Structure of PDB 6wbz Chain B Binding Site BS04

Receptor Information
>6wbz 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
AILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGT
GDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVV
LQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNV
ARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEY
MEKIKQRLFENLRMLP
Ligand information
Ligand IDTV7
InChIInChI=1S/C32H45N5O4/c1-4-32(39,40)14-10-6-7-13-26(35-29(38)24-20-31(24)15-17-37(5-2)18-16-31)28-33-21-27(34-28)23-19-22-11-8-9-12-25(22)36-30(23)41-3/h8-9,11-12,19,21,24,26,39-40H,4-7,10,13-18,20H2,1-3H3,(H,33,34)(H,35,38)/t24-,26+/m1/s1
InChIKeyYPIRISRXAGVBOC-RSXGOPAZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCN1CCC2(CC1)C[C@@H]2C(=O)N[C@@H](CCCCCC(O)(O)CC)c3[nH]c(cn3)c4cc5ccccc5nc4OC
OpenEye OEToolkits 2.0.7CCC(CCCCCC(c1[nH]c(cn1)c2cc3ccccc3nc2OC)NC(=O)C4CC45CCN(CC5)CC)(O)O
OpenEye OEToolkits 2.0.7CCC(CCCCC[C@@H](c1[nH]c(cn1)c2cc3ccccc3nc2OC)NC(=O)[C@H]4CC45CCN(CC5)CC)(O)O
ACDLabs 12.01C(C)C(CCCCCC(c3ncc(c1c(nc2c(c1)cccc2)OC)n3)NC(=O)C5CC45CCN(CC)CC4)(O)O
CACTVS 3.385CCN1CCC2(CC1)C[CH]2C(=O)N[CH](CCCCCC(O)(O)CC)c3[nH]c(cn3)c4cc5ccccc5nc4OC
FormulaC32 H45 N5 O4
Name(1S)-N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-6-ethyl-6-azaspiro[2.5]octane-1-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6wbz Chain B Residue 408 [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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PDB6wbz Discovery of ethyl ketone-based HDACs 1, 2, and 3 selective inhibitors for HIV latency reactivation.
Resolution1.32 Å
Binding residue
(original residue number in PDB)		H29 P30 E99 D100 H141 H142 G150 F151 H179 F206 L272 G302 Y304
Binding residue
(residue number reindexed from 1)		H20 P21 E90 D91 H132 H133 G141 F142 H170 F197 L263 G293 Y295
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:6wbz, PDBe:6wbz, PDBj:6wbz
PDBsum6wbz
PubMed32331932
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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