Structure of PDB 6xec Chain B Binding Site BS04

Receptor Information
>6xec 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 IDV1S
InChIInChI=1S/C28H38FN5O3/c1-3-28(36,37)12-6-4-5-7-22(32-26(35)21-17-27(21)13-15-34(2)16-14-27)24-23(18-30)31-25(33-24)19-8-10-20(29)11-9-19/h8-11,21-22,36-37H,3-7,12-17H2,1-2H3,(H,31,33)(H,32,35)/t21-,22+/m1/s1
InChIKeyHQQQLMWKYHVCDC-YADHBBJMSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01N#Cc1c(nc(n1)c2ccc(cc2)F)C(NC(C4C3(CCN(C)CC3)C4)=O)CCCCCC(CC)(O)O
CACTVS 3.385CCC(O)(O)CCCCC[CH](NC(=O)[CH]1CC12CCN(C)CC2)c3nc([nH]c3C#N)c4ccc(F)cc4
CACTVS 3.385CCC(O)(O)CCCCC[C@H](NC(=O)[C@H]1CC12CCN(C)CC2)c3nc([nH]c3C#N)c4ccc(F)cc4
OpenEye OEToolkits 2.0.7CCC(CCCCCC(c1c([nH]c(n1)c2ccc(cc2)F)C#N)NC(=O)C3CC34CCN(CC4)C)(O)O
OpenEye OEToolkits 2.0.7CCC(CCCCC[C@@H](c1c([nH]c(n1)c2ccc(cc2)F)C#N)NC(=O)[C@H]3CC34CCN(CC4)C)(O)O
FormulaC28 H38 F N5 O3
Name(1S)-N-{(1S)-1-[5-cyano-2-(4-fluorophenyl)-1H-imidazol-4-yl]-7,7-dihydroxynonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6xec 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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PDB6xec Development of a selective HDAC inhibitor aimed at reactivating the HIV latent reservoir.
Resolution1.701 Å
Binding residue
(original residue number in PDB)
P30 E99 D100 H141 H142 G150 F151 H179 F206 G302 Y304
Binding residue
(residue number reindexed from 1)
P21 E90 D91 H132 H133 G141 F142 H170 F197 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:6xec, PDBe:6xec, PDBj:6xec
PDBsum6xec
PubMed32738976
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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