{"data":[{"id":"10.15782/d6159w","type":"dois","attributes":{"doi":"10.15782/d6159w","identifiers":[],"creators":[{"name":"Drug Design Data Resource (D3R)","affiliation":["University of California, San Diego"],"nameIdentifiers":[{"schemeUri":"https://scicrunch.org/scicrunch/resolver/","nameIdentifier":"SCR:000497","nameIdentifierScheme":"RRID"}]}],"titles":[{"title":"Drug Design Data Resource Grand Challenge 2015 Dataset: HSP90 - Heat shock protein 90"}],"publisher":"Drug Design Data Resource (D3R)","container":{},"publicationYear":2016,"subjects":[{"subject":"HSP90"},{"subject":"aryl-benzimidazolone"},{"subject":"aminopyrimidine"},{"subject":"benzophenone"}],"contributors":[{"name":"AbbVie Inc.","affiliation":[],"contributorType":"DataCollector","nameIdentifiers":[{"schemeUri":"SCR:010484","nameIdentifier":"SCR:010484","nameIdentifierScheme":"RRID"}]},{"name":"Community Structure-Activity Resource","affiliation":[],"contributorType":"DataCollector","nameIdentifiers":[{"schemeUri":"SCR:010484","nameIdentifier":"SCR:002206","nameIdentifierScheme":"RRID"}]}],"dates":[{"date":"2016-09-02","dateType":"Updated"},{"date":"2016","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Protein-ligand binding data","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsDocumentedBy","relatedIdentifier":"https://drugdesigndata.org/about/grand-challenge-2015","relatedIdentifierType":"URL"}],"relatedItems":[],"sizes":["539KB"],"formats":["application/vnd.ms-excel"],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"As detailed elsewhere [Symon Gathiaka, Shuai Liu, Michael Chiu, Jeanne A Stuckey, You Na Kang, Huanwang Yang, Stephen K. Burley, W. Patrick Walters, Jim Delproposto, Ginger Kubish, James B. Dunbar, Jr., Heather A. Carlson, Rommie E. Amaro, Victoria A. Feher and Michael K. Gilson. D3R Grand Challenge 2015: Evaluation of Protein-Ligand Pose and Affinity Predictions. JCAMD, 2016, (in press)], the HSP90 dataset is based on enzyme inhibition data contributed by Abbvie Pharmaceuticals to CSAR, D3R’s predecessor, which further developed the dataset by adding new compounds and binding data. The Abbvie dataset contains a set of small molecules with their IC50 values for binding to the protein’s N-terminal ATP-binding domain, measured with a time-resolved fluorescence energy transfer (TR-FRET) assay. The dataset was expanded to a total of 180 with an additional set of 17 ligands, which were designed by the CSAR team, synthesized by WuXi AppTech and assayed by the same TR-FRET method. Some of the compounds were analyzed further by isothermal titration calorimetry and the OctetRed method. These compounds may be classified into three chemical series: aryl-benzimidazolones, pyrimidin-2-amines and benzophenone-like compounds. Each series includes approximately 11 compounds for which binding was undetectable by the TR-FRET assay, corresponding to an IC50 greater than ~50µM. IC50 values ranged from 5.2 nM to \u0026gt;50μM. The CSAR team also obtained co-crystal structures using exactly the same truncated form of the protein used in the binding assays with eight of the ligands. Resolution limits for the resulting co-crystal structures range from 1.60 – 1.95 Å, and the crystallization methods and conditions can be found in www.RCSB.org.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://drugdesigndata.org/about/datasets/408","contentUrl":[],"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2016-09-02T18:54:24Z","registered":"2016-09-02T18:54:25Z","published":null,"updated":"2025-04-17T01:44:44Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.15782/d6wc7z","type":"dois","attributes":{"doi":"10.15782/d6wc7z","identifiers":[],"creators":[{"name":"Drug Design Data Resource (D3R)","affiliation":["University of California, San Diego"],"nameIdentifiers":[{"schemeUri":"https://scicrunch.org/scicrunch/resolver/","nameIdentifier":"SCR:000497","nameIdentifierScheme":"RRID"}]}],"titles":[{"title":"Drug Design Data Resource Grand Challenge 2015 Dataset: MAP4K4 - Mitogen-activated protein kinase kinase kinase kinase 4"}],"publisher":"Drug Design Data Resource (D3R)","container":{},"publicationYear":2016,"subjects":[{"subject":"MAP4K4"},{"subject":"4-aminopyrimidine"},{"subject":"6-quinazoline"},{"subject":"aminopyridine"},{"subject":"pyrazole"},{"subject":"azaindole"},{"subject":"benzofuran"},{"subject":"furan-2-carboxamide"},{"subject":"benzoxepine"},{"subject":"indazole"}],"contributors":[{"name":"Genentech Inc.","affiliation":[],"contributorType":"DataCollector","nameIdentifiers":[{"schemeUri":"https://scicrunch.org/scicrunch/resolver/","nameIdentifier":"SCR:003997","nameIdentifierScheme":"RRID"}]}],"dates":[{"date":"2016-09-02","dateType":"Updated"},{"date":"2016","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Protein-ligand binding data","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsDocumentedBy","relatedIdentifier":"https://drugdesigndata.org/about/grand-challenge-2015","relatedIdentifierType":"URL"}],"relatedItems":[],"sizes":["109KB"],"formats":["application/vnd.ms-excel"],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"As detailed elsewhere [Symon Gathiaka, Shuai Liu, Michael Chiu, Jeanne A Stuckey, You Na Kang, Huanwang Yang, Stephen K. Burley, W. Patrick Walters, Jim Delproposto, Ginger Kubish, James B. Dunbar, Jr., Heather A. Carlson, Rommie E. Amaro, Victoria A. Feher and Michael K. Gilson. D3R Grand Challenge 2015: Evaluation of Protein-Ligand Pose and Affinity Predictions. JCAMD, 2016, (in press)], the MAP4K4 dataset was contributed by Genentech, Inc., and comprises 30 crystal structures of the enzyme’s catalytic domain bound to 30 chemically varied ligands. IC50 values were measured by an ATP consumption assay, for 18 of the 30 compounds, and Ki values for 15 of the compounds determined by a Surface Plasmon Resonance (SPR)-based fragment screen. The IC50 values ranged from 0.0031 to 10 μM while the resolution of the co-crystal structures is \u0026lt; 2.5Å. In general, these compounds are diverse, ranging in size from that of fragments with high ligand efficiency to drug-like, with 65% of the dataset having double digit nM inhibition.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://drugdesigndata.org/about/datasets/409","contentUrl":[],"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2016-09-02T18:54:30Z","registered":"2016-09-02T18:54:31Z","published":null,"updated":"2025-04-17T01:44:42Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.15782/d6rp4p","type":"dois","attributes":{"doi":"10.15782/d6rp4p","identifiers":[],"creators":[{"name":"Drug Design Data Resource (D3R)","affiliation":["University of California, San Diego"],"nameIdentifiers":[{"schemeUri":"https://scicrunch.org/scicrunch/resolver/","nameIdentifier":"https://scicrunch.org/scicrunch/resolver/SCR:000497","nameIdentifierScheme":"RRID"}]}],"titles":[{"lang":"en-us","title":"Drug Design Data Resource Grand Challenge 2 Dataset: FXR - Farnesoid X receptor"}],"publisher":"Drug Design Data Resource (D3R)","container":{},"publicationYear":2017,"subjects":[{"subject":"FXR"},{"subject":"Benzimidazoles"},{"subject":"Spiros"},{"subject":"Sulfonamides"},{"subject":"Isoxazoles"}],"contributors":[{"name":"Roche Inc.","affiliation":[],"contributorType":"DataCollector","nameIdentifiers":[{"schemeUri":"https://scicrunch.org/scicrunch/resolver/","nameIdentifier":"https://scicrunch.org/scicrunch/resolver/SCR:001326","nameIdentifierScheme":"RRID"}]}],"dates":[{"date":"2017-04-13","dateType":"Updated"},{"date":"2017","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Protein-ligand binding data","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["71.5MB"],"formats":["application/x-zip-compressed"],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"lang":"en-us","description":"The Farnesoid X receptor (FXR) dataset, contributed by Roche, comprises 36 co-crystal structures of FXR with chemically varied ligands, one apo structure, and 102 IC50s measured with a Scintillation Proximity Assay. Among these compounds, 96 belong to four chemical series (benzimidazoles, isoxazoles, spiros and sulfonamides) and six are classified as miscellaneous. For 92 of the compounds, IC50 values range from 0.000335 to 62.37 μM, while the remaining ten IC50s are greater than 100 μM. Some of the compounds were synthesized as racemates, diastereomers and epimers, as noted within the dataset. The 37 co-crystal and apo structures have resolutions ranging from 1.8 to 2.6 Å and contain representatives from each of the four chemical series.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://drugdesigndata.org/about/datasets/882","contentUrl":[],"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":null,"isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2017-04-13T18:20:11Z","registered":"2017-04-13T18:20:13Z","published":null,"updated":"2020-10-10T14:48:22Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}}],"meta":{"total":3,"totalPages":1,"page":1},"links":{"self":"https://api.datacite.org/dois?prefix=10.15782"}}