Structure of PDB 4ly1 Chain A Binding Site BS03

Receptor Information
>4ly1 Chain A (length=368) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRP
HKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGL
FEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDI
VLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFP
GTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSA
VVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIR
NVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTP
EYMEKIKQRLFENLRMLP
Ligand information
Ligand ID20Y
InChIInChI=1S/C19H17N3O2S/c1-12(23)21-15-7-4-13(5-8-15)19(24)22-17-11-14(6-9-16(17)20)18-3-2-10-25-18/h2-11H,20H2,1H3,(H,21,23)(H,22,24)
InChIKeyABZSPJVXTTUFAA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(Nc1ccc(cc1)C(=O)Nc2c(N)ccc(c2)c3sccc3)C
CACTVS 3.385CC(=O)Nc1ccc(cc1)C(=O)Nc2cc(ccc2N)c3sccc3
OpenEye OEToolkits 1.7.6CC(=O)Nc1ccc(cc1)C(=O)Nc2cc(ccc2N)c3cccs3
FormulaC19 H17 N3 O2 S
Name4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide
ChEMBLCHEMBL235842
DrugBank
ZINCZINC000014970815
PDB chain4ly1 Chain A Residue 407 [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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PDB4ly1 Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability.
Resolution1.57 Å
Binding residue
(original residue number in PDB)		Y29 M35 L144 H145 H146 G154 F155 C156 D181 H183 F210 L276 G305 G306 Y308
Binding residue
(residue number reindexed from 1)		Y18 M24 L133 H134 H135 G143 F144 C145 D170 H172 F199 L265 G294 G295 Y297
Annotation score1
Binding affinityMOAD: Kd=0.0552uM
PDBbind-CN: -logKd/Ki=7.26,Kd=0.0552uM
BindingDB: IC50=100nM,Ki=1.5nM,Kd=55.2nM
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:4ly1, PDBe:4ly1, PDBj:4ly1
PDBsum4ly1
PubMed23897821
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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