Structure of PDB 6xdm Chain C Binding Site BS04

Receptor Information
>6xdm Chain C (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 IDV1D
InChIInChI=1S/C24H30FN5O4/c1-30-14-16(15-30)23(31)28-19(9-3-2-6-11-24(32,33)21-10-12-34-29-21)22-26-13-20(27-22)17-7-4-5-8-18(17)25/h4-5,7-8,10,12-13,16,19,32-33H,2-3,6,9,11,14-15H2,1H3,(H,26,27)(H,28,31)/t19-/m0/s1
InChIKeyKTQGXHKWGKIKPU-IBGZPJMESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1CC(C1)C(=O)N[CH](CCCCCC(O)(O)c2ccon2)c3[nH]cc(n3)c4ccccc4F
CACTVS 3.385CN1CC(C1)C(=O)N[C@@H](CCCCCC(O)(O)c2ccon2)c3[nH]cc(n3)c4ccccc4F
OpenEye OEToolkits 2.0.7CN1CC(C1)C(=O)NC(CCCCCC(c2ccon2)(O)O)c3[nH]cc(n3)c4ccccc4F
OpenEye OEToolkits 2.0.7CN1CC(C1)C(=O)N[C@@H](CCCCCC(c2ccon2)(O)O)c3[nH]cc(n3)c4ccccc4F
ACDLabs 12.01Fc1ccccc1c2cnc(n2)C(NC(C3CN(C)C3)=O)CCCCCC(c4ccon4)(O)O
FormulaC24 H30 F N5 O4
NameN-[(1S)-1-[4-(2-fluorophenyl)-1H-imidazol-2-yl]-7,7-dihydroxy-7-(1,2-oxazol-3-yl)heptyl]-1-methylazetidine-3-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6xdm Chain C Residue 410 [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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PDB6xdm Selective Class I HDAC Inhibitors Based on Aryl Ketone Zinc Binding Induce HIV-1 Protein for Clearance.
Resolution1.56 Å
Binding residue
(original residue number in PDB)		G28 P30 M31 D100 L140 H141 H142 G150 F151 C152 H179 F206 G301 G302 Y304
Binding residue
(residue number reindexed from 1)		G19 P21 M22 D91 L131 H132 H133 G141 F142 C143 H170 F197 G292 G293 Y295
Annotation score1
Binding affinityMOAD: ic50=0.1nM
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:6xdm, PDBe:6xdm, PDBj:6xdm
PDBsum6xdm
PubMed32676157
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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