Structure of PDB 7kbh Chain B Binding Site BS04

Receptor Information
>7kbh Chain B (length=366) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHK
ATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFE
FCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVL
AILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYYFPG
TGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAV
VLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRN
VARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPE
YMEKIKQRLFENLRML
Ligand information
Ligand IDWB4
InChIInChI=1S/C30H29N5O2S2/c1-38-26-12-5-4-10-23(26)29(36)32-15-7-6-11-24(35-30(37)27-18-31-19-39-27)28-33-17-25(34-28)22-14-13-20-8-2-3-9-21(20)16-22/h2-5,8-10,12-14,16-19,24H,6-7,11,15H2,1H3,(H,32,36)(H,33,34)(H,35,37)/t24-/m0/s1
InChIKeyIBVNIPPBTCWYJG-DEOSSOPVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CSc1ccccc1C(=O)NCCCC[C@@H](c2[nH]c(cn2)c3ccc4ccccc4c3)NC(=O)c5cncs5
ACDLabs 12.01C(NC(=O)c1cncs1)(CCCCNC(=O)c2c(cccc2)SC)c3nc(cn3)c4cc5ccccc5cc4
CACTVS 3.385CSc1ccccc1C(=O)NCCCC[C@H](NC(=O)c2scnc2)c3[nH]c(cn3)c4ccc5ccccc5c4
OpenEye OEToolkits 2.0.7CSc1ccccc1C(=O)NCCCCC(c2[nH]c(cn2)c3ccc4ccccc4c3)NC(=O)c5cncs5
CACTVS 3.385CSc1ccccc1C(=O)NCCCC[CH](NC(=O)c2scnc2)c3[nH]c(cn3)c4ccc5ccccc5c4
FormulaC30 H29 N5 O2 S2
NameN-{(1S)-5-{[2-(methylsulfanyl)benzene-1-carbonyl]amino}-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide
ChEMBLCHEMBL4763995
DrugBank
ZINC
PDB chain7kbh Chain B Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7kbh Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on a 2-Substituted Benzamide Zinc Binding Group.
Resolution2.68 Å
Binding residue
(original residue number in PDB)		G28 H29 P30 M31 D100 H142 G150 F151 C152 H179 F207 D266 L273 G302 G303
Binding residue
(residue number reindexed from 1)		G19 H20 P21 M22 D91 H133 G141 F142 C143 H170 F198 D257 L264 G293 G294
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity

View graph for
Molecular Function
External links
PDB RCSB:7kbh, PDBe:7kbh, PDBj:7kbh
PDBsum7kbh
PubMed33335670
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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