Structure of PDB 6xeb Chain B Binding Site BS04

Receptor Information
>6xeb 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 IDV1P
InChIInChI=1S/C24H35N5O4/c1-3-24(32,33)13-9-5-8-12-18(26-23(31)17-14-29(2)15-17)19-20(21(25)30)28-22(27-19)16-10-6-4-7-11-16/h4,6-7,10-11,17-18,32-33H,3,5,8-9,12-15H2,1-2H3,(H2,25,30)(H,26,31)(H,27,28)/t18-/m0/s1
InChIKeyMYVMGGDKZVVQFO-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCC(O)(O)CCCCC[C@H](NC(=O)C1CN(C)C1)c2[nH]c(nc2C(N)=O)c3ccccc3
OpenEye OEToolkits 2.0.7CCC(CCCCC[C@@H](c1c(nc([nH]1)c2ccccc2)C(=O)N)NC(=O)C3CN(C3)C)(O)O
OpenEye OEToolkits 2.0.7CCC(CCCCCC(c1c(nc([nH]1)c2ccccc2)C(=O)N)NC(=O)C3CN(C3)C)(O)O
CACTVS 3.385CCC(O)(O)CCCCC[CH](NC(=O)C1CN(C)C1)c2[nH]c(nc2C(N)=O)c3ccccc3
ACDLabs 12.01O=C(C1CN(C)C1)NC(CCCCCC(CC)(O)O)c3nc(c2ccccc2)nc3C(N)=O
FormulaC24 H35 N5 O4
Name5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6xeb 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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PDB6xeb Development of a selective HDAC inhibitor aimed at reactivating the HIV latent reservoir.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		G28 P30 D100 H141 H142 G150 F151 H179 F206 Y304
Binding residue
(residue number reindexed from 1)		G19 P21 D91 H132 H133 G141 F142 H170 F197 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:6xeb, PDBe:6xeb, PDBj:6xeb
PDBsum6xeb
PubMed32738976
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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