14628", - }, - pdb: { - dbId: "7ZCE", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-CoV-2, Spike, single chain fragment, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-14628", - pdbId: "7ZCE", - source: "CERES", - method: "PHENIX", - filename: "7zce_14628_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7zce_14628/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "10665", - name: "Spike glycoprotein,Fibritin", - details: "", - altNames: - "S glycoprotein,E2,Peplomer protein,Collar protein,Whisker antigen control protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P10104", - organism: "9606", - name: "scFv76 single chain fragment", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Chaves-Sanjuan, A. (0000-0003-3287-9024)", - "Bolognesi, M. (0000-0002-9253-5170)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "hexameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36114671", - title: - "Spike mutation resilient scFv76 antibody counteracts SARS-CoV-2 lung damage upon aerosol delivery.", - journal: "Mol.Ther. 31: 362-373 (2022), 1525-0024", - doi: "https://doi.org/10.1016/j.ymthe.2022.09.010", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36114671", - pubDate: "2022", - abstract: "", - authors: [ - "Milazzo, F.M.", - "Chaves-Sanjuan, A.", - "Minenkova, O.", - "Santapaola, D.", - "Anastasi, A.M.", - "Battistuzzi, G.", - "Chiapparino, C.", - "Rosi, A.", - "Merlo Pich, E.", - "Albertoni, C.", - "Marra, E.", - "Luberto, L.", - "Viollet, C.", - "Spagnoli, L.G.", - "Riccio, A.", - "Rossi, A.", - "Santoro, M.G.", - "Ballabio, F.", - "Paissoni, C.", - "Camilloni, C.", - "Bolognesi, M.", - "De Santis, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zce_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zce", - }, - }, - { - title: - "SARS-CoV-2 Spike RBD in complex with the single chain fragment scFv76 (Focused Refinement)", - emdb: { - dbId: "EMD-14629", - emMethod: "SINGLE PARTICLE", - resolution: "4.0", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-14629/400_14629.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-14629", - }, - pdb: { - dbId: "7ZCF", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-CoV-2, Spike, single chain fragment, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-14629", - pdbId: "7ZCF", - source: "CERES", - method: "PHENIX", - filename: "7zcf_14629_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7zcf_14629/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "10665", - name: "Spike glycoprotein,Fibritin", - details: "", - altNames: - "S glycoprotein,E2,Peplomer protein,Collar protein,Whisker antigen control protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P10104", - organism: "9606", - name: "scFv76 single chain fragment", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Chaves-Sanjuan, A. (0000-0003-3287-9024)", - "Bolognesi, M. (0000-0002-9253-5170)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36114671", - title: - "Spike mutation resilient scFv76 antibody counteracts SARS-CoV-2 lung damage upon aerosol delivery.", - journal: "Mol.Ther. 31: 362-373 (2022), 1525-0024", - doi: "https://doi.org/10.1016/j.ymthe.2022.09.010", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36114671", - pubDate: "2022", - abstract: "", - authors: [ - "Milazzo, F.M.", - "Chaves-Sanjuan, A.", - "Minenkova, O.", - "Santapaola, D.", - "Anastasi, A.M.", - "Battistuzzi, G.", - "Chiapparino, C.", - "Rosi, A.", - "Merlo Pich, E.", - "Albertoni, C.", - "Marra, E.", - "Luberto, L.", - "Viollet, C.", - "Spagnoli, L.G.", - "Riccio, A.", - "Rossi, A.", - "Santoro, M.G.", - "Ballabio, F.", - "Paissoni, C.", - "Camilloni, C.", - "Bolognesi, M.", - "De Santis, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zcf_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zcf", - }, - }, - { - title: "Cryo-EM structure of Human ACE2 bound to a high-affinity SARS CoV-2 mutant", - emdb: { - dbId: "EMD-14666", - emMethod: "SINGLE PARTICLE", - resolution: "3.2", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-14666/400_14666.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-14666", - }, - pdb: { - dbId: "7ZDQ", - method: "ELECTRON MICROSCOPY", - keywords: "SARS CoV-2, RBD, ACE2, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-14666", - pdbId: "7ZDQ", - source: "CERES", - method: "PHENIX", - filename: "7zdq_14666_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7zdq_14666/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Processed angiotensin-converting enzyme 2", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Bate, N.", - "Savva, C.G.", - "Moody, P.C.E.", - "Brown, E.A.", - "Schwabe, W.R.", - "Brindle, N.P.J.", - "Ball, J.K.", - "Sale, J.E.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "dimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35849637", - title: - "In vitro evolution predicts emerging SARS-CoV-2 mutations with high affinity for ACE2 and cross-species binding.", - journal: "Plos Pathog. 18: e1010733-e1010733 (2022), 1553-7374", - doi: "https://doi.org/10.1371/journal.ppat.1010733", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35849637", - pubDate: "2022", - abstract: "", - authors: [ - "Bate, N.", - "Savva, C.G.", - "Moody, P.C.E.", - "Brown, E.A.", - "Evans, S.E.", - "Ball, J.K.", - "Schwabe, J.W.R.", - "Sale, J.E.", - "Brindle, N.P.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7zdq_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7zdq", - }, - }, - { - title: "Delta SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue.", - emdb: { - dbId: "EMD-14750", - emMethod: "SINGLE PARTICLE", - resolution: "2.6", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-14750/400_14750.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-14750", - }, - pdb: { - dbId: "7ZJL", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-CoV-2, REGN10987, Fab, cryo-EM, S-protein, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-14750", - pdbId: "7ZJL", - source: "CERES", - method: "PHENIX", - filename: "7zjl_14750_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7zjl_14750/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "REGN10987 Fab homologue (Light chain)", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "REGN10987 Fab homologue (Heavy chain)", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Pichkur, E.B. 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(0000-0001-6768-3406)", - "Kern, D.M.", - "Hoel, C.M.", - "Kotecha, A.", - "Brohawn, S.G.", - ], - }, - { - pmID: "32587976", - title: - "Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs.", - journal: "Biorxiv (2021)", - doi: "https://doi.org/10.1101/2020.06.17.156554", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32587976", - pubDate: "2021", - abstract: "", - authors: [ - "Kern, D.M. (0000-0001-8529-9045)", - "Sorum, B.", - "Mali, S.S.", - "Hoel, C.M. (0000-0002-1344-0780)", - "Sridharan, S.", - "Remis, J.P.", - "Toso, D.B.", - "Kotecha, A. (0000-0002-4480-5439)", - "Bautista, D.M.", - "Brohawn, S.G. (0000-0001-6768-3406)", - "Kern, D.M.", - "Hoel, C.M.", - "Kotecha, A.", - "Brohawn, S.G.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/6xdc_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/6xdc", - }, - }, - { - title: - "Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralizing antibodies", - emdb: { - dbId: "EMD-22137", - emMethod: "SINGLE PARTICLE", - resolution: "3.9", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-22137/400_22137.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-22137", - }, - pdb: { - dbId: "6XDG", - method: "ELECTRON MICROSCOPY", - keywords: - "SARS-CoV-2, therapeutic antibody, antiviral, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: "EMD-22137", - pdbId: "6XDG", - source: "CERES", - method: "PHENIX", - filename: "6xdg_22137_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/6xdg_22137/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "REGN10933 antibody Fab fragment light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "REGN10933 antibody Fab fragment heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "REGN10987 antibody Fab fragment heavy chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "REGN10987 antibody Fab fragment light chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhou, Y.", - "Romero Hernandez, A.", - "Saotome, K.", - "Franklin, M.C. 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(0000-0001-9943-8819)", - "Ho, D.D.", - "Rapp, M. 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}, - { - uniprotAcc: "P46782", - organism: null, - name: "40S ribosomal protein S5", - details: "", - altNames: "Small ribosomal subunit protein uS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46783", - organism: null, - name: "40S ribosomal protein S10", - details: "", - altNames: "Small ribosomal subunit protein eS10", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P25398", - organism: null, - name: "40S ribosomal protein S12", - details: "", - altNames: "Small ribosomal subunit protein eS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62841", - organism: null, - name: "40S ribosomal protein S15", - details: "", - altNames: "RIG protein,Small ribosomal subunit protein uS19", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62249", - organism: null, - name: "40S ribosomal protein S16", - details: "", - altNames: "Small ribosomal subunit protein uS9", - 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isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P61247", - organism: null, - name: "40S ribosomal protein S3a", - details: "", - altNames: - "Small ribosomal subunit protein eS1,v-fos transformation effector protein,Fte-1", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P15880", - organism: null, - name: "40S ribosomal protein S2", - details: "", - altNames: - "40S ribosomal protein S4,Protein LLRep3,Small ribosomal subunit protein uS5", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62701", - organism: null, - name: "40S ribosomal protein S4, X isoform", - details: "", - altNames: - "SCR10,Single copy abundant mRNA protein,Small ribosomal subunit protein eS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62753", - organism: null, - name: "40S ribosomal protein S6", - details: "", - altNames: "Phosphoprotein NP33,Small ribosomal subunit protein eS6", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62081", - organism: null, - name: "40S ribosomal protein S7", - details: "", - altNames: "Small ribosomal subunit protein eS7", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62241", - organism: null, - name: "40S ribosomal protein S8", - details: "", - altNames: "Small ribosomal subunit protein eS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P46781", - organism: null, - name: "40S ribosomal protein S9", - details: "", - altNames: "Small ribosomal subunit protein uS4", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62280", - organism: null, - name: "40S ribosomal protein S11", - details: "", - altNames: "Small ribosomal subunit protein uS17", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62277", - organism: null, - name: "40S ribosomal protein S13", - details: "", - altNames: "Small ribosomal subunit protein uS15", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62263", - organism: null, - name: "40S ribosomal protein S14", - details: "", - altNames: "Small ribosomal subunit protein uS11", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P63220", - organism: null, - name: "40S ribosomal protein S21", - details: "", - altNames: "Small ribosomal subunit protein eS21", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62244", - organism: null, - name: "40S ribosomal protein S15a", - details: "", - altNames: "Small ribosomal subunit protein uS8", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62266", - organism: null, - name: "40S ribosomal protein S23", - details: "", - altNames: "Small ribosomal subunit protein uS12", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62847", - organism: null, - name: "40S ribosomal protein S24", - details: "", - altNames: "Small ribosomal subunit protein eS24", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62854", - organism: null, - name: "40S ribosomal protein S26", - details: "", - altNames: "Small ribosomal subunit protein eS26", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P42677", - organism: null, - name: "40S ribosomal protein S27", - details: "", - altNames: - "Metallopan-stimulin 1,MPS-1,Small ribosomal subunit protein eS27", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62861", - organism: null, - name: "40S ribosomal protein S30", - details: "", - altNames: "Small ribosomal subunit protein eS30", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "P62945", - organism: null, - name: "60S ribosomal protein L41", - details: "", - altNames: "HG12,Large ribosomal subunit protein eL41", - 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(0000-0002-7788-2123)", - "Shi, M.", - "Wu, H. (0000-0002-7281-8579)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli BL21", - assembly: "36-meric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32995777", - title: - "SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.09.18.302901", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32995777", - pubDate: "2020", - abstract: "", - authors: [ - "Shi, M.", - "Wang, L.", - "Fontana, P.", - "Vora, S.", - "Zhang, Y.", - "Fu, T.M.", - "Lieberman, J.", - "Wu, H.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k5i_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k5i", - }, - }, - { - title: - "Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C002 (state 1)", - emdb: { - dbId: "EMD-22729", - emMethod: "SINGLE PARTICLE", - resolution: "3.4", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-22729/400_22729.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-22729", - }, - pdb: { - dbId: "7K8S", - method: "ELECTRON MICROSCOPY", - keywords: - "SARS-CoV-2, spike glycoprotein, COVID-19, monoclonal antibody, neutralizing antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: "EMD-22729", - pdbId: "7K8S", - source: "CERES", - method: "PHENIX", - filename: "7k8s_22729_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7k8s_22729/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "C002 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - 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"Bjorkman, P.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7k8s_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7k8s", - }, - }, - { - title: - "Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C002 (State 2)", - emdb: { - dbId: "EMD-22730", - emMethod: "SINGLE PARTICLE", - resolution: "3.4", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-22730/400_22730.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-22730", - }, - pdb: { - dbId: "7K8T", - method: "ELECTRON MICROSCOPY", - keywords: - "SARS-CoV-2, spike glycoprotein, COVID-19, monoclonal antibody, neutralizing antibody, PROTEIN-IMMUNE SYSTEM complex, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: "EMD-22730", - pdbId: "7K8T", - source: "CERES", - method: "PHENIX", - filename: "7k8t_22730_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7k8t_22730/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "C002 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "C002 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Bjorkman, P.J.", "Barnes, C.O.", "Malyutin, A.G."], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "nonameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "33045718", - title: - "SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.", - journal: "Nature 588: 682-687 (2020), 1476-4687", - 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method: "ELECTRON MICROSCOPY", - keywords: - "SARS-CoV-2, spike glycoprotein, COVID-19, monoclonal antibody, neutralizing antibody, PROTEIN-IMMUNE SYSTEM complex, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: "EMD-22731", - pdbId: "7K8U", - source: "CERES", - method: "PHENIX", - filename: "7k8u_22731_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7k8u_22731/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "C104 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "C104 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - 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(0000-0002-0089-277X)", - ], - }, - { - pmID: "33052347", - title: - "D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.10.11.335299", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33052347", - pubDate: "2020", - abstract: "", - authors: [ - "Gobeil, S.M.", - "Janowska, K.", - "McDowell, S.", - "Mansouri, K.", - "Parks, R.", - "Manne, K.", - "Stalls, V.", - "Kopp, M.F.", - "Henderson, R.", - "Edwards, R.J.", - "Haynes, B.F.", - "Acharya, P.", - "Gobeil, S. (0000-0002-0057-2477)", - "Kopp, M.", - "Henderson, R. (0000-0002-4301-6382)", - "Acharya, P. (0000-0002-0089-277X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kdk_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kdk", - }, - }, - { - title: - "SARS-CoV-2 D614G 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G)", - emdb: { - dbId: "EMD-22826", - emMethod: "SINGLE PARTICLE", - resolution: "2.96", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-22826/400_22826.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-22826", - }, - pdb: { - dbId: "7KDL", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-CoV-2 Spike Protein Trimer, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-22826", - pdbId: "7KDL", - source: "CERES", - method: "PHENIX", - filename: "7kdl_22826_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7kdl_22826/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Acharya, P. 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(0000-0002-0089-277X)", - ], - }, - { - pmID: "33052347", - title: - "D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction.", - journal: "Biorxiv (2020)", - doi: "https://doi.org/10.1101/2020.10.11.335299", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/33052347", - pubDate: "2020", - abstract: "", - authors: [ - "Gobeil, S.M.", - "Janowska, K.", - "McDowell, S.", - "Mansouri, K.", - "Parks, R.", - "Manne, K.", - "Stalls, V.", - "Kopp, M.F.", - "Henderson, R.", - "Edwards, R.J.", - "Haynes, B.F.", - "Acharya, P.", - "Gobeil, S. (0000-0002-0057-2477)", - "Kopp, M.", - "Henderson, R. (0000-0002-4301-6382)", - "Acharya, P. 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(0000-0002-5736-4388)", - "Verba, K.A. (0000-0002-2238-8590)", - "Basler, C.F. (0000-0003-4195-425X)", - "Vignuzzi, M. (0000-0002-4400-771X)", - "Peden, A.A. (0000-0003-0144-7712)", - "Beltrao, P. (0000-0002-2724-7703)", - "Krogan, N.J. (0000-0003-4902-337X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7kdt_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7kdt", - }, - }, - { - title: - "SARS-CoV-2 D614G 3 RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G Sub-class)", - emdb: { - dbId: "EMD-22831", - emMethod: "SINGLE PARTICLE", - resolution: "3.21", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-22831/400_22831.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-22831", - }, - pdb: { - dbId: "7KE4", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-CoV-2 Spike Protein Trimer, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-22831", - pdbId: "7KE4", - source: "CERES", - method: "PHENIX", - filename: "7ke4_22831_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7ke4_22831/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Acharya, P. 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(0000-0002-4301-6382)", - "Gobeil, S.M.-C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m0j_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m0j", - }, - }, - { - title: - "Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of neutralizing antibodies REGN10985 and REGN10989", - emdb: { - dbId: "EMD-23662", - emMethod: "SINGLE PARTICLE", - resolution: "3.3", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-23662/400_23662.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-23662", - }, - pdb: { - dbId: "7M42", - method: "ELECTRON MICROSCOPY", - keywords: - "SARS-Cov-2, RBD, neutralizing antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: "EMD-23662", - pdbId: "7M42", - source: "CERES", - method: "PHENIX", - filename: "7m42_23662_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7m42_23662/07_2023", - details: "", - 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"Carrion Jr., R.", - "Ali, S.", - "Norton, T.", - "Somersan-Karakaya, S.", - "Sivapalasingam, S.", - "Herman, G.A.", - "Weinreich, D.M.", - "Lipsich, L.", - "Stahl, N.", - "Murphy, A.J.", - "Yancopoulos, G.D.", - "Kyratsous, C.A.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m42_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m42", - }, - }, - { - title: - "Structural basis for SARS-CoV-2 envelope protein in recognition of human cell junction protein PALS1", - emdb: { - dbId: "EMD-23665", - emMethod: "SINGLE PARTICLE", - resolution: "3.65", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-23665/400_23665.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-23665", - }, - pdb: { - dbId: "7M4R", - method: "ELECTRON MICROSCOPY", - keywords: - "SARS-CoV-2 envelope protein, PDZ-binding motif, complex, pathogen-host interaction, CELL ADHESION-VIRAL PROTEIN complex", - refModels: [ - { - emdbId: "EMD-23665", - 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title: - "Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG1-22", - emdb: { - dbId: "EMD-23694", - emMethod: "SINGLE PARTICLE", - resolution: "3.9", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-23694/400_23694.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-23694", - }, - pdb: { - dbId: "7M6F", - method: "ELECTRON MICROSCOPY", - keywords: - "SARS-CoV-2, Coronavirus, COVID-19, antibody, neutralizing antibody, receptor binding domain, spike glycoprotein, ANTIVIRAL PROTEIN, VIRAL PROTEIN-ANTIVIRAL PROTEIN complex", - refModels: [ - { - emdbId: "EMD-23694", - pdbId: "7M6F", - source: "CERES", - method: "PHENIX", - filename: "7m6f_23694_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7m6f_23694/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - 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"Barnes, C.O.", - "Eraslan, B.", - "Hudak, A.", - "Keeffe, J.R.", - "Cosimi, L.A.", - "Brown, E.M.", - "Muecksch, F.", - "Weisblum, Y.", - "Zhang, S.", - "Delorey, T.", - "Woolley, A.E.", - "Ghantous, F.", - "Park, S.M.", - "Phillips, D.", - "Tusi, B.", - "Huey-Tubman, K.E.", - "Cohen, A.A.", - "Gnanapragasam, P.N.P.", - "Rzasa, K.", - "Hatziioanno, T.", - "Durney, M.A.", - "Gu, X.", - "Tada, T.", - "Landau, N.R.", - "West Jr., A.P.", - "Rozenblatt-Rosen, O.", - "Seaman, M.S.", - "Baden, L.R.", - "Graham, D.B.", - "Deguine, J.", - "Bieniasz, P.D.", - "Regev, A.", - "Hung, D.", - "Bjorkman, P.J.", - "Xavier, R.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7m6f_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7m6f", - }, - }, - { - title: - "Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG7-15", - emdb: { - dbId: "EMD-23695", - emMethod: "SINGLE PARTICLE", - 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(0000-0003-1829-0117)", "Yang, Y. (0000-0001-9061-3828)"], - details: [ - { - sample: { - name: "", - exprSystem: "Escherichia coli", - assembly: "tetradecameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "34315827", - title: - "Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme.", - journal: "Science 373: 1142-1146 (2021), 1095-9203", - doi: "https://doi.org/10.1126/science.abi9310", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/34315827", - pubDate: "2021", - abstract: "", - authors: [ - "Liu, C. (0000-0003-1829-0117)", - "Shi, W. (0000-0002-0741-6813)", - "Becker, S.T. (0000-0002-6730-803X)", - "Schatz, D.G. (0000-0002-5669-1176)", - "Liu, B. (0000-0002-6581-780X)", - "Yang, Y. 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}, - }, - { - title: - "SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(1)-RTC", - emdb: { - dbId: "EMD-24431", - emMethod: "SINGLE PARTICLE", - resolution: "3.17", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-24431/400_24431.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-24431", - }, - pdb: { - dbId: "7RE2", - method: "ELECTRON MICROSCOPY", - keywords: - "RNA-dependent RNA polymerase, viral replication-transcription complex, transcription, viral proteins, REPLICATION-TRANSCRIPTION complex", - refModels: [ - { - emdbId: "EMD-24431", - pdbId: "7RE2", - source: "CERES", - method: "PHENIX", - filename: "7re2_24431_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7re2_24431/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTD1", - organism: "2697049", - name: "RNA-directed RNA polymerase", - details: "", - altNames: "Pol, RdRp, Non-structural protein 12, nsp12", - isAntibody: false, - 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(0000-0003-3205-8832)", - ], - }, - { - pmID: "35262076", - title: - "Flipped Over U: Structural Basis for dsRNA Cleavage by the SARS-CoV-2 Endoribonuclease.", - journal: "Biorxiv (2022), 2692-8205", - doi: "https://doi.org/10.1101/2022.03.02.480688", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35262076", - pubDate: "2022", - abstract: "", - authors: [ - "Frazier, M.N.", - "Wilson, I.M.", - "Krahn, J.M.", - "Butay, K.J.", - "Dillard, L.B.", - "Borgnia, M.J.", - "Stanley, R.E. (0000-0002-2106-3102)", - "Frazier, M.N. 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(0000-0002-3305-0034)", - "Murali-Krishna, K. (0000-0002-6275-1710)", - "Chandele, A. 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details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "nonameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36370711", - title: - "Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes.", - journal: "Immunity 55: 2419-2435.e10 (2022), 1074-7613", - doi: "https://doi.org/10.1016/j.immuni.2022.10.019", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36370711", - pubDate: "2022", - abstract: "", - authors: [ - "Fan, C.", - "Cohen, A.A.", - "Park, M.", - "Hung, A.F.", - "Keeffe, J.R.", - "Gnanapragasam, P.N.P.", - "Lee, Y.E.", - "Gao, H.", - "Kakutani, L.M.", - "Wu, Z.", - "Kleanthous, H.", - "Malecek, K.E.", - "Williams, J.C.", - "Bjorkman, P.J.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7uz6_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7uz6", - }, - }, - { - title: - "Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-31", - 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(0000-0002-1878-0581)", - "May, A.J. (0000-0003-2262-9750)", - "Acharya, P. (0000-0002-0089-277X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Local refinement of SARS-CoV-2 vaccine induced antibody Ab026500 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain", - journal: "To Be Published", - doi: "", - pmidLink: "", - pubDate: "", - abstract: "", - authors: [ - "Stalls, V. (0000-0002-1878-0581)", - "Acharya, P.", - "May, A.J.", - "Malewana, D.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dpz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dpz", - }, - }, - { - title: - "Cryo-EM structure of spike binding to Fab of neutralizing antibody (locally refined)", - emdb: { - dbId: "EMD-27690", - emMethod: "SINGLE PARTICLE", - resolution: "3.3", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-27690/400_27690.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-27690", - }, - pdb: { - dbId: "8DT3", - method: "ELECTRON MICROSCOPY", - keywords: "SARS-COV2, antibody, neutralizing, VIRAL PROTEIN-IMMUNE SYSTEM complex", - refModels: [ - { - emdbId: "EMD-27690", - pdbId: "8DT3", - source: "CERES", - method: "PHENIX", - filename: "8dt3_27690_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/8dt3_27690/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "Heavy chain Fab of SW186", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "10090", - name: "Light chain Fab of SW186", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Sun, P.C. (0000-0002-7549-1161)", - "Fang, Y. (0000-0003-1275-8276)", - "Bai, X.C. (0000-0002-4234-5686)", - "Chen, Z.J. (0000-0002-8475-8251)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Cricetulus griseus", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "35926067", - title: - "An antibody that neutralizes SARS-CoV-1 and SARS-CoV-2 by binding to a conserved spike epitope outside the receptor binding motif.", - journal: "Sci Immunol 7: eabp9962-eabp9962 (2022), 2470-9468", - doi: "https://doi.org/10.1126/sciimmunol.abp9962", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/35926067", - pubDate: "2022", - abstract: "", - authors: [ - "Fang, Y. (0000-0003-1275-8276)", - "Sun, P.", - "Xie, X. (0000-0003-0918-016X)", - "Du, M. (0000-0002-9464-4098)", - "Du, F. (0000-0002-7689-5918)", - "Ye, J. (0000-0002-4160-6389)", - "Kalveram, B.K.", - "Plante, J.A. (0000-0002-4768-7458)", - "Plante, K.S. (0000-0002-7485-3167)", - "Li, B. (0000-0002-8617-900X)", - "Bai, X.C. (0000-0002-4234-5686)", - "Shi, P.Y. (0000-0001-5553-1616)", - "Chen, Z.J. 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(0000-0001-8951-1074)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8dt8_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8dt8", - }, - }, - { - title: - "Structure of RBD directed antibody DH1047 in complex with SARS-CoV-2 spike: Local refinement of RBD-Fab interace", - emdb: { - dbId: "EMD-27703", - emMethod: "SINGLE PARTICLE", - resolution: "3.77", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-27703/400_27703.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-27703", - }, - pdb: { - dbId: "8DTK", - method: "ELECTRON MICROSCOPY", - keywords: "RBD, Fab, Viral Protein, Viral Protein-Immune System Complex", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike protein S1", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "DH1047 Fab Light Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: null, - organism: "9606", - name: "DH1047 Fab Heavy Chain", - details: "", - altNames: "", - isAntibody: true, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "May, A.J. 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}, - }, - { - title: - "SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to computationally engineered ACE2 mimetic CVD293", - emdb: { - dbId: "EMD-27731", - emMethod: "SINGLE PARTICLE", - resolution: "3.5", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-27731/400_27731.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-27731", - }, - pdb: { - dbId: "8DV2", - method: "ELECTRON MICROSCOPY", - keywords: - "SARS-CoV-2, Spike, Receptor-binding domain, ACE2 receptor traps, ANTIVIRAL PROTEIN, VIRAL PROTEIN-ANTIVIRAL PROTEIN complex", - refModels: [ - { - emdbId: "EMD-27731", - pdbId: "8DV2", - source: "CERES", - method: "PHENIX", - filename: "8dv2_27731_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/8dv2_27731/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - 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details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "nonameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "36264829", - title: - "Imprinted antibody responses against SARS-CoV-2 Omicron sublineages.", - journal: "Science 378: 619-627 (2022), 1095-9203", - doi: "https://doi.org/10.1126/science.adc9127", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/36264829", - pubDate: "2022", - abstract: "", - authors: [ - "Park, Y.J.", - "Pinto, D.", - "Walls, A.C.", - "Liu, Z.", - "De Marco, A.", - "Benigni, F.", - "Zatta, F.", - "Silacci-Fregni, C.", - "Bassi, J.", - "Sprouse, K.R.", - "Addetia, A.", - "Bowen, J.E.", - "Stewart, C.", - "Giurdanella, M.", - "Saliba, C.", - "Guarino, B.", - "Schmid, M.A.", - "Franko, N.M.", - "Logue, J.K.", - "Dang, H.V.", - "Hauser, K.", - "di Iulio, J.", - "Rivera, W.", - "Schnell, G.", - "Rajesh, A.", - "Zhou, J.", - "Farhat, N.", - "Kaiser, H.", - "Montiel-Ruiz, M.", - "Noack, J.", - "Lempp, F.A.", - "Janer, J.", - 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(0000-0003-1822-1701)", - "Zhu, Q. (0000-0001-7020-2044)", - "Wang, G. (0000-0002-2100-5439)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "nonameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32970990", - title: - "Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.", - journal: "Cell 183: 1013-1023.e13 (2020), 1097-4172", - doi: "https://doi.org/10.1016/j.cell.2020.09.035", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32970990", - pubDate: "2020", - abstract: "", - authors: [ - "Du, S.", - "Cao, Y.", - "Zhu, Q.", - "Yu, P.", - "Qi, F.", - "Wang, G.", - "Du, X.", - "Bao, L.", - "Deng, W.", - "Zhu, H.", - "Liu, J.", - "Nie, J.", - "Zheng, Y.", - "Liang, H.", - "Liu, R.", - "Gong, S.", - "Xu, H.", - "Yisimayi, A.", - "Lv, Q.", - "Wang, B.", - "He, R.", - "Han, Y.", - "Zhao, W.", - "Bai, Y.", - "Qu, Y.", - "Gao, X.", - "Ji, C.", - "Wang, Q.", - "Gao, N.", - "Huang, W.", - "Wang, Y.", - "Xie, X.S.", - 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"Wang, C.", - "Ma, C.", - "Chen, T.", - "Ho, M.", - "Chang, Y.", - "Lo, J.M.", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "32755598", - title: - "A Carbohydrate-Binding Protein from the Edible Lablab Beans Effectively Blocks the Infections of Influenza Viruses and SARS-CoV-2.", - journal: "Cell Rep 32: 108016-108016 (2020), 2211-1247", - doi: "https://doi.org/10.1016/j.celrep.2020.108016", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/32755598", - pubDate: "2020", - abstract: "", - authors: [ - "Liu, Y.M.", - "Shahed-Al-Mahmud, M.", - "Chen, X.", - "Chen, T.H.", - "Liao, K.S.", - "Lo, J.M.", - "Wu, Y.M.", - "Ho, M.C.", - "Wu, C.Y.", - "Wong, C.H.", - "Jan, J.T.", - "Ma, C.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/7cn9_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/7cn9", - }, - }, - { - title: "S protein of SARS-CoV-2 in complex bound with T-ACE2", - emdb: { - dbId: "EMD-30460", - emMethod: "SINGLE PARTICLE", - resolution: "4", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-30460/400_30460.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-30460", - }, - pdb: { - dbId: "7CT5", - method: "ELECTRON MICROSCOPY", - keywords: "S-ECD, ACE2, VIRAL PROTEIN", - refModels: [ - { - emdbId: "EMD-30460", - pdbId: "7CT5", - source: "CERES", - method: "PHENIX", - filename: "7ct5_30460_trim_real_space_refined_000.pdb", - externalLink: "https://cci.lbl.gov/ceres/goto_entry/7ct5_30460/07_2023", - details: "", - }, - ], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "Q9BYF1", - organism: "9606", - name: "Angiotensin-converting enzyme 2", - details: "", - altNames: - 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(0000-0002-5617-9228)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8t25_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8t25", - }, - }, - { - title: - "Cryo-EM structure of mink variant Y453F trimeric spike protein bound to one mink ACE2 receptors", - emdb: { - dbId: "EMD-41143", - emMethod: "SINGLE PARTICLE", - resolution: "3.75", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-41143/400_41143.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-41143", - }, - pdb: { - dbId: "8TAZ", - method: "ELECTRON MICROSCOPY", - keywords: "Coronavirus, Spike, ACE2, Mink, protein binding, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - { - uniprotAcc: "G1TEF4", - organism: "9986", - name: "Angiotensin-converting enzyme", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Fan, X.", - "Ahn, H.M. (0000-0002-5353-4845)", - "Calderon, B. (0000-0003-1130-0386)", - "Gao, Y. (0000-0001-6787-2397)", - "Horgan, N.", - "Liang, B. (0000-0002-5617-9228)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "tetrameric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37842796", - title: - "Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS-CoV-2.", - journal: "J Med Virol 95: e29163-e29163 (2023), 1096-9071", - doi: "https://doi.org/10.1002/jmv.29163", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37842796", - pubDate: "2023", - abstract: "", - authors: [ - "Ahn, H.", - "Calderon, B.M.", - "Fan, X.", - "Gao, Y.", - "Horgan, N.L.", - "Jiang, N. (0000-0003-3375-4805)", - "Blohm, D.S.", - "Hossain, J.", - "Rayyan, N.W.K.", - "Osman, S.H.", - "Lin, X.", - "Currier, M.", - "Steel, J.", - "Wentworth, D.E.", - "Zhou, B.", - "Liang, B. (0000-0002-5617-9228)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8taz_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8taz", - }, - }, - { - title: - "Gaussian mixture model based single particle refinement - SARS (SARS-CoV-2 Spike Proteins on intact virions from EMPIAR-10492)", - emdb: { - dbId: "EMD-41841", - emMethod: "SINGLE PARTICLE", - resolution: "3.1", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-41841/400_41841.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-41841", - }, - pdb: { - dbId: "8U28", - method: "ELECTRON MICROSCOPY", - keywords: "coronavirus spike protein, VIRUS", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: ["Chen, M.", "Pintilie, G."], - details: [ - { - sample: { - name: "", - exprSystem: "Severe acute respiratory syndrome coronavirus 2", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models", - journal: "Nat.Methods (2023), 1548-7105", - doi: "https://doi.org/10.1038/s41592-023-02082-9", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: ["Chen, M.", "Schmid, M.F.", "Chiu, W."], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8u28_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8u28", - }, - }, - { - title: "Prototypic SARS-CoV-2 spike (containing K417) in the closed conformation", - emdb: { - dbId: "EMD-42589", - emMethod: "SINGLE PARTICLE", - resolution: "3.2", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-42589/400_42589.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-42589", - }, - pdb: { - dbId: "8UUL", - method: "ELECTRON MICROSCOPY", - keywords: "Prototypic SARS-CoV-2 spike, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Li, F. (0000-0002-1958-366X)", - "Geng, Q. (0000-0003-4872-2400)", - "Liu, B. (0000-0002-6581-780X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37991488", - title: - "Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein.", - journal: "Elife 12 (2023), 2050-084X", - doi: "https://doi.org/10.7554/eLife.74060", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37991488", - pubDate: "2023", - abstract: "", - authors: [ - "Geng, Q.", - "Wan, Y.", - "Hsueh, F.C.", - "Shang, J.", - "Ye, G. (0000-0001-6034-2174)", - "Bu, F.", - "Herbst, M.", - "Wilkens, R.", - "Liu, B. (0000-0002-6581-780X)", - "Li, F. (0000-0002-1958-366X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8uul_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8uul", - }, - }, - { - title: "Prototypic SARS-CoV-2 spike (containing K417) in the open conformation", - emdb: { - dbId: "EMD-42590", - emMethod: "SINGLE PARTICLE", - resolution: "3.9", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-42590/400_42590.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-42590", - }, - pdb: { - dbId: "8UUM", - method: "ELECTRON MICROSCOPY", - keywords: "Prototypic SARS-CoV-2 spike, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["WQZGKKKJIJFFOK-QTVWNMPRSA-N", "OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Li, F. (0000-0002-1958-366X)", - "Geng, Q. (0000-0003-4872-2400)", - "Liu, B. (0000-0002-6581-780X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37991488", - title: - "Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein.", - journal: "Elife 12 (2023), 2050-084X", - doi: "https://doi.org/10.7554/eLife.74060", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37991488", - pubDate: "2023", - abstract: "", - authors: [ - "Geng, Q.", - "Wan, Y.", - "Hsueh, F.C.", - "Shang, J.", - "Ye, G. (0000-0001-6034-2174)", - "Bu, F.", - "Herbst, M.", - "Wilkens, R.", - "Liu, B. (0000-0002-6581-780X)", - "Li, F. (0000-0002-1958-366X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8uum_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8uum", - }, - }, - { - title: "Prototypic SARS-CoV-2 spike (containing V417) in the closed conformation", - emdb: { - dbId: "EMD-42591", - emMethod: "SINGLE PARTICLE", - resolution: "3.8", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-42591/400_42591.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-42591", - }, - pdb: { - dbId: "8UUN", - method: "ELECTRON MICROSCOPY", - keywords: "Prototypic SARS-CoV-2 spike V417, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N"], - dbauthors: [ - "Li, F. (0000-0002-1958-366X)", - "Geng, Q. (0000-0003-4872-2400)", - "Liu, B. (0000-0002-6581-780X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37991488", - title: - "Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein.", - journal: "Elife 12 (2023), 2050-084X", - doi: "https://doi.org/10.7554/eLife.74060", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37991488", - pubDate: "2023", - abstract: "", - authors: [ - "Geng, Q.", - "Wan, Y.", - "Hsueh, F.C.", - "Shang, J.", - "Ye, G. (0000-0001-6034-2174)", - "Bu, F.", - "Herbst, M.", - "Wilkens, R.", - "Liu, B. (0000-0002-6581-780X)", - "Li, F. (0000-0002-1958-366X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8uun_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8uun", - }, - }, - { - title: "Prototypic SARS-CoV-2 spike (containing V417) in the open conformation", - emdb: { - dbId: "EMD-42592", - emMethod: "SINGLE PARTICLE", - resolution: "3.9", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-42592/400_42592.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-42592", - }, - pdb: { - dbId: "8UUO", - method: "ELECTRON MICROSCOPY", - keywords: "Prototypic SARS-CoV-2 spike V417, VIRAL PROTEIN", - refModels: [], - entities: [ - { - uniprotAcc: "P0DTC2", - organism: "2697049", - name: "Spike glycoprotein", - details: "", - altNames: "S glycoprotein,E2,Peplomer protein", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: ["OVRNDRQMDRJTHS-FMDGEEDCSA-N", "WQZGKKKJIJFFOK-QTVWNMPRSA-N"], - dbauthors: [ - "Li, F. (0000-0002-1958-366X)", - "Geng, Q. (0000-0003-4872-2400)", - "Liu, B. (0000-0002-6581-780X)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "Homo sapiens", - assembly: "trimeric (author_defined_assembly)", - genes: [], - }, - refdoc: [ - { - pmID: "37991488", - title: - "Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein.", - journal: "Elife 12 (2023), 2050-084X", - doi: "https://doi.org/10.7554/eLife.74060", - pmidLink: "https://pubmed.ncbi.nlm.nih.gov/37991488", - pubDate: "2023", - abstract: "", - authors: [ - "Geng, Q.", - "Wan, Y.", - "Hsueh, F.C.", - "Shang, J.", - "Ye, G. (0000-0001-6034-2174)", - "Bu, F.", - "Herbst, M.", - "Wilkens, R.", - "Liu, B. (0000-0002-6581-780X)", - "Li, F. (0000-0002-1958-366X)", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8uuo_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8uuo", - }, - }, - { - title: "SARS-CoV-2 5' proximal stem-loop 5", - emdb: { - dbId: "EMD-42818", - emMethod: "SINGLE PARTICLE", - resolution: "4.7", - imageLink: "https://www.ebi.ac.uk/emdb/images/entry/EMD-42818/400_42818.gif", - externalLink: "https://www.ebi.ac.uk/emdb/entry/EMD-42818", - }, - pdb: { - dbId: "8UYS", - method: "ELECTRON MICROSCOPY", - keywords: "SL5, coronavirus, 5' UTR, RNA", - refModels: [], - entities: [ - { - uniprotAcc: null, - organism: null, - name: "SARS-CoV-2 RNA SL5 domain.", - details: "", - altNames: "", - isAntibody: false, - isNanobody: false, - isSybody: false, - }, - ], - ligands: [], - dbauthors: [ - "Zhang, K. (0000-0003-0414-4776)", - "Zheludev, I.N. (0000-0002-9572-0574)", - "Li, S. (0000-0002-7041-5960)", - "Chiu, W. (0000-0002-8910-3078)", - "Das, R. (0000-0001-7497-0972)", - "Kretsch, R.C. (0000-0002-6935-518X)", - "Xu, L. (0000-0002-1200-8937)", - "Zhou, X. (0000-0002-0722-7334)", - "Huang, R. (0009-0009-6136-8013)", - "Nye, G. (0009-0001-6698-9988)", - ], - details: [ - { - sample: { - name: "", - exprSystem: "", - assembly: "", - genes: [], - }, - refdoc: [ - { - pmID: "", - title: - "Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses", - journal: "Biorxiv (2023), 2692-8205", - doi: "https://doi.org/10.1101/2023.11.22.567964", - pmidLink: "", - pubDate: "2023", - abstract: "", - authors: [ - "Kretsch, R.C.", - "Xu, L.", - "Zheludev, I.N.", - "Zhou, X.", - "Huang, R.", - "Nye, G.", - "Li, S.", - "Zhang, K.", - "Chiu, W.", - "Das, R.", - ], - }, - ], - }, - ], - imageLink: - "https://www.ebi.ac.uk/pdbe/static/entry/8uys_deposited_chain_front_image-200x200.png", - externalLink: "https://www.ebi.ac.uk/pdbe/entry/pdb/8uys", - }, + { + source: "NMR", + name: "NMR", + description: + "NMR-based screening using a fragment library for binding to 25 SCoV2 proteins and identification of hits also against previously unexplored SCoV2 proteins. Computational mapping has been used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets.", + externalLink: "", }, ], + Structures: [], }; diff --git a/app/assets/javascripts/covid19/src/data/repositories/Covid19InfoApiRepository.ts b/app/assets/javascripts/covid19/src/data/repositories/Covid19InfoApiRepository.ts new file mode 100644 index 000000000..9ca4a4eb9 --- /dev/null +++ b/app/assets/javascripts/covid19/src/data/repositories/Covid19InfoApiRepository.ts @@ -0,0 +1,368 @@ +import _ from "lodash"; +import { + Covid19Info, + Details, + Maybe, + PdbValidation, + Structure, + ValidationMethod, + ValidationSource, +} from "../../domain/entities/Covid19Info"; +import { + Covid19InfoRepository, + GetOptions, + SortingFields, +} from "../../domain/repositories/Covid19InfoRepository"; +import { data } from "../covid19-data"; +import { routes } from "../../routes"; +import { getJSONData } from "../utils/request-utils"; +import { FutureData } from "../../domain/entities/FutureData"; +import { Future } from "../utils/future"; + +export class Covid19InfoApiRepository implements Covid19InfoRepository { + get(options: GetOptions): FutureData { + const covidInfo$ = Future.joinObj({ + pdbEntries: getPdbEntries(options), + validationSources: getPdbRefModelSources(), + }).map(({ pdbEntries, validationSources }) => ({ + count: pdbEntries.count, + structures: pdbEntries.structures, + validationSources, + })); + + return covidInfo$; + } + + autoSuggestions(search: string): FutureData { + const { bionotesApi } = routes; + + const params = new URLSearchParams({ + q: search, + }); + + const suggestions$ = getJSONData<{ results: string[] }>( + `${bionotesApi}/complete/search?${params.toString()}` + ).map(({ results }) => + _(results) + .map(v => v.trim()) + .uniq() + .value() + ); + + return suggestions$; + } +} + +function getPdbRefModelSources(): FutureData { + return Future.success( + data.RefModelSources.map( + (source): ValidationSource => ({ + ...source, + methods: data.RefModelMethods.filter(method => method.source === source.name).map( + (method): ValidationMethod => _.omit(method, ["source"]) + ), + }) + ) + ); +} + +const sortingFields: Record = { + pdb: "dbId", + title: "title", + releaseDate: "relDate", + emdb: "emdbs__dbId", +}; + +function getPdbEntries( + options: GetOptions +): FutureData<{ count: number; structures: Structure[] }> { + const { bionotesApi } = routes; + const { page, pageSize, filter: f, sort, query } = options; + + const filterParams = { + is_antibody: f.antibodies, + is_nanobody: f.nanobodies, + is_sybody: f.sybodies, + is_pdb_redo: f.pdbRedo, + is_cstf: f.cstf, + is_ceres: f.ceres, + is_idr: f.idr, + q: query ?? "", + }; + + const params = new URLSearchParams( + _.mapValues( + { + limit: pageSize, + page: page, + ordering: `${sort.order === "asc" ? "" : "-"}${sortingFields[sort.field]}`, + ..._.pickBy(filterParams, v => Boolean(v)), + }, + v => v.toString() + ) + ); + + const pagination$ = getJSONData>( + `${bionotesApi}/pdbentry/?${params.toString()}` + ); + + return pagination$.map(({ count, results: pdbEntries }) => ({ + count, + structures: pdbEntries.map(buildStructure), + })); +} + +function buildStructure(pdbEntry: PdbEntry): Structure { + const { emdbs } = pdbEntry; + + const emdb = _.first(emdbs); + + const entities = pdbEntry.entities.map(e => ({ + ...e, + uniprotAcc: e.uniprotAcc?.dbId ?? null, + organism: e.organism?.ncbi_taxonomy_id ?? null, + targets: + e.uniprotAcc?.uniprotentities.flatMap(t => { + if (!e.uniprotAcc) return []; + + return [ + { + start: t.start, + end: t.end, + name: t.targetName, + uniprotId: e.uniprotAcc.dbId, + }, + ]; + }) || [], + })); + + const organisms = pdbEntry.entities + .flatMap(e => (e.organism ? [e.organism] : [])) + .map(o => ({ + id: o.ncbi_taxonomy_id, + name: o.scientific_name, + commonName: o.common_name, + externalLink: o.externalLink, + })); + + const ligands = pdbEntry.ligands.map(l => ({ + id: l.dbId, + name: l.name, + imageLink: l.imageLink, + externalLink: l.externalLink, + inChI: l.IUPACInChIkey, + hasIDR: l.well.length > 0, + })); + + const queryLink = `/${pdbEntry.dbId.toLowerCase()}${emdb ? emdb.dbId.toUpperCase() : ""}`; + const pdbQueryLink = `/${pdbEntry.dbId.toLowerCase()}${ + emdb ? "+!" + emdb.dbId.toUpperCase() : "" + }`; + + return { + id: pdbEntry.dbId, + title: pdbEntry.title, + entities: _.uniqBy(entities, "name"), + pdb: { + id: pdbEntry.dbId, + method: pdbEntry.method, + ligands: pdbEntry.ligands.map(ligand => ligand.IUPACInChIkey), + keywords: pdbEntry.keywords, + queryLink: pdbQueryLink, + imageUrl: pdbEntry.imageLink, + externalLinks: [{ url: pdbEntry.externalLink, text: "EBI" }], + entities, + }, + emdb: emdb && { + id: emdb.dbId, + queryLink: `/${ + pdbEntry ? "!" + pdbEntry.dbId.toLowerCase() : "" + }+${emdb.dbId.toUpperCase()}`, + emMethod: emdb.emMethod, + imageUrl: + emdb.imageLink || + `https://www.ebi.ac.uk/pdbe/static/entry/EMD-${emdb.dbId}/400_${emdb.dbId}.gif`, + externalLinks: [{ url: emdb.externalLink, text: "EBI" }], + resolution: emdb.resolution, + }, + organisms: _.uniqBy(organisms, "id"), + ligands: _.uniqBy(ligands, "id"), + details: getDetails(pdbEntry.details), + validations: { pdb: getPdbValidations(pdbEntry, emdb ?? null), emdb: [] }, + queryLink: queryLink, + }; +} + +function getValidationQueryLink(pdbId: string, validation: RefModel) { + switch (validation.source) { + case "PDB-REDO": + return pdbId + "-pdbRedo"; + case "CSTF": + return pdbId + "-cstf"; + case "CERES": + return pdbId + "-ceres"; + default: + console.error(`Validation not supported: "${validation.source}"`); + return undefined; + } +} + +function getPdbValidations(pdb: PdbEntry, emdb: Emdb | null): PdbValidation[] { + const pdbId = pdb.dbId.toLowerCase(); + const emdbId = emdb && emdb.dbId.toUpperCase(); + + const pdbValidation = (validation: RefModel): PdbValidation | undefined => { + const validationQuery = getValidationQueryLink(pdbId, validation); + const queryLink = `/${pdbId}${emdbId ? "+" + emdbId : ""}|${validationQuery}`; + + switch (validation.source) { + case "PDB-REDO": + return { + ...validation, + queryLink, + badgeColor: "w3-orange", + }; + case "CSTF": + return { + ...validation, + queryLink, + badgeColor: "w3-cyan", + }; + case "CERES": + return { + ...validation, + queryLink: undefined, + badgeColor: "w3-blue", + }; + default: + console.error(`Validation not supported: "${validation.source}"`); + return undefined; + } + }; + + return _.compact(pdb.refModels.map(pdbValidation)); +} + +function getDetails(details: Detail[]): Maybe
{ + const detail = _.first(details); + if (!detail) return; + + return { + ...detail, + refdoc: detail.refdoc?.map(ref => { + return { id: ref.pmID, idLink: ref.pmidLink, ...ref }; + }), + }; +} + +type Pagination = { + count: number; + next: string; + results: T[]; +}; + +interface PdbEntry { + dbId: string; + title: string; + emdbs: Emdb[]; + method: string; + keywords: string; + refModels: RefModel[]; + entities: Entity[]; + ligands: Ligand[]; + dbauthors: string[]; + details: Detail[]; + imageLink: string; + externalLink: string; +} + +interface Emdb { + dbId: string; + title: string; + emMethod: string; + resolution: string; + status: string; + details: string; + imageLink: string; + externalLink: string; +} + +type PdbSourceName = "PDB-REDO" | "CSTF" | "CERES"; +type PdbMethodName = "PDB-Redo" | "Isolde" | "Refmac" | "PHENIX"; + +interface RefModel { + source: PdbSourceName; + method: PdbMethodName; + filename: string; + externalLink: string; + details: string; +} + +interface NMRTarget { + start: number; + end: number; + targetName: string; +} + +interface Entity { + uniprotAcc?: UniprotAcc; + organism?: Organism; + name: string; + details: string; + altNames: string; + isAntibody: boolean; + isNanobody: boolean; + isSybody: boolean; +} + +interface UniprotAcc { + dbId: string; + name: string; + externalLink: string; + uniprotentities: NMRTarget[]; +} + +interface Organism { + ncbi_taxonomy_id: string; + scientific_name: string; + common_name: string; + externalLink: string; +} + +interface Ligand { + IUPACInChIkey: string; + dbId: string; + name: string; + formula: string; + formula_weight: number; + imageLink: string; + externalLink: string; + pubChemCompoundId: string; + IUPACInChI: string; + isomericSMILES: string; + canonicalSMILES: string; + well: string[]; +} + +interface Detail { + sample: Sample; + refdoc: Refdoc[]; +} + +interface Sample { + name: string; + exprSystem: string; + assembly: string; + genes: any[]; +} + +interface Refdoc { + pmID: string; + title: string; + journal: string; + doi: string; + pmidLink: string; + pubDate: string; + abstract: string; + authors: any[]; +} diff --git a/app/assets/javascripts/covid19/src/data/repositories/Covid19InfoFromJsonRepository.ts b/app/assets/javascripts/covid19/src/data/repositories/Covid19InfoFromJsonRepository.ts deleted file mode 100644 index 6a50424b4..000000000 --- a/app/assets/javascripts/covid19/src/data/repositories/Covid19InfoFromJsonRepository.ts +++ /dev/null @@ -1,422 +0,0 @@ -import _ from "lodash"; -import MiniSearch, { Options, SearchResult } from "minisearch"; -import { - Covid19Info, - Details, - Emdb, - Entity, - Covid19Filter, - filterEntities, - Maybe, - Ligand, - Organism, - Pdb, - Structure, - PdbValidation, - filterPdbValidations, - ValidationSource, - ValidationMethod, - filterLigands, -} from "../../domain/entities/Covid19Info"; -import { - Covid19InfoRepository, - SearchOptions, -} from "../../domain/repositories/Covid19InfoRepository"; -import { SearchOptions as MiniSearchSearchOptions } from "minisearch"; -import { cache } from "../../utils/cache"; -import { data } from "../covid19-data"; -import * as Data from "../Covid19Data.types"; - -export class Covid19InfoFromJsonRepository implements Covid19InfoRepository { - info: Covid19Info; - searchOptions: MiniSearchSearchOptions = { combineWith: "AND" }; - - constructor() { - this.info = { - structures: getStructures(), - validationSources: getValidationSources(), - }; - } - - get(): Covid19Info { - return this.info; - } - - search(options: SearchOptions): Covid19Info { - const { data, search = "", filter: filterState } = options; - const { structures } = data; - const isTextFilterEnabled = Boolean(search.trim()); - - const exactMatch = extractExactMatches(search); - - const structuresFilteredByText = isTextFilterEnabled - ? this.searchByText(structures, exactMatch.search, exactMatch.matches) - : structures; - - const structuresFilteredByTextAndBody = filterState - ? this.filter(structuresFilteredByText, filterState) - : structuresFilteredByText; - return { ...data, structures: structuresFilteredByTextAndBody }; - } - - autoSuggestions(search: string): string[] { - const miniSearch = this.getMiniSearch(); - const structuresByText = miniSearch - .autoSuggest(search, this.searchOptions) - .map(result => result.suggestion); - return structuresByText; - } - - private filter(structures: Structure[], filterState: Covid19Filter): Structure[] { - const isEntitiesStateEnabled = - filterState.antibodies || filterState.nanobodies || filterState.sybodies; - const isPdbValidationsFilterEnabled = - filterState.pdbRedo || filterState.cstf || filterState.ceres; - const isIDREnabled = filterState.idr; - - if (!isEntitiesStateEnabled && !isPdbValidationsFilterEnabled && !isIDREnabled) - return structures; - const structuresWithValidations = isPdbValidationsFilterEnabled - ? structures.filter(structure => - !_.isEmpty(structure.validations.pdb) - ? filterPdbValidations(structure.validations.pdb, filterState) - : false - ) - : structures; - const structuresWithEntities = isEntitiesStateEnabled - ? structuresWithValidations.filter( - structure => !_.isEmpty(filterEntities(structure.entities, filterState)) - ) - : structuresWithValidations; - const structuresWithIDR = isIDREnabled - ? structuresWithEntities.filter( - structure => !_.isEmpty(filterLigands(structure.ligands)) - ) - : structuresWithEntities; - return structuresWithIDR; - } - - private searchByText( - structures: Structure[], - search: string, - matches: string[] = [] - ): Structure[] { - const miniSearch = this.getMiniSearch(); - const searchOptions = !_.isEmpty(matches) - ? { - ...this.searchOptions, - filter: (result: SearchResult) => - _.isEmpty( - _.difference( - matches.map(m => m.toLowerCase()), - result.terms.map(m => m.toLowerCase()) - ) - ), - } - : this.searchOptions; - const results = miniSearch.search(search, searchOptions); - const matchingIds = results.map(getId); - return _(structures).keyBy(getId).at(matchingIds).compact().value(); - } - - @cache() - private getMiniSearch() { - return getMiniSearch(this.info.structures); - } -} - -function getStructureQueryLink( - pdb: Data.Pdb | null, - emdb: Data.Emdb | null, - validations: Data.RefModel[] -) { - const pdbUrlId = pdb && pdb.dbId.toLowerCase(); - const emdbUrlId = emdb && "+" + emdb.dbId.toUpperCase(); - const validationUrlIds = - pdbUrlId && "|" + validations.map(v => getValidationQueryLink(pdbUrlId, v)).join("+"); - - return `/${pdbUrlId || ""}${emdbUrlId || ""}${validationUrlIds || ""}`; -} - -function getStructures(): Structure[] { - const structures: Covid19Info["structures"] = _.flatten(data.Structures).map( - (structure): Structure => ({ - ..._.omit(structure, ["ligand", "organism", "entities"]), - title: structure.title, - id: getStructureId(structure), - pdb: structure.pdb ? getPdb(structure.pdb, structure.emdb) : undefined, - emdb: structure.emdb ? getEmdb(structure.emdb, structure.pdb) : undefined, - entities: getEntitiesForStructure(structure), - organisms: getOrganismsForStructure(data, structure), - ligands: structure.pdb === null ? [] : getLigands(data.Ligands, structure.pdb.ligands), - details: structure.pdb ? getDetails(structure.pdb) : undefined, - validations: { - pdb: structure.pdb === null ? [] : getPdbValidations(structure.pdb, structure.emdb), - emdb: [], - }, - queryLink: getStructureQueryLink( - structure.pdb, - structure.emdb, - structure.pdb?.refModels ?? [] - ), - }) - ); - - const repeatedIds = _(structures) - .countBy(structure => structure.id) - .toPairs() - .map(([structureId, structuresCount]) => (structuresCount > 1 ? structureId : null)) - .compact() - .value(); - - if (!_.isEmpty(repeatedIds)) { - console.error(`Repeated structure IDs: ${repeatedIds.join(", ")}`); - } - - return _.uniqBy(structures, getId); -} - -function extractExactMatches(search: string) { - const matches = search.match(/"[^"]+"/g)?.map(match => match.slice(1, -1)) ?? []; - return { - search: search.replace('"', ""), - matches, - }; -} - -function getValidationSources(): ValidationSource[] { - return data.RefModelSources.map( - (source): ValidationSource => ({ - ...source, - methods: data.RefModelMethods.filter(method => method.source === source.name).map( - (method): ValidationMethod => _.omit(method, ["source"]) - ), - }) - ); -} - -function getStructureId(structure: Data.Structure): string { - const parts = [structure.pdb?.dbId, structure.emdb?.dbId]; - return _(parts).compact().join("-"); -} - -function getOrganismsForStructure(data: Data.Covid19Data, structure: Data.Structure): Organism[] { - const organismsById = _(data.Organisms) - .map( - (organism): Organism => ({ - id: organism.ncbi_taxonomy_id, - name: organism.scientific_name, - commonName: organism.common_name, - externalLink: organism.externalLink, - }) - ) - .keyBy(getId); - - return _(structure.pdb?.entities) - .map(ref => (ref.organism ? organismsById.get(ref.organism) : null)) - .compact() - .uniqBy(getId) - .value(); -} - -function getLigands( - dataLigands: Data.Covid19Data["Ligands"], - ligandRefs: Data.Pdb["ligands"] -): Ligand[] { - const ligandsByInChI = _(dataLigands) - .map( - (ligand): Ligand => ({ - id: ligand.dbId, - inChI: ligand.IUPACInChIkey, - hasIDR: !!ligand.xRef, - ...ligand, - }) - ) - .keyBy(ligand => ligand.inChI) - .value(); - - return _(ligandRefs) - .map(ligandInChI => ligandsByInChI[ligandInChI]) - .compact() - .value(); -} - -function getEntitiesForStructure(structure: Data.Structure): Entity[] { - return _(structure.pdb?.entities).compact().value(); -} - -function getId(obj: T): string { - return obj.id; -} - -function getPdb(pdb: Data.Pdb, emdb: Data.Emdb | null): Pdb { - const entities = pdb.entities.map(entity => ({ id: pdb.dbId, ...entity })); - const pdbE: Pdb = { - id: pdb.dbId, - method: pdb.method, - ligands: pdb.ligands, - keywords: pdb.keywords, - queryLink: `/${pdb.dbId.toLowerCase()}${emdb ? "+!" + emdb.dbId.toUpperCase() : ""}`, - imageUrl: - pdb.imageLink || - `https://www.ebi.ac.uk/pdbe/static/entry/${pdb.dbId}_deposited_chain_front_image-200x200.png`, - externalLinks: pdb.externalLink.includes("www.ebi") - ? [{ url: pdb.externalLink, text: "EBI" }] - : [], - entities, - }; - return pdbE; -} - -function getEmdb(emdb: Data.Emdb, pdb: Data.Pdb | null): Emdb { - const emdbE: Emdb = { - id: emdb.dbId, - queryLink: `/${pdb ? "!" + pdb.dbId.toLowerCase() : ""}+${emdb.dbId.toUpperCase()}`, - emMethod: emdb.emMethod, - imageUrl: - emdb.imageLink || - `https://www.ebi.ac.uk/pdbe/static/entry/EMD-${emdb.dbId}/400_${emdb.dbId}.gif`, - externalLinks: emdb.externalLink.includes("www.ebi") - ? [{ url: emdb.externalLink, text: "EBI" }] - : [], - }; - return emdbE; -} - -function getDetails(pdb: Data.Pdb): Maybe
{ - const details = pdb.details?.[0]; - if (!details) return; - - return { - ...details, - refdoc: details.refdoc?.map(ref => { - return { id: ref.pmID, idLink: ref.pmidLink, ...ref }; - }), - }; -} - -function getValidationQueryLink(pdbId: string, validation: Data.RefModel) { - switch (validation.source) { - case "PDB-REDO": - return pdbId + "-pdbRedo"; - case "CSTF": - return pdbId + "-cstf"; - case "CERES": - return pdbId + "-ceres"; - default: - console.error(`Validation not supported: "${validation.source}"`); - return undefined; - } -} - -function getPdbValidations(pdb: Data.Pdb, emdb: Data.Emdb | null): PdbValidation[] { - const pdbId = pdb.dbId.toLowerCase(); - const emdbId = emdb && emdb.dbId.toUpperCase(); - const getQueryLink = (validation: Data.RefModel) => { - return `/${pdbId}${emdbId ? "+" + emdbId : ""}|${getValidationQueryLink( - pdbId, - validation - )}`; - }; - return pdb.refModels - ? _.compact( - pdb.refModels?.map((validation): PdbValidation | undefined => { - switch (validation.source) { - case "PDB-REDO": - return { - ...validation, - queryLink: getQueryLink(validation), - badgeColor: "w3-orange", - }; - case "CSTF": - return { - ...validation, - queryLink: getQueryLink(validation), - badgeColor: "w3-cyan", - }; - case "CERES": - return { - ...validation, - queryLink: undefined, - badgeColor: "w3-blue", - }; - default: - console.error(`Validation not supported: "${validation.source}"`); - return undefined; - } - }) - ) - : []; -} - -/* Search */ - -function getFields(objs: Obj[], keys: Array): string { - return _(objs) - .flatMap(obj => _.at(obj, keys)) - .compact() - .join(" - "); -} - -const fields = ["title", "details", "pdb", "emdb", "organisms", "ligands", "entities"] as const; - -type Field = typeof fields[number]; - -function getMiniSearch(structures: Structure[]): MiniSearch { - const miniSearch = new MiniSearch({ - fields: Array.from(fields), - storeFields: [], - searchOptions: { - prefix: true, - fuzzy: 0, - boost: { - title: 2, - }, - }, - extractField: extractField as Options["extractField"], - }); - miniSearch.addAll(structures); - return miniSearch; -} - -function extractField(structure: Structure, field: Field): string { - switch (field) { - case "pdb": - return structure.pdb?.id || ""; - case "emdb": - return structure.emdb?.id || ""; - case "organisms": - return getFields(structure.organisms, ["id", "name", "commonName"]); - case "ligands": - return getFields(structure.ligands, ["id", "name", "details"]); - case "details": { - if (!structure.details) return ""; - const { sample, refdoc } = structure.details; - - const valuesList = [ - _.flatMap(refdoc, getValuesFromObject), - getValuesFromObject(sample), - ]; - - return _(valuesList) - .flatten() - .reject(value => value.startsWith("http")) - .uniq() - .join(" "); - } - case "entities": - return getFields(structure.entities, [ - "uniprotAcc", - "name", - "altNames", - "details", - "organism", - ]); - default: - return structure[field] || ""; - } -} - -function getValuesFromObject(obj: object | undefined): string[] { - return _.compact(_.flatten(_.values(obj))); -} diff --git a/app/assets/javascripts/covid19/src/data/repositories/EntitiesApiRepository.ts b/app/assets/javascripts/covid19/src/data/repositories/EntitiesApiRepository.ts new file mode 100644 index 000000000..6eec30ba4 --- /dev/null +++ b/app/assets/javascripts/covid19/src/data/repositories/EntitiesApiRepository.ts @@ -0,0 +1,179 @@ +import _, { pick } from "lodash"; +import { routes } from "../../routes"; +import { RequestError, getValidatedJSON } from "../utils/request-utils"; +import { FutureData } from "../../domain/entities/FutureData"; +import { BasicNSPTarget, NSPTarget } from "../../domain/entities/Covid19Info"; +import { NMRPagination, EntitiesRepository } from "../../domain/repositories/EntitiesRepository"; +import { nmrFragmentCodec, NMRScreeningFragment } from "../NMRScreening"; +import { getResults, paginationCodec } from "../codec-utils"; +import { Future } from "../utils/future"; +import { lookup } from "mime-types"; +import FileSaver from "file-saver"; +import i18n from "../../utils/i18n"; + +export class EntitiesApiRepository implements EntitiesRepository { + getPartialNMRTarget( + target: BasicNSPTarget, + pagination: NMRPagination + ): FutureData<{ target: NSPTarget; pagination: NMRPagination }> { + const { uniprotId, start: _start, end: _end, name } = target; //don't want to remove start & end + const { bionotesApi } = routes; + const nmrTarget$ = getValidatedJSON( + `${bionotesApi}/nmr/${uniprotId}/?target=${name}&limit=${pagination.pageSize}&page=${ + pagination.page + 1 + }`, + paginationCodec(nmrFragmentCodec) + ).flatMap(p => + getNMRTarget(uniprotId, getResults(p)).map(target => ({ + pagination: p + ? { ...pagination, page: pagination.page - 1, count: p.count } + : pagination, + target, + })) + ); + + return nmrTarget$; + } + + getNMRTarget(target: BasicNSPTarget): FutureData { + const { uniprotId, start: _start, end: _end, name } = target; + const { bionotesApi } = routes; + const chunkSize = 50; + const targetChunk$ = (page: number) => + getValidatedJSON( + `${bionotesApi}/nmr/${uniprotId}/?target=${name}&limit=${chunkSize}&page=${ + page + 1 + }`, + paginationCodec(nmrFragmentCodec) + ).flatMap(pagination => getNMRTarget(uniprotId, getResults(pagination))); + + const nmrTarget$ = getValidatedJSON( + `${bionotesApi}/nmr/${uniprotId}/?target=${name}&limit=1`, + paginationCodec(nmrFragmentCodec) + ) + .flatMap(pagination => { + const pages = Math.ceil((pagination?.count ?? 0) / chunkSize); + return Future.sequential(_.times(pages).map(page => targetChunk$(page))); + }) + .flatMap( + (targets): Future => + _.isEmpty(targets) + ? Future.error({ message: "No targets" }) + : Future.success(targets) + ) + .map(targets => + targets.reduce((acc, v) => ({ + ...acc, + bindingCount: acc.bindingCount + v.bindingCount, + notBindingCount: acc.notBindingCount + v.notBindingCount, + fragments: [...acc.fragments, ...v.fragments], + })) + ); + + return nmrTarget$; + } + + saveNMRTarget(target: NSPTarget) { + const targetKeys = ["name", "uniprotId", "start", "end", "fragments"]; + const fragmentKeys = ["name", "ligand", "binding"]; + const ligandKeys = ["formula", "inChI", "name", "pubchemId", "smiles"]; + + const fragments = target.fragments.map(f => { + const fragment = { + ...f, + ligand: pick(f.ligand, ligandKeys), + }; + + return pick(fragment, fragmentKeys); + }); + + const t = { + ...target, + fragments, + }; + + const content = pick(t, targetKeys); + const contents = JSON.stringify(content, null, 4); + + return this.save({ + contents, + name: `${target.name.toLowerCase().replaceAll(/\s/g, "-")}`, + extension: "json", + }); + } + + private save(options: { name: string; contents: string; extension: string }) { + const { name, extension, contents } = options; + const filename = `${name}.${extension}`; + const mimeType = lookup(filename); + const blob = new Blob([contents], { type: mimeType || undefined }); + FileSaver.saveAs(blob, filename); + } +} + +export function getNMRTarget( + uniprotId: string, + nmrScreenings: NMRScreeningFragment[] +): FutureData { + const fragments = nmrScreenings.map(nmr => ({ + ...nmr, + binding: !nmr.details.type.toLowerCase().includes("not"), + })); + + const targets = _(fragments) + .groupBy(i => i.details.entity) + .toPairs() + .value(); + + const target = targets[0]; + if (!target) + return Future.error({ + message: i18n.t("NMR Error: no target found", { nsSeparator: false }), + }); + if (targets.length > 1) + return Future.error({ + message: i18n.t( + `NMR Error: target should only be one. Instead received ${targets.length}.`, + { nsSeparator: false } + ), + }); + + const [targetName, targetFragments] = target; + + const tFragments = targetFragments.map( + ({ name, description, externalLink, binding, ligandentity, start, end }) => ({ + name, + description, + externalLink, + binding, + ligand: { + ...ligandentity, + inChI: ligandentity.IUPACInChIkey, + smiles: ligandentity.canonicalSMILES, + pubchemId: ligandentity.pubChemCompoundId, + }, + start, + end, + }) + ); + + const start = _.first(fragments.map(({ start }) => start)); + const end = _.first(fragments.map(({ end }) => end)); + if (!start || !end) + return Future.error({ + message: i18n.t( + "NMR Unexpected Error: no start / no end on fragments. Unable to get target.", + { nsSeparator: false } + ), + }); + + return Future.success({ + name: targetName, + uniprotId, + fragments: tFragments, + bindingCount: fragments.filter(({ binding }) => binding).length, + notBindingCount: fragments.filter(({ binding }) => !binding).length, + start, + end, + }); +} diff --git a/app/assets/javascripts/covid19/src/data/repositories/LocalStorageCacheRepository.ts b/app/assets/javascripts/covid19/src/data/repositories/LocalStorageCacheRepository.ts deleted file mode 100644 index e3d788810..000000000 --- a/app/assets/javascripts/covid19/src/data/repositories/LocalStorageCacheRepository.ts +++ /dev/null @@ -1,13 +0,0 @@ -import { CacheRepository } from "../../domain/repositories/CacheRepository"; - -export class LocalStorageCacheRepository implements CacheRepository { - get(key: string): T | undefined { - const value = localStorage.getItem(key); - return value === null ? undefined : (JSON.parse(value) as T); - } - - set(key: string, value: T): void { - const json = JSON.stringify(value); - localStorage.setItem(key, json); - } -} diff --git a/app/assets/javascripts/covid19/src/data/repositories/SourcesApiRepository.ts b/app/assets/javascripts/covid19/src/data/repositories/SourcesApiRepository.ts new file mode 100644 index 000000000..5d08a8a8b --- /dev/null +++ b/app/assets/javascripts/covid19/src/data/repositories/SourcesApiRepository.ts @@ -0,0 +1,87 @@ +import { Codec, exactly, string } from "purify-ts"; +import { FutureData } from "../../domain/entities/FutureData"; +import { Source } from "../../domain/entities/Source"; +import { SourcesRepository } from "../../domain/repositories/SourcesRepository"; +import { routes } from "../../routes"; +import { getResults, paginationCodec } from "../codec-utils"; +import { Future } from "../utils/future"; +import { getValidatedJSON } from "../utils/request-utils"; + +export class SourcesApiRepository implements SourcesRepository { + get(): FutureData { + const { bionotesApi } = routes; + + const refinedModelSources$ = getValidatedJSON( + `${bionotesApi}/refinedModelSources/`, + paginationCodec(modelSourcesCodec) + ).map(getResults); + + const refinedModelMethods$ = getValidatedJSON( + `${bionotesApi}/refinedModelMethods/`, + paginationCodec(modelMethodsCodec) + ).map(getResults); + + const nmr$ = getValidatedJSON( + `${bionotesApi}/nmr/source/`, + paginationCodec(nmrMethodCodec) + ).map(getResults); + + return Future.joinObj({ + refinedModelSources: refinedModelSources$, + refinedModelMethods: refinedModelMethods$, + nmr: nmr$, + }).map(({ refinedModelSources, refinedModelMethods, nmr }) => { + // Manually adding NMR and IDR sources + // BWS should be grouped in only one endpoint for all sources, and grouping even methods + const nmrSource: Source = { + name: "NMR", + description: "The COVID19-NMR Consortium", + externalLink: "https://covid19-nmr.de/", + methods: nmr, + }; + + const refinedSources = refinedModelSources.map(source => ({ + ...source, + methods: refinedModelMethods.filter(method => method.source === source.name), + })); + + return [...refinedSources, idrSource, nmrSource]; + }); + } +} + +const refinedSources = ["CERES", "CSTF", "PDB-REDO"] as const; + +const modelSourcesCodec = Codec.interface({ + name: exactly(...refinedSources), + description: string, + externalLink: string, +}); + +const modelMethodsCodec = Codec.interface({ + source: exactly(...refinedSources), + name: string, + description: string, + externalLink: string, +}); + +const nmrMethodCodec = Codec.interface({ + name: string, + description: string, + externalLink: string, +}); + +const idrSource: Source = { + name: "IDR", + description: + "The Image Data Resource (IDR) is a public repository of image datasets from published scientific studies, where the community can submit, search and access high-quality bio-image data.", + externalLink: "https://idr.openmicroscopy.org/", + methods: [ + { + name: "IDR", + description: + "High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets. (Source Accession: EFO_0007553)", + externalLink: "https://idr.openmicroscopy.org/", + }, + ], +}; diff --git a/app/assets/javascripts/covid19/src/data/utils/future.ts b/app/assets/javascripts/covid19/src/data/utils/future.ts index e2bd117c9..a29a79ed2 100644 --- a/app/assets/javascripts/covid19/src/data/utils/future.ts +++ b/app/assets/javascripts/covid19/src/data/utils/future.ts @@ -60,6 +60,10 @@ export class Future { return new Future(instance); } + static sequential(futures: Array>): Future> { + return Future.parallel(futures, { maxConcurrency: 1 }); + } + static parallel( futures: Array>, options: { maxConcurrency?: number } = {} diff --git a/app/assets/javascripts/covid19/src/data/utils/request-utils.ts b/app/assets/javascripts/covid19/src/data/utils/request-utils.ts index 5dd5bc25a..332446c6d 100644 --- a/app/assets/javascripts/covid19/src/data/utils/request-utils.ts +++ b/app/assets/javascripts/covid19/src/data/utils/request-utils.ts @@ -5,10 +5,11 @@ import { axiosRequest, defaultBuilder, RequestResult } from "../utils/future-axi import { Future } from "../utils/future"; import { Maybe } from "../utils/ts-utils"; import { FutureData } from "../../domain/entities/FutureData"; +import i18n from "../../utils/i18n"; export type RequestError = { message: string }; -const timeout = 20e3; +const timeout = 75e3; export function getFromUrl(url: string): Future { return request({ method: "GET", url, timeout }).map(res => res.data); @@ -20,6 +21,7 @@ export function getTextFromUrl(url: string): Future { url, timeout, responseType: "text", + timeoutErrorMessage: i18n.t("Request timed out: " + timeout / 1000 + " seconds"), transformResponse: [data => data], }).map(res => res.data); } diff --git a/app/assets/javascripts/covid19/src/domain/entities/Covid19Info.ts b/app/assets/javascripts/covid19/src/domain/entities/Covid19Info.ts index 09837672b..01b15a3a7 100644 --- a/app/assets/javascripts/covid19/src/domain/entities/Covid19Info.ts +++ b/app/assets/javascripts/covid19/src/domain/entities/Covid19Info.ts @@ -2,6 +2,7 @@ import _ from "lodash"; import i18n from "../../utils/i18n"; export interface Covid19Info { + count: number; structures: Structure[]; validationSources: ValidationSource[]; } @@ -35,18 +36,26 @@ export interface Entity { isAntibody: boolean; isNanobody: boolean; isSybody: boolean; + targets: BasicNSPTarget[]; } export interface Ligand { id: Id; name: string; - details: string; imageLink: Url; externalLink: Url; inChI: string; //IUPACInChIkey hasIDR: boolean; } +export interface NMRLigand { + name: string; + inChI: string; //IUPACInChIkey + smiles: string; + formula: string; + pubchemId: string; +} + export interface LigandInstance { info: Ligand; instances: number; @@ -110,43 +119,28 @@ export interface ValidationSource { } export interface ValidationMethod { - name: MethodName; + name: string; description: string; externalLink: string; } -export interface Validation { +interface Validation { externalLink?: Url; queryLink?: Url; badgeColor: W3Color; } export interface PdbValidation extends Validation { - source: PdbSourceName; - method: PdbMethodName; -} - -export interface EmdbValidation extends Validation { - source: EmdbSourceName; - method: EmdbMethodName; + source: SourceName; + method: string; } export interface Validations { pdb: PdbValidation[]; - emdb: EmdbValidation[]; + emdb: never[]; } -export type SourceName = PdbSourceName | EmdbSourceName | "IDR"; - -export type MethodName = PdbMethodName | EmdbMethodName | "IDR"; - -export type PdbSourceName = "PDB-REDO" | "CSTF" | "CERES"; - -export type PdbMethodName = "PDB-Redo" | "Isolde" | "Refmac" | "PHENIX"; - -export type EmdbSourceName = ""; - -export type EmdbMethodName = "DeepRes" | "MonoRes" | "BlocRes" | "Map-Q" | "FSC-Q"; +export type SourceName = "PDB-REDO" | "CSTF" | "CERES" | "IDR" | "NMR"; export interface Pdb extends DbItem { keywords: string; @@ -204,6 +198,26 @@ export interface Details { refdoc?: RefDoc[]; } +export interface BasicNSPTarget { + uniprotId: string; + start: number; + end: number; + name: string; +} + +export interface NSPTarget extends BasicNSPTarget { + name: string; + fragments: NMRFragment[]; + bindingCount: number; + notBindingCount: number; +} + +export interface NMRFragment { + name: string; + binding: boolean; + ligand: NMRLigand; +} + export const filterKeys = [ "antibodies", "nanobodies", @@ -212,46 +226,13 @@ export const filterKeys = [ "cstf", "ceres", "idr", + "nmr", ] as const; export type FilterKey = typeof filterKeys[number]; export type Covid19Filter = Record; -export function filterEntities(entities: Entity[], filterState: Covid19Filter): Entity[] { - return entities.filter( - entity => - entity.isAntibody === filterState.antibodies && - entity.isNanobody === filterState.nanobodies && - entity.isSybody === filterState.sybodies - ); -} - -export function filterLigands(ligands: Ligand[]): Ligand[] { - return ligands.filter(ligand => ligand.hasIDR); -} - -export function filterPdbValidations( - PdbValidations: PdbValidation[], - filterState: Covid19Filter -): boolean { - return ( - (!filterState.pdbRedo || _.some(PdbValidations, v => v?.source === "PDB-REDO")) && - (!filterState.cstf || _.some(PdbValidations, v => v?.source === "CSTF")) && - (!filterState.ceres || _.some(PdbValidations, v => v?.source === "CERES")) - ); -} - -export function updateStructures(data: Covid19Info, structures: Structure[]): Covid19Info { - if (_.isEmpty(structures)) return data; - const structuresById = _.keyBy(structures, structure => structure.id); - const structures2 = data.structures.map(structure => structuresById[structure.id] || structure); - const hasChanges = _(data.structures) - .zip(structures2) - .some(([s1, s2]) => s1 !== s2); - return hasChanges ? { ...data, structures: structures2 } : data; -} - export function getTranslations() { return { filterKeys: { @@ -262,6 +243,7 @@ export function getTranslations() { cstf: i18n.t("CSTF"), ceres: i18n.t("CERES"), idr: i18n.t("IDR"), + nmr: i18n.t("CV19-NMR-C"), } as Record, }; } diff --git a/app/assets/javascripts/covid19/src/domain/entities/Source.ts b/app/assets/javascripts/covid19/src/domain/entities/Source.ts new file mode 100644 index 000000000..2458c302b --- /dev/null +++ b/app/assets/javascripts/covid19/src/domain/entities/Source.ts @@ -0,0 +1,16 @@ +/* Transition from JSON to API, co-existing with ValidationSource[] for now */ + +type Reference = { + name: string; + description: string; + externalLink: string; +}; + +type Method = Reference; + +export type Source = Reference & { + name: SourceName; + methods: Method[]; +}; + +type SourceName = "CERES" | "CSTF" | "PDB-REDO" | "IDR" | "NMR"; diff --git a/app/assets/javascripts/covid19/src/domain/repositories/CacheRepository.ts b/app/assets/javascripts/covid19/src/domain/repositories/CacheRepository.ts deleted file mode 100644 index 0f4500502..000000000 --- a/app/assets/javascripts/covid19/src/domain/repositories/CacheRepository.ts +++ /dev/null @@ -1,20 +0,0 @@ -export interface CacheRepository { - get(key: string): T | undefined; - set(key: string, value: T): void; -} - -export async function fromCache( - repository: CacheRepository, - options: { key: string; get: () => Promise } -): Promise { - const { key, get } = options; - const valueFromCache = repository.get(key); - - if (valueFromCache !== undefined) { - return valueFromCache; - } else { - const value = await get(); - repository.set(key, value); - return value; - } -} diff --git a/app/assets/javascripts/covid19/src/domain/repositories/Covid19InfoRepository.ts b/app/assets/javascripts/covid19/src/domain/repositories/Covid19InfoRepository.ts index a6bf62afe..786e8d615 100644 --- a/app/assets/javascripts/covid19/src/domain/repositories/Covid19InfoRepository.ts +++ b/app/assets/javascripts/covid19/src/domain/repositories/Covid19InfoRepository.ts @@ -1,13 +1,20 @@ import { Covid19Info, Covid19Filter } from "../entities/Covid19Info"; +import { FutureData } from "../entities/FutureData"; export interface Covid19InfoRepository { - get(): Covid19Info; - search(options: SearchOptions): Covid19Info; - autoSuggestions(search: string): string[]; + get(options: GetOptions): FutureData; + autoSuggestions(search: string): FutureData; } -export interface SearchOptions { - data: Covid19Info; - search?: string; - filter?: Covid19Filter; +export type SortingFields = "pdb" | "emdb" | "title" | "releaseDate"; + +export interface GetOptions { + page: number; + pageSize: number; + filter: Covid19Filter; + sort: { + field: SortingFields; + order: "asc" | "desc"; + }; + query?: string; } diff --git a/app/assets/javascripts/covid19/src/domain/repositories/EntitiesRepository.ts b/app/assets/javascripts/covid19/src/domain/repositories/EntitiesRepository.ts new file mode 100644 index 000000000..557385794 --- /dev/null +++ b/app/assets/javascripts/covid19/src/domain/repositories/EntitiesRepository.ts @@ -0,0 +1,17 @@ +import { BasicNSPTarget, NSPTarget } from "../entities/Covid19Info"; +import { FutureData } from "../entities/FutureData"; + +export interface EntitiesRepository { + getPartialNMRTarget: ( + target: BasicNSPTarget, + pagination: NMRPagination + ) => FutureData<{ target: NSPTarget; pagination: NMRPagination }>; + getNMRTarget: (target: BasicNSPTarget) => FutureData; + saveNMRTarget: (target: NSPTarget) => void; +} + +export interface NMRPagination { + page: number; + pageSize: number; + count: number; +} diff --git a/app/assets/javascripts/covid19/src/domain/repositories/SourcesRepository.ts b/app/assets/javascripts/covid19/src/domain/repositories/SourcesRepository.ts new file mode 100644 index 000000000..0ca11544b --- /dev/null +++ b/app/assets/javascripts/covid19/src/domain/repositories/SourcesRepository.ts @@ -0,0 +1,6 @@ +import { FutureData } from "../entities/FutureData"; +import { Source } from "../entities/Source"; + +export interface SourcesRepository { + get(): FutureData; +} diff --git a/app/assets/javascripts/covid19/src/domain/usecases/AddDynamicInfoToCovid19InfoUseCase.ts b/app/assets/javascripts/covid19/src/domain/usecases/AddDynamicInfoToCovid19InfoUseCase.ts deleted file mode 100644 index 9cec6774d..000000000 --- a/app/assets/javascripts/covid19/src/domain/usecases/AddDynamicInfoToCovid19InfoUseCase.ts +++ /dev/null @@ -1,26 +0,0 @@ -import _ from "lodash"; -import { Covid19Info, Structure } from "../entities/Covid19Info"; -import { CacheRepository } from "../repositories/CacheRepository"; -import { Covid19InfoRepository } from "../repositories/Covid19InfoRepository"; - -export class AddDynamicInfoToCovid19InfoUseCase { - constructor( - private covid19InfoRepository: Covid19InfoRepository, - private cacheRepository: CacheRepository - ) {} - - execute(data: Covid19Info, options: { ids: string[] }): Promise { - return this.getStructures(data, options); - } - - async getStructures(data: Covid19Info, options: { ids: string[] }): Promise { - if (_.isEmpty(options.ids)) return []; - - const structuresById = _.keyBy(data.structures, structure => structure.id); - const structuresToUpdate = _(structuresById).at(options.ids).compact().value(); - - const structuresUpdated$ = structuresToUpdate; - - return Promise.all(structuresUpdated$); - } -} diff --git a/app/assets/javascripts/covid19/src/domain/usecases/GetCovid19InfoUseCase.ts b/app/assets/javascripts/covid19/src/domain/usecases/GetCovid19InfoUseCase.ts index a0b65ec6c..9b6413cbd 100644 --- a/app/assets/javascripts/covid19/src/domain/usecases/GetCovid19InfoUseCase.ts +++ b/app/assets/javascripts/covid19/src/domain/usecases/GetCovid19InfoUseCase.ts @@ -1,9 +1,12 @@ -import { Covid19InfoRepository } from "../repositories/Covid19InfoRepository"; +import _ from "lodash"; +import { Covid19InfoRepository, GetOptions } from "../repositories/Covid19InfoRepository"; +import { FutureData } from "../entities/FutureData"; +import { Covid19Info } from "../entities/Covid19Info"; export class GetCovid19InfoUseCase { constructor(private covid19InfoRepository: Covid19InfoRepository) {} - execute() { - return this.covid19InfoRepository.get(); + execute(options: GetOptions): FutureData { + return this.covid19InfoRepository.get(options); } } diff --git a/app/assets/javascripts/covid19/src/domain/usecases/GetPartialNMRTargetUseCase.ts b/app/assets/javascripts/covid19/src/domain/usecases/GetPartialNMRTargetUseCase.ts new file mode 100644 index 000000000..85c00a8f6 --- /dev/null +++ b/app/assets/javascripts/covid19/src/domain/usecases/GetPartialNMRTargetUseCase.ts @@ -0,0 +1,10 @@ +import { BasicNSPTarget } from "../entities/Covid19Info"; +import { EntitiesRepository, NMRPagination } from "../repositories/EntitiesRepository"; + +export class GetPartialNMRTargetUseCase { + constructor(private entitiesRepository: EntitiesRepository) {} + + execute(target: BasicNSPTarget, pagination: NMRPagination) { + return this.entitiesRepository.getPartialNMRTarget(target, pagination); + } +} diff --git a/app/assets/javascripts/covid19/src/domain/usecases/GetSourcesUseCase.ts b/app/assets/javascripts/covid19/src/domain/usecases/GetSourcesUseCase.ts new file mode 100644 index 000000000..865b6fd27 --- /dev/null +++ b/app/assets/javascripts/covid19/src/domain/usecases/GetSourcesUseCase.ts @@ -0,0 +1,11 @@ +import { FutureData } from "../entities/FutureData"; +import { Source } from "../entities/Source"; +import { SourcesRepository } from "../repositories/SourcesRepository"; + +export class GetSourcesUseCase { + constructor(private sourcesRepository: SourcesRepository) {} + + execute(): FutureData { + return this.sourcesRepository.get(); + } +} diff --git a/app/assets/javascripts/covid19/src/domain/usecases/SaveNMRTargetUseCase.ts b/app/assets/javascripts/covid19/src/domain/usecases/SaveNMRTargetUseCase.ts new file mode 100644 index 000000000..2dcda4f26 --- /dev/null +++ b/app/assets/javascripts/covid19/src/domain/usecases/SaveNMRTargetUseCase.ts @@ -0,0 +1,12 @@ +import { BasicNSPTarget } from "../entities/Covid19Info"; +import { EntitiesRepository } from "../repositories/EntitiesRepository"; + +export class SaveNMRTargetUseCase { + constructor(private entitiesRepository: EntitiesRepository) {} + + execute(target: BasicNSPTarget) { + return this.entitiesRepository + .getNMRTarget(target) + .map(target => this.entitiesRepository.saveNMRTarget(target)); + } +} diff --git a/app/assets/javascripts/covid19/src/domain/usecases/SearchCovid19InfoUseCase.ts b/app/assets/javascripts/covid19/src/domain/usecases/SearchCovid19InfoUseCase.ts deleted file mode 100644 index f6660e9e8..000000000 --- a/app/assets/javascripts/covid19/src/domain/usecases/SearchCovid19InfoUseCase.ts +++ /dev/null @@ -1,9 +0,0 @@ -import { Covid19InfoRepository, SearchOptions } from "../repositories/Covid19InfoRepository"; - -export class SearchCovid19InfoUseCase { - constructor(private covid19InfoRepository: Covid19InfoRepository) {} - - execute(options: SearchOptions) { - return this.covid19InfoRepository.search(options); - } -} diff --git a/app/assets/javascripts/covid19/src/domain/usecases/common/StorageProvider.ts b/app/assets/javascripts/covid19/src/domain/usecases/common/StorageProvider.ts new file mode 100644 index 000000000..6b8c2c1f0 --- /dev/null +++ b/app/assets/javascripts/covid19/src/domain/usecases/common/StorageProvider.ts @@ -0,0 +1,3 @@ +export interface StorageProvider { + get(options: { key: string; getter: () => T }): T; +} diff --git a/app/assets/javascripts/covid19/src/routes.ts b/app/assets/javascripts/covid19/src/routes.ts index fd1975331..d8524de01 100644 --- a/app/assets/javascripts/covid19/src/routes.ts +++ b/app/assets/javascripts/covid19/src/routes.ts @@ -1,7 +1,8 @@ /* On DEV, proxy requests (to circumvent CORS) and cache them (see src/setupProxy.js) */ -const isDev = process.env.NODE_ENV === "development"; +export const isDev = process.env.NODE_ENV === "development"; +const route = process.env.REACT_APP_BWS; export const routes = { - bionotesApi: isDev ? "http://3dbionotes.cnb.csic.es/bws/api" : `/bws/api`, + bionotesApi: isDev ? `${route}/api` : `/bws/api`, }; diff --git a/app/assets/javascripts/covid19/src/utils/analytics.ts b/app/assets/javascripts/covid19/src/utils/analytics.ts index 47013eb9c..d9c9dba62 100644 --- a/app/assets/javascripts/covid19/src/utils/analytics.ts +++ b/app/assets/javascripts/covid19/src/utils/analytics.ts @@ -1,6 +1,8 @@ +declare function gtag(type: "event", name: string, data?: object): void; + export function sendAnalytics(name: string, data?: object) { if (window.gtag !== undefined) - window.gtag( + gtag( "event", name, data && { @@ -10,5 +12,4 @@ export function sendAnalytics(name: string, data?: object) { location_href: window.location.href, } ); - else throw new Error("gtag() function has not been declared."); } diff --git a/app/assets/javascripts/covid19/src/webapp/components/app/App.tsx b/app/assets/javascripts/covid19/src/webapp/components/app/App.tsx index 2dd7a4a5f..fed29a110 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/app/App.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/app/App.tsx @@ -1,7 +1,8 @@ import React from "react"; +import { SnackbarProvider } from "@eyeseetea/d2-ui-components/snackbar"; import { getCompositionRoot } from "../../../compositionRoot"; import { Covid19Info } from "../../../domain/entities/Covid19Info"; -import { AppContext } from "../../contexts/app-context"; +import { AppContext, AppContextState } from "../../contexts/app-context"; import { Root } from "./Root"; import "./App.css"; @@ -11,15 +12,25 @@ declare global { } } -interface AppProps {} +const compositionRoot = getCompositionRoot(); -export const App: React.FC = React.memo(() => { - const compositionRoot = getCompositionRoot(); - const appContext = { compositionRoot, config: {} }; +export const App = React.memo(() => { + const [appContext, setAppContext] = React.useState({ + compositionRoot, + sources: [], + }); + + React.useEffect(() => { + compositionRoot.getSources + .execute() + .run(sources => setAppContext({ compositionRoot, sources }), console.error); + }, []); return ( - + + + ); }); diff --git a/app/assets/javascripts/covid19/src/webapp/components/loader-mask/LoaderMask.tsx b/app/assets/javascripts/covid19/src/webapp/components/loader-mask/LoaderMask.tsx new file mode 100644 index 000000000..14d3f0334 --- /dev/null +++ b/app/assets/javascripts/covid19/src/webapp/components/loader-mask/LoaderMask.tsx @@ -0,0 +1,56 @@ +import React from "react"; +import { Backdrop, CircularProgress, makeStyles } from "@material-ui/core"; +import { Cancel as CancelIcon } from "@material-ui/icons"; +import { isDev } from "../../../routes"; +import styled from "styled-components"; + +interface LoaderProps { + open: boolean; + title?: string; + errorThrown?: boolean; +} + +export const LoaderMask: React.FC = React.memo(props => { + const classes = useStyles(); + const { open, title, errorThrown } = props; + + return ( + + + {errorThrown ? : } + {title &&

{title}

} +
+
+ ); +}); + +const useStyles = makeStyles(theme => ({ + backdrop: { + height: !isDev ? "calc(100vh - 85px)" : undefined, + top: !isDev ? 85 : undefined, + zIndex: theme.zIndex.tooltip + 1, + color: "#fff", + backgroundColor: "rgba(0, 0, 0, 0.7)", + position: "fixed", + pointerEvents: "none", + }, + title: { + fontWeight: "bold", + fontSize: "1em", + marginTop: "1em", + letterSpacing: "0.25px", + }, +})); + +const Container = styled.div` + & { + display: flex; + flex-direction: column; + align-items: center; + justify-content: center; + } + + & .MuiCircularProgress-colorPrimary { + color: #fff !important; + } +`; diff --git a/app/assets/javascripts/covid19/src/webapp/components/proteome/ProteomePath.tsx b/app/assets/javascripts/covid19/src/webapp/components/proteome/ProteomePath.tsx index 069988330..b26adf4cf 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/proteome/ProteomePath.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/proteome/ProteomePath.tsx @@ -20,7 +20,7 @@ export const ProteomePath: React.FC = React.memo(props => { const triggerSearch = React.useCallback(() => { setSearch( - details && details.gen === "Nucleoprotein" ? `${details.gen} ${name}` : `"${name}"` + details && details.gen === "Nucleoprotein" ? `${details.gen} ${name}` : `${name}` ); setProteomeSelected(true); toggleProteome(); diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/Columns.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Columns.tsx index 2780fc9ab..af3997e13 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/Columns.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Columns.tsx @@ -1,28 +1,21 @@ import React from "react"; -import { - GridColDef, - GridCellValue, - GridSortCellParams, - GridStateApi, -} from "@material-ui/data-grid"; +import { GridColDef } from "@material-ui/data-grid"; import _ from "lodash"; import i18n from "../../../utils/i18n"; -import { - Covid19Info, - Ligand, - Structure, - ValidationSource, -} from "../../../domain/entities/Covid19Info"; +import { Covid19Info, Ligand, NSPTarget, Structure } from "../../../domain/entities/Covid19Info"; import { TitleCell } from "./cells/TitleCell"; import { DetailsCell } from "./cells/DetailsCell"; import { PdbCell } from "./cells/PdbCell"; import { EmdbCell } from "./cells/EmdbCell"; -import { EntityCell } from "./cells/EntityCell"; +import { EntitiyCellProps, EntityCell } from "./cells/EntityCell"; import { LigandsCell, LigandsCellProps } from "./cells/LigandsCell"; import { OrganismCell } from "./cells/OrganismCell"; import { LigandImageData } from "../../../domain/entities/LigandImageData"; import { OnClickDetails } from "./badge/BadgeDetails"; import { OnClickIDR } from "./badge/BadgeLigands"; +import { OnClickNMR } from "./badge/BadgeEntities"; +import { NMRPagination } from "../../../domain/repositories/EntitiesRepository"; +import { SetNMROptions } from "./StructuresTable"; type Row = Structure; export type Field = keyof Row; @@ -34,6 +27,19 @@ export interface IDROptions { error?: string; } +export interface NMROptions { + target?: NSPTarget; + pagination?: NMRPagination; + setPagination?: SetNMRPagination; + error?: string; + loading?: boolean; +} + +export interface SetNMRPagination { + setPage: (page: number) => void; + setPageSize: (pageSize: number) => void; +} + export interface DetailsDialogOptions { row: Structure; field: Field; @@ -43,7 +49,6 @@ export interface CellProps { data: Covid19Info; row: Row; moreDetails?: boolean; - validationSources?: ValidationSource[]; onClickDetails?: OnClickDetails; } @@ -51,7 +56,7 @@ export interface ColumnAttrs extends Omit { headerName: string; field: F; - renderCell: React.FC | React.FC; + renderCell: React.FC | React.FC | React.FC; renderString(row: Row): string | undefined; } @@ -59,47 +64,54 @@ function column(field: F, options: Omit, "field" return { ...options, field, hide: false, headerAlign: "center" }; } +export const columnsWidths = { + title: 220, + pdb: 150, + emdb: 120, + related: 180, +}; + export type Columns = ColumnAttrs[]; export const columnsBase: Columns = [ column("title", { headerName: i18n.t("Title"), sortable: true, - width: 220, + width: columnsWidths.title, renderCell: TitleCell, renderString: row => row.title, }), column("pdb", { headerName: i18n.t("PDB"), - width: 150, + width: columnsWidths.pdb, + sortable: true, renderCell: PdbCell, - sortComparator: compareIds, renderString: row => row.pdb?.id, }), column("emdb", { headerName: i18n.t("EMDB"), - width: 120, + width: columnsWidths.emdb, + sortable: true, renderCell: EmdbCell, - sortComparator: compareIds, renderString: row => row.emdb?.id, }), column("entities", { headerName: i18n.t("Entities"), - width: 180, + width: columnsWidths.related, sortable: false, renderCell: EntityCell, renderString: row => row.entities.map(entity => entity.name).join(", "), }), column("ligands", { headerName: i18n.t("Ligands"), - width: 180, + width: columnsWidths.related, sortable: false, renderCell: LigandsCell, renderString: row => row.ligands.map(ligand => ligand.name).join(", "), }), column("organisms", { headerName: i18n.t("Organisms"), - width: 180, + width: columnsWidths.related, sortable: false, renderCell: OrganismCell, renderString: row => @@ -116,7 +128,7 @@ export const columnsBase: Columns = [ column("details", { headerName: i18n.t("Details"), hide: false, - width: 200, + flex: 1, sortable: false, renderCell: DetailsCell, renderString: row => { @@ -157,6 +169,8 @@ export function getColumns( options: { onClickDetails: OnClickDetails; onClickIDR: OnClickIDR; + onClickNMR: OnClickNMR; + setNMROptions: SetNMROptions; } ): { definition: GridColDef[]; base: Columns } { const definition = columnsBase.map( @@ -174,7 +188,8 @@ export function getColumns( data={data} onClickDetails={options.onClickDetails} onClickIDR={options.onClickIDR} - validationSources={data.validationSources} + onClickNMR={options.onClickNMR} + setNMROptions={options.setNMROptions} /> ); @@ -186,31 +201,6 @@ export function getColumns( return { definition, base: columnsBase }; } -type Ref = { id?: string }; - -/* Compare IDs keeping always empty values to the end (it only supports single column sorting) */ -function compareIds( - cell1: GridCellValue | undefined, - cell2: GridCellValue | undefined, - cellParams1: GridSortCellParams -): number { - const id1 = (cell1 as Ref)?.id; - const id2 = (cell2 as Ref)?.id; - - const isAsc = (cellParams1.api as GridStateApi).state.sorting.sortModel[0]?.sort === "asc"; - const emptyCmpValue = isAsc ? -1 : +1; - - if (id1 && id2) { - return id1 === id2 ? 0 : id1 > id2 ? +1 : -1; - } else if (id1 && !id2) { - return emptyCmpValue; - } else if (!id1 && id2) { - return -emptyCmpValue; - } else { - return 0; - } -} - export const styles = { link: { textDecoration: "none" }, column: { lineHeight: 1 }, // Allows multi-line values in cells diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/CustomCheckboxFilter.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/CustomCheckboxFilter.tsx index ba7fb6a93..b3331f3ec 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/CustomCheckboxFilter.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/CustomCheckboxFilter.tsx @@ -14,15 +14,16 @@ import { } from "../../../domain/entities/Covid19Info"; import { HtmlTooltip } from "./HtmlTooltip"; import i18n from "../../../utils/i18n"; +import { useAppContext } from "../../contexts/app-context"; export interface CustomCheckboxFilterProps { setFilterState: (value: React.SetStateAction) => void; - validationSources: ValidationSource[]; filterState: Covid19Filter; } export const CustomCheckboxFilter: React.FC = React.memo(props => { - const { filterState, setFilterState, validationSources } = props; + const { filterState, setFilterState } = props; + const { sources: validationSources } = useAppContext(); const [anchorEl, setAnchorEl] = React.useState(null); const isOpen = Boolean(anchorEl); const openMenu = React.useCallback(event => setAnchorEl(event.currentTarget), []); @@ -67,6 +68,7 @@ export const CustomCheckboxFilter: React.FC = React.m cstf: getTooltip(getValidationSource(validationSources, "CSTF")), ceres: getTooltip(getValidationSource(validationSources, "CERES")), idr: getTooltip(getValidationSource(validationSources, "IDR")), + nmr: getTooltip(getValidationSource(validationSources, "NMR")), }), [validationSources, getTooltip] ); @@ -132,6 +134,12 @@ export const CustomCheckboxFilter: React.FC = React.m setFilterState={setFilterState} tooltip={filterTooltips.idr} /> + diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/CustomGridPagination.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/CustomGridPagination.tsx index dae147235..d0e09f64b 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/CustomGridPagination.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/CustomGridPagination.tsx @@ -1,50 +1,72 @@ import React from "react"; import TablePagination from "@material-ui/core/TablePagination"; -import { DataGrid } from "../../../domain/entities/DataGrid"; +import { useSnackbar } from "@eyeseetea/d2-ui-components/snackbar"; +import { useBooleanState } from "../../hooks/useBoolean"; +import { makeStyles } from "@material-ui/styles"; export interface CustomGridPaginationProps { - dataGrid: DataGrid; + count: number; page: number; pageSize: number | undefined; pageSizes: number[]; - setPage: (param: number) => void; - setPageSize: (param: number) => void; + isLoading: boolean; + setPageSize: (pageSize: number) => void; + setPage: (newPage: number) => void; } export const CustomGridPagination: React.FC = React.memo(props => { - const { dataGrid, page, pageSize, pageSizes, setPage, setPageSize } = props; + const { count, page, pageSize, pageSizes, setPage, setPageSize, isLoading } = props; + const [showInfo, { disable: hideInfo }] = useBooleanState(true); + const snackbar = useSnackbar(); + const classes = useStyles(); - const handleChangePage = React.useCallback( + const maxPage = Math.ceil(count / (pageSize ?? 10)); + + const setPageFromEvent = React.useCallback( (_event: React.MouseEvent | null, newPage: number) => { - setPage(newPage); + setPage(newPage + 1); }, [setPage] ); - const handleChangeRowsPerPage = React.useCallback( + const changePageSize = React.useCallback( (event: React.ChangeEvent) => { - setPageSize(parseInt(event.target.value, 10)); - setPage(0); + const pageSize = parseInt(event.target.value, 10); + if (pageSize > 25 && showInfo) { + snackbar.info("Please note that larger page size may take longer to load."); + hideInfo(); + } + setPageSize(pageSize); }, - [setPageSize, setPage] + [setPageSize, snackbar, showInfo, hideInfo] + ); + + const tableProps = React.useMemo( + () => ({ + backIconButtonProps: { disabled: isLoading || page === 1 }, + nextIconButtonProps: { disabled: isLoading || page === maxPage }, + SelectProps: { disabled: isLoading }, + rowsPerPage: pageSize || 10, + }), + [isLoading, maxPage, page, pageSize] ); return ( ); }); -const styles = { - table: { float: "right" as const, borderBottom: "none" as const, padding: 0 }, -}; +const useStyles = makeStyles({ + table: { borderBottom: "none", padding: 0 }, +}); diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/DetailsDialog.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/DetailsDialog.tsx index 232f0c198..dc1782d1f 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/DetailsDialog.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/DetailsDialog.tsx @@ -5,6 +5,7 @@ import { Accordion, AccordionSummary, AccordionDetails, Typography } from "@mate import { ExpandMore as ExpandMoreIcon } from "@material-ui/icons"; import { Covid19Info, Structure } from "../../../domain/entities/Covid19Info"; import { OnClickIDR } from "./badge/BadgeLigands"; +import { OnClickNMR } from "./badge/BadgeEntities"; import { Field } from "./Columns"; import { PdbCell } from "./cells/PdbCell"; import { EmdbCell } from "./cells/EmdbCell"; @@ -13,6 +14,7 @@ import { LigandsCell } from "./cells/LigandsCell"; import { OrganismCell } from "./cells/OrganismCell"; import { DetailsCell } from "./cells/DetailsCell"; import { Dialog } from "./Dialog"; +import { SetNMROptions } from "./StructuresTable"; import i18n from "../../../utils/i18n"; export interface DetailsDialogProps { @@ -22,22 +24,39 @@ export interface DetailsDialogProps { row: Structure; data: Covid19Info; onClickIDR: OnClickIDR; + onClickNMR: OnClickNMR; + setNMROptions: SetNMROptions; } export const DetailsDialog: React.FC = React.memo(props => { - const { onClose, expandedAccordion, row, data, open, onClickIDR } = props; + const { + onClose, + expandedAccordion, + row, + data, + open, + onClickIDR, + onClickNMR, + setNMROptions, + } = props; return ( - +
- + = React.memo(props => { row={row} moreDetails={false} onClickIDR={onClickIDR} - validationSources={data.validationSources} /> diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/Dialog.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Dialog.tsx index 984a3a398..9a90c7998 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/Dialog.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Dialog.tsx @@ -9,31 +9,45 @@ export interface DialogProps { open: boolean; headerChildren?: React.ReactNode; maxWidth?: "xs" | "sm" | "md" | "lg" | "xl" | false; + fullWidth?: boolean; + scroll?: "paper" | "body"; onClose(): void; } -export const Dialog: React.FC = React.memo( - ({ onClose, className, title, open, children, maxWidth, headerChildren }) => { - return ( - - - {title} - {headerChildren} - - - - +export const Dialog: React.FC = React.memo(props => { + const { + onClose, + className, + title, + open, + children, + maxWidth, + headerChildren, + scroll, + fullWidth, + } = props; - {children} - - ); - } -); + return ( + + + {title} + {headerChildren} + + + + + + {children} + + ); +}); const StyledDialog = styled(MuiDialog)` .MuiDialog-paper { diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/Footer.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Footer.tsx new file mode 100644 index 000000000..cc94b9314 --- /dev/null +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Footer.tsx @@ -0,0 +1,91 @@ +import React from "react"; +import { Box, InputBaseComponentProps, TextField, Typography } from "@material-ui/core"; +import { CustomGridPagination, CustomGridPaginationProps } from "./CustomGridPagination"; +import { Badge } from "./badge/Badge"; +import { Maybe } from "../../../data/utils/ts-utils"; +import i18n from "../../../utils/i18n"; +import styled from "styled-components"; + +export const Footer: React.FC = React.memo(props => { + const { count, pageSize, page, setPage: handlePageChange, isLoading } = props; + + const [inputPage, setInputPage] = React.useState>(1); + + const interpolation = { + pageCount: Math.ceil(count / (pageSize ?? 10)), + }; + + const disabled = isLoading || !inputPage || inputPage === page; + + const inputProps: InputBaseComponentProps = React.useMemo( + () => ({ + min: 1, + max: Math.ceil(count / (pageSize ?? 10)), + }), + [count, pageSize] + ); + + const onInputChange = React.useCallback( + (event: React.ChangeEvent) => { + if (!event.target.value) setInputPage(undefined); + else + setInputPage( + Math.max(1, Math.min(inputProps.max, parseInt(event.target.value) || 1)) + ); + }, + [inputProps.max] + ); + + const goToPage = React.useCallback(() => { + if (!disabled && inputPage) handlePageChange(inputPage); + }, [disabled, handlePageChange, inputPage]); + + const onKeyPress = React.useCallback( + (event: React.KeyboardEvent) => { + if (event.key === "Enter") goToPage(); + }, + [goToPage] + ); + + const onInputBlur = React.useCallback(() => { + if (inputPage === undefined) setInputPage(page); + }, [inputPage, page]); + + React.useEffect(() => { + setInputPage(page); + }, [page]); + + return ( + + + {i18n.t("Page")} + + {i18n.t("of {{pageCount}}", interpolation)} + + {i18n.t("Go to page")} + + + + + ); +}); + +const StyledTextField = styled(TextField)<{ length?: number; placeholder: string }>` + .MuiFilledInput-inputMarginDense { + padding: 0.75em 0.5em; + min-width: 3em; + width: ${props => (props.length ? props.length + 2 : props.placeholder.length)}em; + } +`; diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/IDRDialog.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/IDRDialog.tsx index e836da106..17d838644 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/IDRDialog.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/IDRDialog.tsx @@ -122,7 +122,9 @@ const ListItem: React.FC = React.memo(props => { ); }); -const AssayFC: React.FC = React.memo(({ assay, dataSource }) => ( +export const NoBulletListItem = ListItem; + +export const AssayFC: React.FC = React.memo(({ assay, dataSource }) => ( <> {assay.type.reduce(reduceOntologyType, [])} diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/NMRDialog.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/NMRDialog.tsx new file mode 100644 index 000000000..3fb71b222 --- /dev/null +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/NMRDialog.tsx @@ -0,0 +1,377 @@ +import _ from "lodash"; +import React from "react"; +import styled from "styled-components"; +import { + Button, + Table, + TableBody, + TableCell, + TableContainer, + TableHead, + TablePagination, + TableRow, + Typography, + LinearProgress, + CircularProgress, + Paper, + makeStyles, +} from "@material-ui/core"; +import { GetApp, Stop as StopIcon } from "@material-ui/icons"; +import { Dialog } from "./Dialog"; +import { NMROptions, SetNMRPagination } from "./Columns"; +import { NSPTarget, getValidationSource } from "../../../domain/entities/Covid19Info"; +import { NMRPagination } from "../../../domain/repositories/EntitiesRepository"; +import { useBooleanState } from "../../hooks/useBoolean"; +import { useAppContext } from "../../contexts/app-context"; +import { NoBulletListItem as ListItem } from "./IDRDialog"; +import { Cancel } from "../../../data/utils/future"; +import i18n from "../../../utils/i18n"; + +export interface NMRDialogProps { + onClose(): void; + nmrOptions: NMROptions; + open: boolean; +} + +export const NMRDialog: React.FC = React.memo(props => { + const { onClose, open } = props; + const { target, error, pagination, setPagination, loading } = props.nmrOptions; + const { compositionRoot, sources } = useAppContext(); + const [isExporting, { enable: showExporting, disable: hideExporting }] = useBooleanState(false); + + const classes = useStyles(); + + const nmrSource = React.useMemo(() => getValidationSource(sources, "NMR"), [sources]); + const nmrMethod = nmrSource?.methods[0]; + + const title = `${i18n.t("NMR-based fragment screening on")}: ${target?.name ?? ""}`; + + const saveTarget = React.useCallback(() => { + if (target) { + showExporting(); + return compositionRoot.entities.saveNMR.execute(target).run( + () => { + hideExporting(); + }, + err => { + console.error(err); + hideExporting(); + } + ); + } + }, [target, compositionRoot, hideExporting, showExporting]); + + const nmrReference = nmrSource && nmrMethod && ( + + + + + + {nmrMethod.externalLink} + + + + + + ); + + const fragmentsTable = target && pagination && setPagination && saveTarget && ( + + {loading && pagination.pageSize >= 25 && } + + +
{loading && }
+
+ ); + + return ( + + {error && ( + +
{error}
+
+ )} + {nmrReference} + {fragmentsTable} +
+ ); +}); + +interface DialogContentProps { + target: NSPTarget; + pagination: NMRPagination; +} + +interface ToolbarProps { + pagination: NMRPagination; + setPagination: SetNMRPagination; + saveTarget: () => Cancel | undefined; + hideExporting: () => void; + isExporting: boolean; +} + +const Toolbar: React.FC = React.memo(props => { + const { + pagination, + setPagination: { setPage, setPageSize }, + isExporting, + saveTarget, + hideExporting, + } = props; + + const { handleChangePage, handleChangeRowsPerPage, onClick, stopSaving } = useToolbar({ + setPage, + setPageSize, + saveTarget, + isExporting, + hideExporting, + }); + + const classes = useStyles(); + + return ( +
+ + +
+ ); +}); + +interface ExportButtonProps { + isProcessing: boolean; + onClick: () => void; + stop: () => void; +} + +const ExportButton: React.FC = React.memo(({ isProcessing, onClick, stop }) => { + const classes = useStyles(); + + return ( +
+ + + {isProcessing && ( +
+ + +
+ )} +
+ ); +}); + +const DialogContent: React.FC = React.memo(({ target, pagination }) => { + const headers = ["Name", "SMILES", "InchiKey", "Formula", "PubChem_ID", "Target", "Result"]; + const Headers = headers.map((h, idx) => ( + + {h} + + )); + + const fragments = React.useMemo(() => _.sortBy(target.fragments, f => !f.binding), [target]); + + return ( + + + + + + {Headers} + + + + {fragments.map((fragment, idx) => { + const { + binding, + ligand: { name: ligandName, smiles, inChI, formula, pubchemId }, + } = fragment; + + return ( + + ); + })} + +
+
+ ); +}); + +interface ItemRowProps extends DialogContentProps { + idx: number; + binding: boolean; + name: string; + smiles: string; + inChI: string; + formula: string; + pubchemId: string; +} + +const ItemRow: React.FC = React.memo(props => { + const { binding, name, smiles, inChI, formula, pubchemId, target, pagination, idx } = props; + + return ( + + {pagination.pageSize * pagination.page + idx + 1} + {name} + {smiles} + {inChI} + {formula} + {pubchemId} + {target.name} + + {binding ? i18n.t("Binding") : i18n.t("Not binding")} + + + ); +}); + +function useToolbar(props: { + setPage: (page: number) => void; + setPageSize: (pageSize: number) => void; + saveTarget: () => Cancel | undefined; + isExporting: boolean; + hideExporting: () => void; +}) { + const { setPage, setPageSize, saveTarget, isExporting, hideExporting } = props; + const [saving, setSaving] = React.useState(); + + const handleChangePage = React.useCallback( + (_event: React.MouseEvent | null, newPage: number) => { + setPage(newPage); + }, + [setPage] + ); + + const handleChangeRowsPerPage = React.useCallback( + (event: React.ChangeEvent) => { + setPageSize(parseInt(event.target.value, 10)); + setPage(1); + }, + [setPage, setPageSize] + ); + + const onClick = React.useCallback(() => { + if (isExporting) return; + const cancel = saveTarget(); + setSaving(_saving => cancel); + }, [isExporting, saveTarget]); + + const stopSaving = React.useCallback(() => { + saving && saving(); + hideExporting(); + }, [hideExporting, saving]); + + return { handleChangePage, handleChangeRowsPerPage, onClick, stopSaving }; +} + +const useStyles = makeStyles({ + toolbar: { + display: "flex", + justifyContent: "space-between", + paddingLeft: "1em", + margin: "0.5em 0 0.25em", + }, + exportButton: { + display: "flex", + alignItems: "center", + color: "#607d8b", + position: "relative", + justifyContent: "center", + }, + exportStopButton: { + cursor: "pointer", + display: "flex", + alignItems: "center", + color: "#009688", + position: "absolute", + justifyContent: "center", + }, + stop: { position: "absolute", fontSize: "14px" }, + bottomProgress: { height: "4px" }, +}); + +const StyledHeadTableRow = styled(TableRow)` + background: #fff; + & .MuiTableCell-root { + border-bottom: unset; + } +`; + +const StyledTableRow = styled(StyledHeadTableRow)<{ binding: boolean }>` + background: ${props => (props.binding ? "#dcedc8" : "#ffcdd2")}; + border: ${props => (props.binding ? "1px solid #9ccc65" : "1px solid #ef5350")}; +`; + +const StyledDialog = styled(Dialog)` + .MuiDialogContent-root { + padding: 0 !important; + } +`; + +const StyledLinearProgress = styled(LinearProgress)` + &.MuiLinearProgress-colorPrimary { + background-color: #c6ece8; + } + & .MuiLinearProgress-barColorPrimary { + background-color: #009688; + } +`; + +const StyledCircularProgress = styled(CircularProgress)` + position: absolute; + &.MuiCircularProgress-colorPrimary { + color: #009688; + } +`; + +const List = styled.ul` + list-style: none; + margin: 1.5rem 2rem; + padding: 0; + box-sizing: border-box; +`; + +const Content = styled(Paper)` + margin: 1.5rem 2rem; +`; diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/SearchBar.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/SearchBar.tsx index 0c3c1b040..615f9b0b3 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/SearchBar.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/SearchBar.tsx @@ -1,13 +1,12 @@ import React from "react"; import _ from "lodash"; -import { TextField, InputAdornment, Chip, CircularProgress } from "@material-ui/core"; -import Autocomplete from "@material-ui/lab/Autocomplete"; +import { TextField, InputAdornment, Chip } from "@material-ui/core"; +import Autocomplete, { AutocompleteRenderOptionState } from "@material-ui/lab/Autocomplete"; import parse from "autosuggest-highlight/parse"; import match from "autosuggest-highlight/match"; import styled from "styled-components"; import { Close as CloseIcon, Search as SearchIcon } from "@material-ui/icons"; import i18n from "../../../utils/i18n"; -import { useDebouncedSetter } from "../../hooks/useDebounce"; import { Covid19Filter, FilterKey, @@ -16,6 +15,7 @@ import { } from "../../../domain/entities/Covid19Info"; import { useAppContext } from "../../contexts/app-context"; import { searchExamples } from "./Toolbar"; +import { useBooleanState } from "../../hooks/useBoolean"; export interface SearchBarProps { value: string; @@ -29,18 +29,22 @@ export interface SearchBarProps { export const SearchBar: React.FC = React.memo(props => { const { compositionRoot } = useAppContext(); const { value, setValue, highlighted, setHighlight, filterState, setFilterState } = props; - const [open, setOpen] = React.useState(false); - const [stateValue, setValueDebounced] = useDebouncedSetter(value, setValue, { delay: 500 }); + const [open, { enable: showAutocomplete, disable: hideAutocomplete }] = useBooleanState(false); + const [searchValue, setSearchValue] = React.useState(value); const [autoSuggestionOptions, setAutoSuggestionOptions] = React.useState(searchExamples); - const [loading, setLoading] = React.useState(false); const selectedFilterNames = filterKeys.filter(key => filterState[key]); React.useEffect(() => { - setLoading(true); - const autoSuggestions = compositionRoot.getAutoSuggestions.execute(stateValue); - setAutoSuggestionOptions(stateValue === "" ? searchExamples : autoSuggestions); - setLoading(false); - }, [stateValue, compositionRoot.getAutoSuggestions]); + setSearchValue(value); + }, [value]); + + React.useEffect(() => { + if (searchValue.length > 2) { + compositionRoot.getAutoSuggestions + .execute(searchValue) + .run(suggestions => setAutoSuggestionOptions(suggestions), console.error); + } + }, [searchValue, compositionRoot.getAutoSuggestions]); const removeChip = React.useCallback( (chipToDelete: FilterKey) => { @@ -61,6 +65,56 @@ export const SearchBar: React.FC = React.memo(props => { const removeHighlight = React.useCallback(() => setHighlight(false), [setHighlight]); + const suggestions = React.useMemo(() => { + if (searchValue === "") { + return searchExamples; + } else { + return _([searchValue.toLowerCase(), ...autoSuggestionOptions]) + .uniq() + .sortBy(s => s !== searchValue) + .value(); + } + }, [autoSuggestionOptions, searchValue]); + + const resetValueIfEmpty = React.useCallback(() => { + if (searchValue === "") setSearchValue(value); + }, [searchValue, value]); + + const renderInput = React.useCallback( + params => ( + setSearchValue(ev.target.value)} + onBlur={resetValueIfEmpty} + onKeyPress={e => { + if (e.key === "Enter") { + setValue(searchValue); + } + }} + placeholder={i18n.t("Search protein/organism/PDB ID/EMDB ID/UniProt ID")} + InputProps={{ + ...params.InputProps, + endAdornment: ( + + setValue(searchValue)} + > + + + + ), + type: "search", + }} + /> + ), + [removeHighlight, searchValue, setValue, resetValueIfEmpty] + ); + return (
@@ -76,66 +130,53 @@ export const SearchBar: React.FC = React.memo(props => {
id="covid19-searchbar-autocomplete" - options={autoSuggestionOptions} - loading={loading} - open={open} + options={suggestions} + open={open && (searchValue.length > 2 || searchValue === "")} fullWidth={true} - onOpen={() => setOpen(true)} - onClose={() => setOpen(false)} + freeSolo={undefined} // weird... + autoComplete={true} + selectOnFocus={true} + autoSelect={true} clearOnBlur={false} - getOptionSelected={(option, value) => - option.toUpperCase() === value.toUpperCase() + clearOnEscape={true} + openOnFocus={true} + onOpen={showAutocomplete} + onClose={hideAutocomplete} + inputValue={searchValue} + onChange={(_event, option, reason) => + reason === "select-option" && option && setValue(option) } - inputValue={stateValue} - onInputChange={(_event, newInputValue) => setValueDebounced(newInputValue)} - renderOption={(option, { inputValue }) => { - const matches = match(option, inputValue); - const parts = parse(option, matches); - return ( -
- {parts.map((part, index) => ( - - {part.text} - - ))} -
- ); + onInputChange={(event, newInputValue) => { + /* Fix bug: if event is null or type blur, somehow, newInputValue randomly picks one of the search examples */ + if (event !== null && event.type !== "blur") setSearchValue(newInputValue); }} - renderInput={params => ( - setValueDebounced(ev.target.value)} - placeholder={i18n.t( - "Search protein/organism/PDB ID/EMDB ID/UniProt ID" - )} - InputProps={{ - ...params.InputProps, - endAdornment: ( - - {loading ? ( - - ) : null} - - - - - ), - type: "search", - }} - /> - )} + renderOption={renderOption} + renderInput={renderInput} />
); }); +function renderOption(option: string, { inputValue }: AutocompleteRenderOptionState) { + const matches = match(option, inputValue); + const parts = parse(option, matches); + return ( +
+ {parts.map((part, index) => ( + + {part.text} + + ))} +
+ ); +} + const StyledAutocomplete = styled(Autocomplete)` &.MuiAutocomplete-hasPopupIcon.MuiAutocomplete-hasClearIcon .MuiAutocomplete-inputRoot[class*="MuiOutlinedInput-root"] { @@ -181,4 +222,7 @@ const styles = { listStyle: "none", margin: 0, }, + searchButton: { + cursor: "pointer", + }, }; diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/Skeleton.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Skeleton.tsx new file mode 100644 index 000000000..2adc64551 --- /dev/null +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Skeleton.tsx @@ -0,0 +1,136 @@ +import _ from "lodash"; +import React from "react"; +import { Box } from "@material-ui/core"; +import { Skeleton as MuiSkeleton } from "@material-ui/lab"; +import { headerHeight, rowHeight } from "./StructuresTable"; +import { columnsWidths } from "./Columns"; + +const columns = columnsWidths; + +export const Skeleton: React.FC = () => ( + + + + + + + + + + + + + + + + + + + + +); + +const TitleSkeleton: React.FC = () => ( + + + + +); + +const PdbSkeleton: React.FC = () => ( + + + + + +); + +const EmdbSkeleton: React.FC = () => ( + + + + + +); + +const RelatedSkeleton: React.FC = () => ( + + + + + +); + +const DetailsSkeleton: React.FC = () => { + return ( + + + + + + + + + + + ); +}; + +const styles = { + details: { container: { flexGrow: 1 } }, + rect: { borderRadius: "0.25em" }, +}; diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/StructuresTable.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/StructuresTable.tsx index fabd5256a..34110fd89 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/StructuresTable.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/StructuresTable.tsx @@ -1,19 +1,28 @@ -import React from "react"; import _ from "lodash"; +import React from "react"; +import styled from "styled-components"; import { makeStyles } from "@material-ui/core"; -import { DataGrid, DataGridProps, GridSortModel } from "@material-ui/data-grid"; -import { updateStructures } from "../../../domain/entities/Covid19Info"; -import { getColumns, IDROptions, DetailsDialogOptions } from "./Columns"; -import { Covid19Filter, Id } from "../../../domain/entities/Covid19Info"; +import { DataGrid } from "@material-ui/data-grid"; +import { getColumns, IDROptions, DetailsDialogOptions, NMROptions } from "./Columns"; +import { Covid19Filter } from "../../../domain/entities/Covid19Info"; +import { LinearProgress } from "@material-ui/core"; +import { GridApi } from "@material-ui/data-grid"; +import { useSnackbar } from "@eyeseetea/d2-ui-components/snackbar"; +import { Covid19Info } from "../../../domain/entities/Covid19Info"; import { Toolbar, ToolbarProps } from "./Toolbar"; -import { useVirtualScrollbarForDataGrid } from "../VirtualScrollbar"; +import { VirtualScrollbarProps, useVirtualScrollbarForDataGrid } from "../VirtualScrollbar"; import { DataGrid as DataGridE } from "../../../domain/entities/DataGrid"; -import { useAppContext } from "../../contexts/app-context"; import { DetailsDialog } from "./DetailsDialog"; -import { sendAnalytics } from "../../../utils/analytics"; +import { sendAnalytics as _sendAnalytics } from "../../../utils/analytics"; import { IDRDialog } from "./IDRDialog"; import { useInfoDialog } from "../../hooks/useInfoDialog"; -import { CustomGridPagination, CustomGridPaginationProps } from "./CustomGridPagination"; +import { CustomGridPaginationProps } from "./CustomGridPagination"; +import { NMRDialog } from "./NMRDialog"; +import { Skeleton } from "./Skeleton"; +import { Footer } from "./Footer"; +import { SelfCancellable, pageSizes, useStructuresTable } from "./useStructuresTable"; +import { useBooleanState } from "../../hooks/useBoolean"; +import { Maybe } from "../../../data/utils/ts-utils"; export interface StructuresTableProps { search: string; @@ -22,104 +31,228 @@ export interface StructuresTableProps { setHighlight: (value: boolean) => void; } -export const rowHeight = 220; +export const StructuresTable: React.FC = React.memo(props => { + const { search, highlighted, setHighlight } = props; + const classes = useStyles(); + const snackbar = useSnackbar(); -const noSort: GridSortModel = []; + const { main, skeleton, cancellable, stop: stopLoading } = useUILoaders(); + const { loading: isLoading, show: showLoading } = main; + const { loading: isSkeletonLoading } = skeleton; + const { loading: isCancellable, show: enableCancellable } = cancellable; -const defaultSort: GridSortModel = [{ field: "emdb", sort: "desc" }]; + const structuresTableProps = { + ...props, + notice: snackbar, + showLoading, + enableCancellable, + stopLoading, + }; -export const StructuresTable: React.FC = React.memo(props => { - const { search, setSearch: setSearch0, highlighted, setHighlight } = props; - const { compositionRoot } = useAppContext(); - const [page, setPage] = React.useState(0); - const [pageSize, setPageSize] = React.useState(pageSizes[0]); - const classes = useStyles(); + const { + data, + page, + pageSize, + sortModel, + filterState, + setFilterState, + cancelRequest, + setSearch, + resetPageAndSorting, + changePage, + changePageSize, + } = useStructuresTable(structuresTableProps); + + const { structures } = data; + + const { + gridApi, + virtualScrollbarProps, + updateScrollBarFromStateChange, + } = useVirtualScrollbarForDataGrid(); + + const structuresTableUIProps = { + data, + gridApi, + virtualScrollbarProps, + search, + setSearch, + highlighted, + setHighlight, + filterState, + setFilterState, + page, + pageSize, + changePage, + changePageSize, + isLoading, + isCancellable, + cancelRequest, + }; + + const { + detailsDialog, + idrDialog, + nmrDialog, + columns, + components, + componentsProps, + } = useStructuresTableUI(structuresTableUIProps); + + const { isOpen: isDetailsOpen, close: closeDetails, data: detailsInfo } = detailsDialog; + const { isOpen: isIDROpen, open: openIDRDialog, close: closeIDR, data: idrOptions } = idrDialog; + const { + isOpen: isNMROpen, + open: openNMRDialog, + close: closeNMR, + data: nmrOptions, + setData: setNMROptions, + } = nmrDialog; + + return ( +
+ + {isLoading && } + {detailsInfo && ( + + )} + {idrOptions && ( + + )} + {nmrOptions && ( + + )} +
+ ); +}); + +type StructuresTableUIProps = { + data: Covid19Info; + gridApi: Maybe; + virtualScrollbarProps: VirtualScrollbarProps; + search: string; + setSearch: (value: string) => void; + highlighted: boolean; + setHighlight: (value: boolean) => void; + filterState: Covid19Filter; + setFilterState: React.Dispatch>; + page: number; + pageSize: number; + changePage: (newPage: number) => void; + changePageSize: (pageSize: number) => void; + isLoading: boolean; + isCancellable: boolean; + cancelRequest: React.MutableRefObject; +}; + +function useStructuresTableUI(props: StructuresTableUIProps) { + const { + data, + gridApi, + virtualScrollbarProps, + search, + setSearch, + highlighted, + setHighlight, + filterState, + setFilterState, + page, + pageSize, + changePage, + changePageSize, + isLoading, + isCancellable, + cancelRequest, + } = props; + + const { structures } = data; + window.app = { data }; const { info: detailsInfo, useDialogState: detailsDialogState, } = useInfoDialog(); const [isDetailsOpen, closeDetails, showDetailsDialog] = detailsDialogState; + const { info: idrOptions, useDialogState: idrDialogState } = useInfoDialog(); const [isIDROpen, closeIDR, showIDRDialog] = idrDialogState; - const [sortModel, setSortModel] = React.useState(defaultSort); - const [filterState, setFilterState0] = React.useState(initialFilterState); + const { + info: nmrOptions, + setInfo: setNMROptions, + useDialogState: nmrDialogState, + } = useInfoDialog(); + const [isNMROpen, closeNMR, showNMRDialog] = nmrDialogState; const openDetailsDialog = React.useCallback( (options: DetailsDialogOptions, gaLabel: string) => { closeIDR(); + closeNMR(); showDetailsDialog(options, gaLabel); }, - [closeIDR, showDetailsDialog] + [closeIDR, showDetailsDialog, closeNMR] ); const openIDRDialog = React.useCallback( (options: IDROptions, gaLabel: string) => { closeDetails(); + closeNMR(); showIDRDialog(options, gaLabel); }, - [closeDetails, showIDRDialog] + [closeDetails, showIDRDialog, closeNMR] ); - const setFilterState = React.useCallback((value: React.SetStateAction) => { - setPage(0); - setFilterState0(value); - }, []); - - const setSearch = React.useCallback( - (value: string) => { - setPage(0); - sendAnalytics("search", { - on: "covid_table", - query: value, - }); - setSearch0(value); - setSortModel(value ? noSort : defaultSort); - }, - [setSearch0] - ); - - const { - gridApi, - virtualScrollbarProps, - updateScrollBarFromStateChange, - } = useVirtualScrollbarForDataGrid(); - - const [renderedRowIds, setRenderedRowsFromState] = useRenderedRows(); - - const onStateChange = React.useCallback>( - params => { - setRenderedRowsFromState(params); - updateScrollBarFromStateChange(params); + const openNMRDialog = React.useCallback( + (options: NMROptions, gaLabel: string) => { + closeDetails(); + closeIDR(); + showNMRDialog(options, gaLabel); }, - [setRenderedRowsFromState, updateScrollBarFromStateChange] + [closeDetails, closeIDR, showNMRDialog] ); - const [data, setData] = React.useState(() => compositionRoot.getCovid19Info.execute()); - window.app = { data }; - - React.useEffect(() => { - compositionRoot.addDynamicInfo.execute(data, { ids: renderedRowIds }).then(structures => { - setData(data => updateStructures(data, structures)); - }); - }, [compositionRoot, data, renderedRowIds]); - - const filteredData = React.useMemo(() => { - return compositionRoot.searchCovid19Info.execute({ data, search, filter: filterState }); - }, [compositionRoot, data, search, filterState]); - - const { structures } = filteredData; - const columns = React.useMemo(() => { return getColumns(data, { onClickDetails: openDetailsDialog, onClickIDR: openIDRDialog, + onClickNMR: openNMRDialog, + setNMROptions: setNMROptions, }); - }, [data, openDetailsDialog, openIDRDialog]); + }, [data, openDetailsDialog, openIDRDialog, openNMRDialog, setNMROptions]); const components = React.useMemo( - () => ({ Toolbar: Toolbar, Pagination: CustomGridPagination }), + () => ({ Toolbar: Toolbar, Footer: Footer, LoadingOverlay: Skeleton }), [] ); @@ -128,7 +261,11 @@ export const StructuresTable: React.FC = React.memo(props }, [columns, structures]); const componentsProps = React.useMemo< - { toolbar: ToolbarProps; pagination: CustomGridPaginationProps } | undefined + | { + toolbar: ToolbarProps; + footer: CustomGridPaginationProps; + } + | undefined >(() => { return gridApi ? { @@ -145,17 +282,23 @@ export const StructuresTable: React.FC = React.memo(props page, pageSize, pageSizes, - setPage, - setPageSize, + setPage: changePage, + setPageSize: changePageSize, + isLoading, + slowLoading: isCancellable, + count: data.count, + cancelRequest: () => cancelRequest.current && cancelRequest.current(), //wrapper validationSources: data.validationSources, }, - pagination: { + footer: { dataGrid, page, pageSize, pageSizes, - setPage, - setPageSize, + setPage: changePage, + setPageSize: changePageSize, + isLoading, + count: data.count, }, } : undefined; @@ -171,63 +314,70 @@ export const StructuresTable: React.FC = React.memo(props virtualScrollbarProps, page, pageSize, - setPage, - setPageSize, data.validationSources, + isLoading, + isCancellable, + changePage, + changePageSize, + data.count, + cancelRequest, ]); - const resetPageAndSorting = React.useCallback>(_modelParams => { - setPage(0); - }, []); - - const setPageFromParams = React.useCallback>(params => { - return setPage(params.page); - }, []); - - const setPageSizeFromParams = React.useCallback>(params => { - return setPageSize(params.pageSize); - }, []); - - return ( -
- - {detailsInfo && ( - - )} - {idrOptions && ( - - )} -
- ); -}); + return { + detailsDialog: { + isOpen: isDetailsOpen, + open: openDetailsDialog, + close: closeDetails, + data: detailsInfo, + }, + idrDialog: { + isOpen: isIDROpen, + open: openIDRDialog, + close: closeIDR, + data: idrOptions, + }, + nmrDialog: { + isOpen: isNMROpen, + open: openNMRDialog, + close: closeNMR, + data: nmrOptions, + setData: setNMROptions, + }, + columns, + components, + componentsProps, + }; +} -type GridProp = NonNullable; +function useUILoaders() { + const [isLoading, { enable: showLoading, disable: hideLoading }] = useBooleanState(true); + const [isSkeletonLoading, { disable: hideSkeleton }] = useBooleanState(true); + const [ + isCancellable, + { enable: enableCancellable, disable: disableCancellable }, + ] = useBooleanState(false); + + const stopLoading = React.useCallback(() => { + hideSkeleton(); + hideLoading(); + disableCancellable(); + }, [hideLoading, disableCancellable, hideSkeleton]); + + return { + main: { + loading: isLoading, + show: showLoading, + }, + skeleton: { + loading: isSkeletonLoading, + }, + cancellable: { + loading: isCancellable, + show: enableCancellable, + }, + stop: stopLoading, + }; +} const useStyles = makeStyles({ root: { @@ -235,45 +385,34 @@ const useStyles = makeStyles({ whiteSpace: "normal", display: "flex", // "flex": center vertically. "block" otherwise }, + "&.MuiDataGrid-root": { + borderTop: "none", + borderRadius: "0 0 4px 4px", + }, "&.MuiDataGrid-root .MuiDataGrid-cellWithRenderer": {}, }, - wrapper: {}, + wrapper: { + position: "relative", + }, }); -const pageSizes = [10, 25, 50, 75, 100]; +export type SetNMROptions = React.Dispatch>; -const sortingOrder = ["asc" as const, "desc" as const]; - -const initialFilterState: Covid19Filter = { - antibodies: false, - nanobodies: false, - sybodies: false, - pdbRedo: false, - cstf: false, - ceres: false, - idr: false, -}; - -function useRenderedRows() { - const [renderedRowIds, setRenderedRowIds] = React.useState([]); - - const setRenderedRowsFromState = React.useCallback>( - gridParams => { - const { api } = gridParams; - const { page, pageSize } = gridParams.state.pagination; - const sortedIds = api.getSortedRowIds() as Id[]; - const visibleIds = Array.from(api.getVisibleRowModels().keys()) as string[]; - - const ids = _(sortedIds) - .intersection(visibleIds) - .drop(page * pageSize) - .take(pageSize) - .value(); - - setRenderedRowIds(prevIds => (_.isEqual(prevIds, ids) ? prevIds : ids)); - }, - [] - ); - - return [renderedRowIds, setRenderedRowsFromState] as const; -} +export const rowHeight = 220; +export const headerHeight = 56; + +const sortingOrder = ["asc" as const, "desc" as const, null]; + +const StyledLinearProgress = styled(LinearProgress)<{ position: "top" | "bottom" }>` + &.MuiLinearProgress-root { + position: absolute; + ${props => props.position}: 0; + width: 100%; + } + &.MuiLinearProgress-colorPrimary { + background-color: #c6ece8; + } + & .MuiLinearProgress-barColorPrimary { + background-color: #009688; + } +`; diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/Toolbar.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Toolbar.tsx index 44b212029..94e609527 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/Toolbar.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/Toolbar.tsx @@ -1,9 +1,9 @@ import _ from "lodash"; import React from "react"; -import HelpOutlineIcon from "@material-ui/icons/HelpOutline"; +import { Stop as StopIcon, HelpOutline as HelpOutlineIcon } from "@material-ui/icons"; import styled from "styled-components"; import { GridApi, GridToolbarColumnsButton, GridToolbarContainer } from "@material-ui/data-grid"; -import { Typography } from "@material-ui/core"; +import { CircularProgress, Typography } from "@material-ui/core"; import { DataGrid } from "../../../domain/entities/DataGrid"; import { Covid19Filter, ValidationSource } from "../../../domain/entities/Covid19Info"; import { VirtualScroll, VirtualScrollbarProps } from "../VirtualScrollbar"; @@ -13,6 +13,7 @@ import { SearchBar } from "./SearchBar"; import { CustomCheckboxFilter } from "./CustomCheckboxFilter"; import { SearchExampleButton } from "./SearchExampleButton"; import { HtmlTooltip } from "./HtmlTooltip"; +import { SelfCancellable } from "./useStructuresTable"; import i18n from "../../../utils/i18n"; import "./Toolbar.css"; @@ -37,11 +38,15 @@ export interface ToolbarProps { dataGrid: DataGrid; virtualScrollbarProps: VirtualScrollbarProps; page: number; - pageSize: number | undefined; + pageSize: number; pageSizes: number[]; setPage: (param: number) => void; setPageSize: (param: number) => void; validationSources: ValidationSource[]; + isLoading: boolean; + slowLoading: boolean; + cancelRequest: SelfCancellable; + count: number; } // Toolbar is called with empty object on initialization @@ -142,7 +147,10 @@ export const Toolbar: React.FC = props => { pageSizes, setPage, setPageSize, - validationSources, + count, + isLoading, + slowLoading, + cancelRequest, } = props; return ( @@ -161,7 +169,6 @@ export const Toolbar: React.FC = props => { = props => { + {isLoading && ( + + + {slowLoading && ( + cancelRequest()} + /> + )} + + )} @@ -203,7 +230,8 @@ export const Toolbar: React.FC = props => { ))} (obj: T | {}): obj is T { @@ -288,3 +318,21 @@ export const StyledTypography = styled(Typography)` font-weight: 500; } `; + +const LoadingContainer = styled.div<{ cancellable: boolean }>` + display: flex; + width: 36px; + margin: 0 10px; + align-items: center; + justify-content: center; + position: relative; + color: #009688; + cursor: ${props => (props.cancellable ? "pointer" : "default")}; +`; + +const StyledCircularProgress = styled(CircularProgress)` + position: absolute; + &.MuiCircularProgress-colorPrimary { + color: #009688; + } +`; diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/Badge.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/Badge.tsx index c803fbb22..51c8f9909 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/Badge.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/Badge.tsx @@ -4,12 +4,13 @@ import { W3Color } from "../../../../domain/entities/Covid19Info"; interface BadgeProps { color?: W3Color; backgroundColor?: W3Color; + disabled?: boolean; } export const Badge = styled.span` display: inline-flex; justify-content: center; - cursor: pointer; + cursor: ${props => (props.disabled ? "default" : "pointer")}; padding: 6px 12px; flex-grow: 1; font-size: 10.5px; @@ -18,7 +19,11 @@ export const Badge = styled.span` white-space: normal; color: ${props => (props.color ? colors[props.color] : "#fff")}; background-color: ${props => - props.backgroundColor ? colors[props.backgroundColor] : "#607d8b"}; + props.disabled + ? "#ccc" + : props.backgroundColor + ? colors[props.backgroundColor] + : "#607d8b"}; font-weight: 700; line-height: 1; text-align: center; diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/BadgeEntities.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/BadgeEntities.tsx new file mode 100644 index 000000000..ffa575ea5 --- /dev/null +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/BadgeEntities.tsx @@ -0,0 +1,143 @@ +import React, { MouseEvent } from "react"; +import styled from "styled-components"; +import { Badge } from "./Badge"; +import { useAppContext } from "../../../contexts/app-context"; +import { NMROptions } from "../Columns"; +import { SetNMROptions } from "../StructuresTable"; +import { LoaderMask } from "../../loader-mask/LoaderMask"; +import { useBooleanState } from "../../../hooks/useBoolean"; +import i18n from "../../../../utils/i18n"; +import { Portal } from "@material-ui/core"; +import { BasicNSPTarget } from "../../../../domain/entities/Covid19Info"; + +export type OnClickNMR = (options: NMROptions, gaLabel: string) => void; + +export interface BadgeEntitiesProps { + moreDetails?: boolean; + onClick?: OnClickNMR; + target: BasicNSPTarget; + setNMROptions: SetNMROptions; +} + +export const BadgeEntities: React.FC = React.memo(props => { + const { moreDetails = true, target, onClick, setNMROptions } = props; + const [loading, { open: showLoading, close: hideLoading }] = useBooleanState(false); + + const getNMR = useNMRPagination(target, setNMROptions); + + const notifyClick = React.useCallback( + (e: MouseEvent) => { + e.preventDefault(); + if (onClick) { + showLoading(); + //This can be extracted to NMR Dialog with useEffect + return getNMR(onClick, hideLoading); + } + }, + [onClick, getNMR, hideLoading, showLoading] + ); + + return ( + <> + {moreDetails ? ( + + + {i18n.t("C19-NMR")} + + + ) : ( + + + {i18n.t("C19-NMR")} + + + )} + + + + + ); +}); + +function useNMRPagination(basicTarget: BasicNSPTarget, setNMROptions: SetNMROptions) { + const [page, setPage] = React.useState(0); + const [pageSize, setPageSize] = React.useState(25); + const [count, setCount] = React.useState(0); + const { compositionRoot } = useAppContext(); + + React.useEffect(() => { + if (count === 0) return; + setNMROptions(nmrOptions => ({ + ...nmrOptions, + loading: true, + })); + + return compositionRoot.entities.getPartialNMR + .execute(basicTarget, { page, pageSize, count }) + .run( + ({ target, pagination }) => { + setCount(pagination.count); + return setNMROptions({ + target, + pagination: { page, pageSize, count: pagination.count }, + setPagination: { + setPage, + setPageSize, + }, + loading: false, + }); + }, + err => { + setNMROptions({ + error: err.message, + loading: false, + }); + } + ); + }, [page, pageSize, count, setPage, setPageSize, setNMROptions, compositionRoot, basicTarget]); + + const getNMR = React.useCallback( + (onClick: OnClickNMR, hideLoading: () => void) => { + return compositionRoot.entities.getPartialNMR + .execute(basicTarget, { page, pageSize, count }) + .run( + ({ target, pagination }) => { + hideLoading(); + setCount(pagination.count); + return onClick( + { + target, + pagination: { page, pageSize, count }, + setPagination: { + setPage, + setPageSize, + }, + }, + `NMR Target entity. Uniprot: ${basicTarget.uniprotId}. Target: ${basicTarget.name}` + ); + }, + err => { + hideLoading(); + return onClick( + { error: err.message }, + `ERROR NMR Target. Uniprot: ${basicTarget.uniprotId}. Target: ${basicTarget.name}` + ); + } + ); + }, + [page, pageSize, count, compositionRoot, setPage, setPageSize, basicTarget] + ); + + return getNMR; +} + +const BadgeGroup = styled.div` + display: flex; + justify-content: center; +`; + +const BadgeInlineGroup = styled.div` + display: inline-flex; + align-items: flex-end; + justify-content: center; +`; diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/BadgeLigands.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/BadgeLigands.tsx index 6f4a39050..05e0730c0 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/BadgeLigands.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/badge/BadgeLigands.tsx @@ -5,6 +5,9 @@ import { IDROptions } from "../Columns"; import { Badge } from "./Badge"; import { useAppContext } from "../../../contexts/app-context"; import i18n from "../../../../utils/i18n"; +import { Portal } from "@material-ui/core"; +import { LoaderMask } from "../../loader-mask/LoaderMask"; +import { useBooleanState } from "../../../hooks/useBoolean"; export type OnClickIDR = (options: IDROptions, gaLabel: string) => void; @@ -18,40 +21,53 @@ export interface BadgeLigandsProps { export const BadgeLigands: React.FC = React.memo(props => { const { ligand, pdbId, onClick, moreDetails = true } = props; const { compositionRoot } = useAppContext(); + const [loading, { enable: showLoading, disable: hideLoading }] = useBooleanState(false); const notifyClick = React.useCallback( (e: MouseEvent) => { e.preventDefault(); if (onClick) { + showLoading(); compositionRoot.ligands.getIDR.execute(ligand.inChI, pdbId).run( - idr => + idr => { + hideLoading(); onClick( { ligand, pdbId, idr }, `IDR Ligand. PDB: ${pdbId}. Ligand: ${ligand.id}. Ligand name: ${ligand.name}` - ), - err => + ); + }, + err => { + hideLoading(); onClick( { ligand, pdbId, error: err.message }, `ERROR IDR Ligand. ID: ${ligand.id}` - ) + ); + } ); } }, - [onClick, ligand, compositionRoot, pdbId] + [onClick, ligand, compositionRoot, pdbId, hideLoading, showLoading] ); - return moreDetails ? ( - - - {i18n.t("IDR")} - - - ) : ( - - - {i18n.t("IDR")} - - + return ( + <> + {moreDetails ? ( + + + {i18n.t("IDR")} + + + ) : ( + + + {i18n.t("IDR")} + + + )} + + + + ); }); diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/EntityCell.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/EntityCell.tsx index e8fb596aa..7cea6ba9c 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/EntityCell.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/EntityCell.tsx @@ -1,53 +1,37 @@ import _ from "lodash"; import React from "react"; -import i18n from "../../../../utils/i18n"; import { CellProps } from "../Columns"; import { Link } from "../Link"; import { Wrapper } from "./Wrapper"; +import { BadgeEntities, OnClickNMR } from "../badge/BadgeEntities"; +import { HtmlTooltip } from "../HtmlTooltip"; +import { + Entity, + Maybe, + ValidationSource, + getValidationSource, +} from "../../../../domain/entities/Covid19Info"; +import { useAppContext } from "../../../contexts/app-context"; +import { SetNMROptions } from "../StructuresTable"; +import i18n from "../../../../utils/i18n"; -export const EntityCell: React.FC = React.memo(props => { - const { row, onClickDetails, moreDetails } = props; +export interface EntitiyCellProps extends CellProps { + onClickNMR?: OnClickNMR; + setNMROptions: SetNMROptions; +} - const entities = React.useMemo(() => { - return row.entities.map(entity => { - const uniprot = entity.uniprotAcc && ( -
- {i18n.t("UniProt")}: {entity.uniprotAcc} -
- ); - const altNames = entity.altNames && ( -
- {i18n.t("Alt Names")}: {entity.altNames} -
- ); - const organism = entity.organism && ( -
- {i18n.t("Organism")}: {entity.organism} -
- ); - const details = entity.details &&
{entity.details}
; - const antibody = entity.isAntibody &&
{i18n.t("Entity is antibody")}
; - const nanobody = entity.isNanobody &&
{i18n.t("Entity is nanobody")}
; - const sybody = entity.isSybody &&
{i18n.t("Entity is sybody")}
; +export const EntityCell: React.FC = React.memo(props => { + const { row, onClickDetails, onClickNMR, moreDetails, setNMROptions } = props; + const { sources: validationSources } = useAppContext(); - return { - name: entity.name, - tooltip: !_.isEmpty( - _.compact([uniprot, altNames, organism, details, antibody, nanobody, sybody]) - ) && ( - - {uniprot} - {altNames} - {organism} - {details} - {antibody} - {nanobody} - {sybody} - - ), - }; - }); - }, [row.entities]); + const nmrValidationSource = React.useMemo( + () => getValidationSource(validationSources ?? [], "NMR"), + [validationSources] + ); + + const entities = React.useMemo(() => { + return row.entities.map(entity => mapEntity(entity, nmrValidationSource)); + }, [nmrValidationSource, row.entities]); return ( = React.memo(props => { field="entities" > {entities.map((entity, idx) => ( - + <> + + {entity.nmr && entity.sourceTooltip && entity.uniprotAcc && ( + + <> + {entity.nmr.map((target, idx) => ( + + + + ))} + + + )} + ))} ); }); + +function mapEntity(entity: Entity, nmrValidationSource: Maybe) { + const uniprot = entity.uniprotAcc && ( +
+ {i18n.t("UniProt")}: {entity.uniprotAcc} +
+ ); + const altNames = entity.altNames && ( +
+ {i18n.t("Alt Names")}: {entity.altNames} +
+ ); + const organism = entity.organism && ( +
+ {i18n.t("Organism")}: {entity.organism} +
+ ); + const details = entity.details &&
{entity.details}
; + const antibody = entity.isAntibody &&
{i18n.t("Entity is antibody")}
; + const nanobody = entity.isNanobody &&
{i18n.t("Entity is nanobody")}
; + const sybody = entity.isSybody &&
{i18n.t("Entity is sybody")}
; + + const nmr = entity.targets; + + const tooltip = !_.isEmpty( + _.compact([uniprot, altNames, organism, details, antibody, nanobody, sybody]) + ) && ( + + {uniprot} + {altNames} + {organism} + {details} + {antibody} + {nanobody} + {sybody} + + ); + + const sourceTooltip = nmrValidationSource && ( +
+ {nmrValidationSource.methods.map(method => ( + <> + {nmrValidationSource.methods.length > 1 ? ( + + {i18n.t(`{{methodName}} Method: `, { + nsSeparator: false, + methodName: method.name, + })} + + ) : ( + {i18n.t("Method: ", { nsSeparator: false })} + )} + {method.description} +
+
+ + ))} + {nmrValidationSource.description && ( + <> + {i18n.t("Source: ", { nsSeparator: false })} + {nmrValidationSource.description} + + )} +
+ ); + + return { + ...entity, + nmr, + tooltip, + sourceTooltip, + }; +} diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/LigandsCell.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/LigandsCell.tsx index bbb3153eb..1b5ae708c 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/LigandsCell.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/LigandsCell.tsx @@ -8,13 +8,15 @@ import { Wrapper } from "./Wrapper"; import { getValidationSource } from "../../../../domain/entities/Covid19Info"; import { HtmlTooltip } from "../HtmlTooltip"; import i18n from "../../../../utils/i18n"; +import { useAppContext } from "../../../contexts/app-context"; export interface LigandsCellProps extends CellProps { onClickIDR?: OnClickIDR; } export const LigandsCell: React.FC = React.memo(props => { - const { row, onClickDetails, onClickIDR, moreDetails = true, validationSources } = props; + const { row, onClickDetails, onClickIDR, moreDetails = true } = props; + const { sources: validationSources } = useAppContext(); const ligands = React.useMemo(() => { return row.ligands.map(ligand => { @@ -30,12 +32,6 @@ export const LigandsCell: React.FC = React.memo(props => { {i18n.t("Name")}: {ligand.name} - {ligand.details !== ligand.name && ( -
- {i18n.t("Details")}: {ligand.details} -
- )} - {ligand.imageLink && ( {ligand.id} )} diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/PdbCell.tsx b/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/PdbCell.tsx index be5af0c5c..606a3f265 100644 --- a/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/PdbCell.tsx +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/cells/PdbCell.tsx @@ -17,24 +17,20 @@ import { BadgeLink } from "../badge/BadgeLink"; import { Badge } from "../badge/Badge"; import { urlPrefix } from "./TitleCell"; import i18n from "../../../../utils/i18n"; +import { useAppContext } from "../../../contexts/app-context"; export const PdbCell: React.FC = React.memo(props => { const { pdb } = props.row; - return pdb ? ( - - ) : null; + return pdb ? : null; }); const PdbCell2: React.FC<{ structure: Structure; pdb: Pdb; - validationSources: ValidationSource[]; }> = React.memo(props => { - const { pdb, structure, validationSources } = props; + const { pdb, structure } = props; + const { sources: validationSources } = useAppContext(); + const [open, setOpen] = React.useState(false); const pdbValidations = structure.validations.pdb; diff --git a/app/assets/javascripts/covid19/src/webapp/components/structures-table/useStructuresTable.ts b/app/assets/javascripts/covid19/src/webapp/components/structures-table/useStructuresTable.ts new file mode 100644 index 000000000..779e21755 --- /dev/null +++ b/app/assets/javascripts/covid19/src/webapp/components/structures-table/useStructuresTable.ts @@ -0,0 +1,194 @@ +import React, { ReactNode } from "react"; +import { DataGridProps, GridSortModel } from "@material-ui/data-grid"; +import { StructuresTableProps } from "./StructuresTable"; +import { useAppContext } from "../../contexts/app-context"; +import { Covid19Filter, Covid19Info } from "../../../domain/entities/Covid19Info"; +import i18n from "../../../utils/i18n"; +import { isElementOfUnion } from "../../../data/utils/ts-utils"; + +type Props = StructuresTableProps & { + notice: NoticeState; + showLoading: () => void; + stopLoading: () => void; + enableCancellable: () => void; +}; + +export function useStructuresTable(props: Props) { + const { + search, + setSearch: setSearch0, + notice, + showLoading, + stopLoading, + enableCancellable, + } = props; + + const { compositionRoot } = useAppContext(); + + //data + const [data, setData] = React.useState({ + count: 0, + structures: [], + validationSources: [], + }); + + //paging + const [page, setPage] = React.useState(1); + const pageSize = React.useRef(pageSizes[0] ?? 10); + + //sort filter + const [sortModel, setSortModel] = React.useState(noSort); + const [filterState, setFilterState] = React.useState(initialFilterState); + + //cancel get request + const cancelLoadDataRef: React.MutableRefObject = React.useRef(() => {}); + + const setSearch = React.useCallback( + (value: string) => { + // ANALYTICS TO BE REBUILD + // sendAnalytics("search", { + // on: "covid_table", + // query: value, + // }); + setSearch0(value.toLowerCase()); + setSortModel(sort => (value ? noSort : sort)); + }, + [setSearch0] + ); + + const resetPageAndSorting = React.useCallback>(modelParams => { + setSortModel(modelParams.sortModel); + }, []); + + const getData = React.useCallback( + (page: number, pageSize: number, onSuccess?: () => void) => { + showLoading(); + if (pageSize > 25) enableCancellable(); + const sortOption = sortModel[0]; + + const sort = + sortOption && isElementOfUnion(sortOption.field, sortingFields) && sortOption.sort + ? { + field: sortOption.field, + order: sortOption.sort, + } + : ({ field: "releaseDate", order: "desc" } as const); + + const cancelGetData = compositionRoot.getCovid19Info + .execute({ page, pageSize, filter: filterState, sort, query: search }) + .run( + data => { + setData(data); + onSuccess && onSuccess(); + cancelLoadDataRef.current = () => {}; + stopLoading(); + }, + err => { + console.error(err.message); + notice.error(err.message); + cancelLoadDataRef.current = () => {}; + stopLoading(); + } + ); + + const cancelData = (self = false) => { + if (!self) { + stopLoading(); + notice.info(i18n.t("Request has been cancelled"), { autoHideDuration: 2000 }); + } + cancelGetData(); + }; + + cancelLoadDataRef.current = cancelData; + + return cancelData; + }, + [ + compositionRoot, + stopLoading, + enableCancellable, + showLoading, + notice, + filterState, + sortModel, + search, + ] + ); + + const changePage = React.useCallback( + (newPage: number) => { + if (cancelLoadDataRef.current) { + cancelLoadDataRef.current(true); + } + getData(newPage, pageSize.current, () => setPage(newPage)); + }, + [setPage, getData] + ); + + const changePageSize = React.useCallback( + (size: number) => { + if (cancelLoadDataRef.current) { + cancelLoadDataRef.current(true); + } + getData(1, size, () => { + pageSize.current = size; + setPage(1); + }); + }, + [setPage, getData] + ); + + const resetPage = React.useCallback(() => { + changePage(1); + }, [changePage]); + + React.useEffect(resetPage, [filterState, resetPage]); + + return { + compositionRoot, + data, + page, + pageSize: pageSize.current, + sortModel, + filterState, + setFilterState, + cancelRequest: cancelLoadDataRef, + setSearch, + resetPageAndSorting, + changePage, + changePageSize, + }; +} + +export const pageSizes = [10, 25, 50, 75, 100]; +const noSort: GridSortModel = []; + +export const initialFilterState: Covid19Filter = { + antibodies: false, + nanobodies: false, + sybodies: false, + pdbRedo: false, + cstf: false, + ceres: false, + idr: false, + nmr: false, +}; + +const sortingFields = ["pdb", "title", "emdb", "releaseDate"] as const; + +type GridProp = NonNullable; +export type SelfCancellable = (self?: boolean) => void; + +type NoticeLevel = "success" | "info" | "warning" | "error"; +type Message = ReactNode; + +export interface NotifyUserOptions { + isOpen: boolean; + message?: Message; + variant?: NoticeLevel; + autoHideDuration?: number | null; +} + +type NoticeState = { + [level in NoticeLevel]: (message: Message, options?: Partial) => void; +}; diff --git a/app/assets/javascripts/covid19/src/webapp/contexts/app-context.ts b/app/assets/javascripts/covid19/src/webapp/contexts/app-context.ts index e53b378e6..e4d764551 100644 --- a/app/assets/javascripts/covid19/src/webapp/contexts/app-context.ts +++ b/app/assets/javascripts/covid19/src/webapp/contexts/app-context.ts @@ -1,10 +1,10 @@ import React, { useContext } from "react"; import { CompositionRoot } from "../../compositionRoot"; -import { Config } from "../../domain/entities/config"; +import { Source } from "../../domain/entities/Source"; export interface AppContextState { compositionRoot: CompositionRoot; - config: Config; + sources: Source[]; } export const AppContext = React.createContext(null); diff --git a/app/assets/javascripts/covid19/src/webapp/hooks/useBoolean.ts b/app/assets/javascripts/covid19/src/webapp/hooks/useBoolean.ts index 35b5cf1a3..efd04b7b2 100644 --- a/app/assets/javascripts/covid19/src/webapp/hooks/useBoolean.ts +++ b/app/assets/javascripts/covid19/src/webapp/hooks/useBoolean.ts @@ -8,17 +8,21 @@ interface UseBooleanActions { set: (newValue: boolean) => void; toggle: Callback; enable: Callback; + open: Callback; disable: Callback; + close: Callback; } -export function useBooleanState(initialValue: boolean): UseBooleanReturn { - const [value, setValue] = React.useState(initialValue); +export function useBooleanState(initialValue?: boolean): UseBooleanReturn { + const [value, setValue] = React.useState(initialValue ?? false); const actions = React.useMemo(() => { return { set: (newValue: boolean) => setValue(newValue), enable: () => setValue(true), + open: () => setValue(true), disable: () => setValue(false), + close: () => setValue(false), toggle: () => setValue(value_ => !value_), }; }, [setValue]); diff --git a/app/assets/javascripts/covid19/src/webapp/hooks/useInfoDialog.ts b/app/assets/javascripts/covid19/src/webapp/hooks/useInfoDialog.ts index 1f196f74c..45bd78c1e 100644 --- a/app/assets/javascripts/covid19/src/webapp/hooks/useInfoDialog.ts +++ b/app/assets/javascripts/covid19/src/webapp/hooks/useInfoDialog.ts @@ -5,6 +5,7 @@ import { useBooleanState } from "./useBoolean"; type UseInfoDialogReturn = { info: Maybe; + setInfo: React.Dispatch>; useDialogState: [ isDialogOpen: boolean, closeDialog: () => void, @@ -27,5 +28,5 @@ export function useInfoDialog(): UseInfoDialogReturn { [openDialog] ); - return { info, useDialogState: [isDialogOpen, closeDialog, showDialog] }; + return { info, setInfo, useDialogState: [isDialogOpen, closeDialog, showDialog] }; } diff --git a/app/assets/javascripts/covid19/yarn.lock b/app/assets/javascripts/covid19/yarn.lock index 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integrity sha1-llxwWGaOgrVde/4E/yM3vItWR/4= @@ -4786,6 +5483,11 @@ boolbase@^1.0.0, boolbase@~1.0.0: resolved "https://registry.yarnpkg.com/boolbase/-/boolbase-1.0.0.tgz#68dff5fbe60c51eb37725ea9e3ed310dcc1e776e" integrity sha1-aN/1++YMUes3cl6p4+0xDcwed24= +bowser@^1.7.3: + version "1.9.4" + resolved "https://registry.yarnpkg.com/bowser/-/bowser-1.9.4.tgz#890c58a2813a9d3243704334fa81b96a5c150c9a" + integrity sha512-9IdMmj2KjigRq6oWhmwv1W36pDuA4STQZ8q6YO9um+x07xgYNCD3Oou+WP/3L1HNz7iqythGet3/p4wvc8AAwQ== + brace-expansion@^1.1.7: version "1.1.11" resolved "https://registry.yarnpkg.com/brace-expansion/-/brace-expansion-1.1.11.tgz#3c7fcbf529d87226f3d2f52b966ff5271eb441dd" @@ -5154,6 +5856,11 @@ caseless@~0.12.0: resolved "https://registry.yarnpkg.com/caseless/-/caseless-0.12.0.tgz#1b681c21ff84033c826543090689420d187151dc" integrity sha1-G2gcIf+EAzyCZUMJBolCDRhxUdw= +chain-function@^1.0.0: + version "1.0.1" + resolved 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static-extend "^0.1.1" +classnames@2.2.6: + version "2.2.6" + resolved "https://registry.yarnpkg.com/classnames/-/classnames-2.2.6.tgz#43935bffdd291f326dad0a205309b38d00f650ce" + integrity sha512-JR/iSQOSt+LQIWwrwEzJ9uk0xfN3mTVYMwt1Ir5mUcSN6pU+V4zQFFaJsclJbPuAUQH+yfWef6tm7l1quW3C8Q== + classnames@^2.3.1: version "2.3.1" resolved "https://registry.npmjs.org/classnames/-/classnames-2.3.1.tgz#dfcfa3891e306ec1dad105d0e88f4417b8535e8e" @@ -5384,10 +6101,10 @@ cloneable-readable@^1.0.0: process-nextick-args "^2.0.0" readable-stream "^2.3.5" -clsx@^1.0.4: - version "1.1.1" - resolved "https://registry.yarnpkg.com/clsx/-/clsx-1.1.1.tgz#98b3134f9abbdf23b2663491ace13c5c03a73188" - integrity sha512-6/bPho624p3S2pMyvP5kKBPXnI3ufHLObBFCfgx+LkeR5lg2XYy2hqZqUf45ypD8COn2bhgGJSUE+l5dhNBieA== +clsx@^1.0.2, clsx@^1.0.4: + version "1.2.1" + resolved "https://registry.yarnpkg.com/clsx/-/clsx-1.2.1.tgz#0ddc4a20a549b59c93a4116bb26f5294ca17dc12" + integrity 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"https://registry.yarnpkg.com/core-js/-/core-js-1.2.7.tgz#652294c14651db28fa93bd2d5ff2983a4f08c636" + integrity sha512-ZiPp9pZlgxpWRu0M+YWbm6+aQ84XEfH1JRXvfOc/fILWI0VKhLC2LX13X1NYq4fULzLMq7Hfh43CSo2/aIaUPA== + core-js@^2.4.0, core-js@^2.5.0: version "2.6.11" resolved "https://registry.yarnpkg.com/core-js/-/core-js-2.6.11.tgz#38831469f9922bded8ee21c9dc46985e0399308c" @@ -5833,6 +6560,14 @@ css-has-pseudo@^0.10.0: postcss "^7.0.6" postcss-selector-parser "^5.0.0-rc.4" +css-in-js-utils@^2.0.0: + version "2.0.1" + resolved "https://registry.yarnpkg.com/css-in-js-utils/-/css-in-js-utils-2.0.1.tgz#3b472b398787291b47cfe3e44fecfdd9e914ba99" + integrity sha512-PJF0SpJT+WdbVVt0AOYp9C8GnuruRlL/UFW7932nLWmFLQTaWEzTBQEx7/hn4BuV+WON75iAViSUJLiU3PKbpA== + dependencies: + hyphenate-style-name "^1.0.2" + isobject "^3.0.1" + css-loader@4.3.0: version "4.3.0" resolved "https://registry.yarnpkg.com/css-loader/-/css-loader-4.3.0.tgz#c888af64b2a5b2e85462c72c0f4a85c7e2e0821e" @@ -6128,6 +6863,13 @@ cypress@6.2.0: url "^0.11.0" yauzl "^2.10.0" +d2@~31.7: + version "31.7.0" + resolved "https://registry.yarnpkg.com/d2/-/d2-31.7.0.tgz#3a843240fecaafdf213da78b55aed9b8611ee22e" + integrity sha512-+ubKyPWKxUz90g5RHCYIt4KxKPzcCOBvDS7X0076XSycecfx4qvtkGBcKyFmXdz27iwTLUpNtruL9pUK9aTi/A== + dependencies: + isomorphic-fetch "^2.2.1" + d@1, d@^1.0.1: version "1.0.1" resolved "https://registry.yarnpkg.com/d/-/d-1.0.1.tgz#8698095372d58dbee346ffd0c7093f99f8f9eb5a" @@ -6429,6 +7171,13 @@ dom-converter@^0.2: dependencies: utila "~0.4" +dom-helpers@^3.2.0: + version "3.4.0" + resolved "https://registry.yarnpkg.com/dom-helpers/-/dom-helpers-3.4.0.tgz#e9b369700f959f62ecde5a6babde4bccd9169af8" + integrity sha512-LnuPJ+dwqKDIyotW1VzmOZ5TONUN7CwkCR5hrgawTUbkBGYdeoNLZo6nNfGkCrjtE1nXXaj7iMMpDa8/d9WoIA== + dependencies: + "@babel/runtime" "^7.1.2" + dom-helpers@^5.0.1: version "5.1.4" resolved "https://registry.yarnpkg.com/dom-helpers/-/dom-helpers-5.1.4.tgz#4609680ab5c79a45f2531441f1949b79d6587f4b" @@ -6522,6 +7271,16 @@ dotenv@8.2.0: resolved "https://registry.yarnpkg.com/dotenv/-/dotenv-8.2.0.tgz#97e619259ada750eea3e4ea3e26bceea5424b16a" integrity sha512-8sJ78ElpbDJBHNeBzUbUVLsqKdccaa/BXF1uPTw3GrvQTBgrQrtObr2mUrE38vzYd8cEv+m/JBfDLioYcfXoaw== +downshift@5.4.2: + version "5.4.2" + resolved "https://registry.yarnpkg.com/downshift/-/downshift-5.4.2.tgz#3f6b7bf4ad7e0ff5503414efe3a398421763ebae" + integrity sha512-IVwIc4iw5OF5Bi/MbITarW2E8/5akm++5b6UL7aXyPoZmuVe4ilFGaQaktdFW/IwuzHieIwaWj4AQgI0lQNslQ== + dependencies: + "@babel/runtime" "^7.9.1" + compute-scroll-into-view "^1.0.13" + prop-types "^15.7.2" + react-is "^16.13.1" + duplexer@^0.1.1: version "0.1.1" resolved "https://registry.yarnpkg.com/duplexer/-/duplexer-0.1.1.tgz#ace6ff808c1ce66b57d1ebf97977acb02334cfc1" @@ -6631,6 +7390,13 @@ encodeurl@~1.0.2: resolved "https://registry.yarnpkg.com/encodeurl/-/encodeurl-1.0.2.tgz#ad3ff4c86ec2d029322f5a02c3a9a606c95b3f59" integrity sha1-rT/0yG7C0CkyL1oCw6mmBslbP1k= +encoding@^0.1.11: + version "0.1.13" + resolved "https://registry.yarnpkg.com/encoding/-/encoding-0.1.13.tgz#56574afdd791f54a8e9b2785c0582a2d26210fa9" + integrity sha512-ETBauow1T35Y/WZMkio9jiM0Z5xjHHmJ4XmjZOq1l/dXz3lr2sRn87nJy20RupqSh1F2m3HHPSp8ShIPQJrJ3A== + dependencies: + iconv-lite "^0.6.2" + encoding@^0.1.12: version "0.1.12" resolved "https://registry.yarnpkg.com/encoding/-/encoding-0.1.12.tgz#538b66f3ee62cd1ab51ec323829d1f9480c74beb" @@ -7355,6 +8121,19 @@ fb-watchman@^2.0.0: dependencies: bser "2.1.1" +fbjs@^0.8.1: + version "0.8.18" + resolved "https://registry.yarnpkg.com/fbjs/-/fbjs-0.8.18.tgz#9835e0addb9aca2eff53295cd79ca1cfc7c9662a" + integrity sha512-EQaWFK+fEPSoibjNy8IxUtaFOMXcWsY0JaVrQoZR9zC8N2Ygf9iDITPWjUTVIax95b6I742JFLqASHfsag/vKA== + dependencies: + core-js "^1.0.0" + isomorphic-fetch "^2.1.1" + loose-envify "^1.0.0" + object-assign "^4.1.0" + promise "^7.1.1" + setimmediate "^1.0.5" + ua-parser-js "^0.7.30" + fd-slicer@~1.1.0: version "1.1.0" resolved 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dependencies: safer-buffer ">= 2.1.2 < 3" +iconv-lite@^0.6.2: + version "0.6.3" + resolved "https://registry.yarnpkg.com/iconv-lite/-/iconv-lite-0.6.3.tgz#a52f80bf38da1952eb5c681790719871a1a72501" + integrity sha512-4fCk79wshMdzMp2rH06qWrJE4iolqLhCUH+OiuIgU++RB0+94NlDL81atO7GX55uUKueo0txHNtvEyI6D7WdMw== + dependencies: + safer-buffer ">= 2.1.2 < 3.0.0" + icss-utils@^4.0.0, icss-utils@^4.1.1: version "4.1.1" resolved "https://registry.yarnpkg.com/icss-utils/-/icss-utils-4.1.1.tgz#21170b53789ee27447c2f47dd683081403f9a467" @@ -8450,6 +9253,14 @@ ini@^1.3.5: resolved "https://registry.yarnpkg.com/ini/-/ini-1.3.5.tgz#eee25f56db1c9ec6085e0c22778083f596abf927" integrity sha512-RZY5huIKCMRWDUqZlEi72f/lmXKMvuszcMBduliQ3nnWbx9X/ZBQO7DijMEYS9EhHBb2qacRUMtC7svLwe0lcw== +inline-style-prefixer@^3.0.8: + version "3.0.8" + resolved "https://registry.yarnpkg.com/inline-style-prefixer/-/inline-style-prefixer-3.0.8.tgz#8551b8e5b4d573244e66a34b04f7d32076a2b534" + integrity 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sha1-TkMekrEalzFjaqH5yNHMvP2reN8= +isomorphic-fetch@^2.1.1, isomorphic-fetch@^2.2.1: + version "2.2.1" + resolved "https://registry.yarnpkg.com/isomorphic-fetch/-/isomorphic-fetch-2.2.1.tgz#611ae1acf14f5e81f729507472819fe9733558a9" + integrity sha512-9c4TNAKYXM5PRyVcwUZrF3W09nQ+sO7+jydgs4ZGW9dhsLG2VOlISJABombdQqQRXCwuYG3sYV/puGf5rp0qmA== + dependencies: + node-fetch "^1.0.1" + whatwg-fetch ">=0.10.0" + isstream@~0.1.2: version "0.1.2" resolved "https://registry.yarnpkg.com/isstream/-/isstream-0.1.2.tgz#47e63f7af55afa6f92e1500e690eb8b8529c099a" @@ -9908,6 +10727,11 @@ jss@^10.0.3, jss@^10.3.0: array-includes "^3.1.2" object.assign "^4.1.2" +keycode@^2.1.8: + version "2.2.1" + resolved "https://registry.yarnpkg.com/keycode/-/keycode-2.2.1.tgz#09c23b2be0611d26117ea2501c2c391a01f39eff" + integrity sha512-Rdgz9Hl9Iv4QKi8b0OlCRQEzp4AgVxyCtz5S/+VIHezDmrDhkp2N2TqBWOLz0/gbeREXOOiI9/4b8BY9uw2vFg== + killable@^1.0.1: version "1.0.1" resolved "https://registry.yarnpkg.com/killable/-/killable-1.0.1.tgz#4c8ce441187a061c7474fb87ca08e2a638194892" @@ -10012,6 +10836,13 @@ lines-and-columns@^1.1.6: resolved "https://registry.yarnpkg.com/lines-and-columns/-/lines-and-columns-1.1.6.tgz#1c00c743b433cd0a4e80758f7b64a57440d9ff00" integrity sha1-HADHQ7QzzQpOgHWPe2SldEDZ/wA= +linkify-it@^2.0.3: + version "2.2.0" + resolved "https://registry.yarnpkg.com/linkify-it/-/linkify-it-2.2.0.tgz#e3b54697e78bf915c70a38acd78fd09e0058b1cf" + integrity sha512-GnAl/knGn+i1U/wjBz3akz2stz+HrHLsxMwHQGofCDfPvlf+gDKN58UtfmUquTY4/MXeE2x7k19KQmeoZi94Iw== + dependencies: + uc.micro "^1.0.1" + listr-silent-renderer@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/listr-silent-renderer/-/listr-silent-renderer-1.1.1.tgz#924b5a3757153770bf1a8e3fbf74b8bbf3f9242e" @@ -10156,6 +10987,11 @@ lodash.memoize@4.x, lodash.memoize@^4.1.2: resolved "https://registry.yarnpkg.com/lodash.memoize/-/lodash.memoize-4.1.2.tgz#bcc6c49a42a2840ed997f323eada5ecd182e0bfe" integrity sha1-vMbEmkKihA7Zl/Mj6tpezRguC/4= +lodash.merge@^4.6.0: + version "4.6.2" + resolved "https://registry.yarnpkg.com/lodash.merge/-/lodash.merge-4.6.2.tgz#558aa53b43b661e1925a0afdfa36a9a1085fe57a" + integrity sha512-0KpjqXRVvrYyCsX1swR/XTK0va6VQkQM6MNo7PqW77ByjAhoARA8EfrP1N4+KlKj8YS0ZUCtRT/YUuhyYDujIQ== + lodash.once@^4.1.1: version "4.1.1" resolved "https://registry.yarnpkg.com/lodash.once/-/lodash.once-4.1.1.tgz#0dd3971213c7c56df880977d504c88fb471a97ac" @@ -10181,6 +11017,11 @@ lodash.templatesettings@^4.0.0: dependencies: lodash._reinterpolate "^3.0.0" +lodash.throttle@^4.1.1: + version "4.1.1" + resolved "https://registry.yarnpkg.com/lodash.throttle/-/lodash.throttle-4.1.1.tgz#c23e91b710242ac70c37f1e1cda9274cc39bf2f4" + integrity sha512-wIkUCfVKpVsWo3JSZlc+8MB5it+2AN5W8J7YVMST30UrvcQNZ1Okbj+rbVniijTWE6FGYy4XJq/rHkas8qJMLQ== + lodash.uniq@^4.5.0: version "4.5.0" resolved "https://registry.yarnpkg.com/lodash.uniq/-/lodash.uniq-4.5.0.tgz#d0225373aeb652adc1bc82e4945339a842754773" @@ -10196,6 +11037,11 @@ lodash@4.17.20, lodash@^4.17.19, lodash@^4.17.20: resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.15.tgz#b447f6670a0455bbfeedd11392eff330ea097548" integrity sha512-8xOcRHvCjnocdS5cpwXQXVzmmh5e5+saE2QGoeQmbKmRS6J3VQppPOIt0MnmE+4xlZoumy0GPG0D0MVIQbNA1A== +lodash@^4.17.10: + version "4.17.21" + resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.21.tgz#679591c564c3bffaae8454cf0b3df370c3d6911c" + integrity sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg== + log-symbols@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/log-symbols/-/log-symbols-1.0.2.tgz#376ff7b58ea3086a0f09facc74617eca501e1a18" @@ -10303,6 +11149,23 @@ map-visit@^1.0.0: dependencies: object-visit "^1.0.0" +material-ui@^0.20.0: + version "0.20.2" + resolved "https://registry.yarnpkg.com/material-ui/-/material-ui-0.20.2.tgz#5fc9b4b62b691d3b16c89d8e54597a0412b52c7d" + integrity sha512-VeqgQkdvtK193w+FFvXDEwlVxI4rWk83eWbpYLeOIHDPWr3rbB9B075JRnJt/8IsI2X8q5Aia5W3+7m4KkleDg== + dependencies: + babel-runtime "^6.23.0" + inline-style-prefixer "^3.0.8" + keycode "^2.1.8" + lodash.merge "^4.6.0" + lodash.throttle "^4.1.1" + prop-types "^15.5.7" + react-event-listener "^0.6.2" + react-transition-group "^1.2.1" + recompose "^0.26.0" + simple-assign "^0.1.0" + warning "^3.0.0" + md5.js@^1.3.4: version "1.3.5" resolved "https://registry.yarnpkg.com/md5.js/-/md5.js-1.3.5.tgz#b5d07b8e3216e3e27cd728d72f70d1e6a342005f" @@ -10557,6 +11420,11 @@ mkdirp@^0.5.1, mkdirp@^0.5.3, mkdirp@^0.5.4, mkdirp@^0.5.5, mkdirp@~0.5.1: dependencies: minimist "^1.2.5" +moment@2.22.2: + version "2.22.2" + resolved "https://registry.yarnpkg.com/moment/-/moment-2.22.2.tgz#3c257f9839fc0e93ff53149632239eb90783ff66" + integrity 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"^1.10.0" +node-fetch@^1.0.1: + version "1.7.3" + resolved "https://registry.yarnpkg.com/node-fetch/-/node-fetch-1.7.3.tgz#980f6f72d85211a5347c6b2bc18c5b84c3eb47ef" + integrity sha512-NhZ4CsKx7cYm2vSrBAr2PvFOe6sWDf0UYLRqA6svUYg7+/TSfVAu49jYC4BvQ4Sms9SZgdqGBgroqfDhJdTyKQ== + dependencies: + encoding "^0.1.11" + is-stream "^1.0.1" + node-forge@^0.10.0: version "0.10.0" resolved "https://registry.npmjs.org/node-forge/-/node-forge-0.10.0.tgz#32dea2afb3e9926f02ee5ce8794902691a676bf3" @@ -12237,6 +13118,13 @@ promise-inflight@^1.0.1: resolved "https://registry.yarnpkg.com/promise-inflight/-/promise-inflight-1.0.1.tgz#98472870bf228132fcbdd868129bad12c3c029e3" integrity sha1-mEcocL8igTL8vdhoEputEsPAKeM= +promise@^7.1.1: + version "7.3.1" + resolved "https://registry.yarnpkg.com/promise/-/promise-7.3.1.tgz#064b72602b18f90f29192b8b1bc418ffd1ebd3bf" + integrity sha512-nolQXZ/4L+bP/UGlkfaIujX9BKxGwmQ9OT4mOt5yvy8iK1h3wqTEJCijzGANTCCl9nWjY41juyAn2K3Q1hLLTg== + dependencies: + asap "~2.0.3" + 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+resize-observer-polyfill@^1.5.1: + version "1.5.1" + resolved "https://registry.yarnpkg.com/resize-observer-polyfill/-/resize-observer-polyfill-1.5.1.tgz#0e9020dd3d21024458d4ebd27e23e40269810464" + integrity sha512-LwZrotdHOo12nQuZlHEmtuXdqGoOD0OhaxopaNFxWzInpEgaLWoVuAMbTzixuosCx2nEG58ngzW3vxdWoxIgdg== + resolve-cwd@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/resolve-cwd/-/resolve-cwd-2.0.0.tgz#00a9f7387556e27038eae232caa372a6a59b665a" @@ -13126,6 +14101,13 @@ rgba-regex@^1.0.0: resolved "https://registry.yarnpkg.com/rgba-regex/-/rgba-regex-1.0.0.tgz#43374e2e2ca0968b0ef1523460b7d730ff22eeb3" integrity sha1-QzdOLiyglosO8VI0YLfXMP8i7rM= +rifm@^0.7.0: + version "0.7.0" + resolved "https://registry.yarnpkg.com/rifm/-/rifm-0.7.0.tgz#debe951a9c83549ca6b33e5919f716044c2230be" + integrity sha512-DSOJTWHD67860I5ojetXdEQRIBvF6YcpNe53j0vn1vp9EUb9N80EiZTxgP+FkDKorWC8PZw052kTF4C1GOivCQ== + dependencies: + "@babel/runtime" "^7.3.1" + rimraf@^2.5.4, rimraf@^2.6.2, rimraf@^2.6.3: version "2.7.1" resolved "https://registry.yarnpkg.com/rimraf/-/rimraf-2.7.1.tgz#35797f13a7fdadc566142c29d4f07ccad483e3ec" @@ -13200,6 +14182,11 @@ run-queue@^1.0.0, run-queue@^1.0.3: dependencies: aproba "^1.1.1" +rxjs-compat@6.6.3: + version "6.6.3" + resolved "https://registry.yarnpkg.com/rxjs-compat/-/rxjs-compat-6.6.3.tgz#141405fcee11f48718d428b99c8f01826f594e5c" + integrity sha512-y+wUqq7bS2dG+7rH2fNMoxsDiJ32RQzFxZQE/JdtpnmEZmwLQrb1tCiItyHxdXJHXjmHnnzFscn3b6PEmORGKw== + rxjs@^6.3.3: version "6.6.0" resolved "https://registry.yarnpkg.com/rxjs/-/rxjs-6.6.0.tgz#af2901eedf02e3a83ffa7f886240ff9018bbec84" @@ -13231,7 +14218,7 @@ safe-regex@^1.1.0: dependencies: ret "~0.1.10" -"safer-buffer@>= 2.1.2 < 3", safer-buffer@^2.0.2, safer-buffer@^2.1.0, safer-buffer@~2.1.0: +"safer-buffer@>= 2.1.2 < 3", "safer-buffer@>= 2.1.2 < 3.0.0", safer-buffer@^2.0.2, safer-buffer@^2.1.0, safer-buffer@~2.1.0: version "2.1.2" resolved 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"https://registry.yarnpkg.com/simple-assign/-/simple-assign-0.1.0.tgz#17fd3066a5f3d7738f50321bb0f14ca281cc4baa" + integrity sha512-otdSSQzuVsmDoe5MnSm4ZgHd5sl0ak6A1CTjW1R/DUHQ8xoZuU1NUzf9x6n9Dvp3nxpvW51WNMQ/7rQ9432xDg== + simple-swizzle@^0.2.2: version "0.2.2" resolved "https://registry.yarnpkg.com/simple-swizzle/-/simple-swizzle-0.2.2.tgz#a4da6b635ffcccca33f70d17cb92592de95e557a" @@ -14180,7 +15172,7 @@ svgo@^1.0.0, svgo@^1.2.2: unquote "~1.1.1" util.promisify "~1.0.0" -symbol-observable@^1.1.0: +symbol-observable@^1.0.4, symbol-observable@^1.1.0: version "1.2.0" resolved "https://registry.yarnpkg.com/symbol-observable/-/symbol-observable-1.2.0.tgz#c22688aed4eab3cdc2dfeacbb561660560a00804" integrity sha512-e900nM8RRtGhlV36KGEU9k65K3mPb1WV70OdjfxlG2EAuM1noi/E/BaW/uMhL7bPEssK8QV57vN3esixjUvcXQ== @@ -14316,6 +15308,11 @@ throat@^5.0.0: resolved "https://registry.yarnpkg.com/throat/-/throat-5.0.0.tgz#c5199235803aad18754a667d659b5e72ce16764b" integrity sha512-fcwX4mndzpLQKBS1DVYhGAcYaYt7vsHNIvQV+WXMvnow5cgjPphq5CaayLaGsjRdSCKZFNGt7/GYAuXaNOiYCA== +throttle-debounce@2.1.0: + version "2.1.0" + resolved "https://registry.yarnpkg.com/throttle-debounce/-/throttle-debounce-2.1.0.tgz#257e648f0a56bd9e54fe0f132c4ab8611df4e1d5" + integrity sha512-AOvyNahXQuU7NN+VVvOOX+uW6FPaWdAOdRP5HfwYxAfCzXTFKRMoIMk+n+po318+ktcChx+F1Dd91G3YHeMKyg== + throttleit@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/throttleit/-/throttleit-1.0.0.tgz#9e785836daf46743145a5984b6268d828528ac6c" @@ -14372,6 +15369,11 @@ tiny-warning@^1.0.0, tiny-warning@^1.0.2, tiny-warning@^1.0.3: resolved "https://registry.yarnpkg.com/tiny-warning/-/tiny-warning-1.0.3.tgz#94a30db453df4c643d0fd566060d60a875d84754" integrity sha512-lBN9zLN/oAf68o3zNXYrdCt1kP8WsiGW8Oo2ka41b2IM5JL/S1CTyX1rW0mb/zSuJun0ZUrDxx4sqvYS2FWzPA== +tlds@^1.199.0: + version "1.251.0" + resolved "https://registry.yarnpkg.com/tlds/-/tlds-1.251.0.tgz#d5a79fe0ddd564dadef7b3ce0b5f7f6e5acd2f99" + integrity 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sha512-8Y75pvTYkLJW2hWQHXxoqRgV7qb9B+9vFEtidML+7koHUFapnVJAZ6cKs+Qjz5Aw3aZWHMC6u0wJE3At+nSGwA== + uglify-js@^3.1.4: version "3.10.0" resolved "https://registry.yarnpkg.com/uglify-js/-/uglify-js-3.10.0.tgz#397a7e6e31ce820bfd1cb55b804ee140c587a9e7" @@ -15022,6 +16034,20 @@ walker@^1.0.7, walker@~1.0.5: dependencies: makeerror "1.0.x" +warning@^3.0.0: + version "3.0.0" + resolved "https://registry.yarnpkg.com/warning/-/warning-3.0.0.tgz#32e5377cb572de4ab04753bdf8821c01ed605b7c" + integrity sha512-jMBt6pUrKn5I+OGgtQ4YZLdhIeJmObddh6CsibPxyQ5yPZm1XExSyzC1LCNX7BzhxWgiHmizBWJTHJIjMjTQYQ== + dependencies: + loose-envify "^1.0.0" + +warning@^4.0.1, warning@^4.0.2: + version "4.0.3" + resolved "https://registry.yarnpkg.com/warning/-/warning-4.0.3.tgz#16e9e077eb8a86d6af7d64aa1e05fd85b4678ca3" + integrity sha512-rpJyN222KWIvHJ/F53XSZv0Zl/accqHR8et1kpaMTD/fLCRxtV8iX8czMzY7sVZupTI3zcUTg8eycS2kNF9l6w== + dependencies: + loose-envify "^1.0.0" + watchpack-chokidar2@^2.0.1: version "2.0.1" resolved "https://registry.yarnpkg.com/watchpack-chokidar2/-/watchpack-chokidar2-2.0.1.tgz#38500072ee6ece66f3769936950ea1771be1c957" @@ -15188,6 +16214,11 @@ whatwg-encoding@^1.0.1, whatwg-encoding@^1.0.5: dependencies: iconv-lite "0.4.24" +whatwg-fetch@>=0.10.0: + version "3.6.20" + resolved "https://registry.yarnpkg.com/whatwg-fetch/-/whatwg-fetch-3.6.20.tgz#580ce6d791facec91d37c72890995a0b48d31c70" + integrity sha512-EqhiFU6daOA8kpjOWTL0olhVOF3i7OrFzSYiGsEMB8GcXS+RrzauAERX65xMeNWVqxA6HXH2m69Z9LaKKdisfg== + whatwg-fetch@^3.4.1: version "3.4.1" resolved "https://registry.npmjs.org/whatwg-fetch/-/whatwg-fetch-3.4.1.tgz#e5f871572d6879663fa5674c8f833f15a8425ab3" diff --git a/app/views/webserver/viewer.html.haml b/app/views/webserver/viewer.html.haml index 6665f6bef..80bd01d73 100644 --- a/app/views/webserver/viewer.html.haml +++ b/app/views/webserver/viewer.html.haml @@ -3,7 +3,7 @@ -# Protvista = javascript_include_tag('//d3js.org/d3.v4.min.js') -= javascript_include_tag('3dbio_viewer/build/protvista-pdb/protvista-pdb-2.0.1-est-2.js') += javascript_include_tag('3dbio_viewer/build/protvista-pdb/protvista-pdb-2.0.1-est-2-beta.1.js') = stylesheet_link_tag("https://ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.3/fonts.css") -# PDBE Molstar