Structure of PDB 5iwg Chain A Binding Site BS03

Receptor Information
>5iwg 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 IDIWX
InChIInChI=1S/C18H19FN2O2/c19-15-4-1-12(2-5-15)14-3-6-16(20)17(11-14)21-18(22)13-7-9-23-10-8-13/h1-6,11,13H,7-10,20H2,(H,21,22)
InChIKeyZFCDNONWGMYBHA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(Nc2cc(c1ccc(F)cc1)ccc2N)C3CCOCC3
OpenEye OEToolkits 2.0.4c1cc(ccc1c2ccc(c(c2)NC(=O)C3CCOCC3)N)F
CACTVS 3.385Nc1ccc(cc1NC(=O)C2CCOCC2)c3ccc(F)cc3
FormulaC18 H19 F N2 O2
NameN-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)oxane-4-carboxamide
ChEMBLCHEMBL3828396
DrugBank
ZINCZINC000145105788
PDB chain5iwg Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5iwg Kinetic and structural insights into the binding of histone deacetylase 1 and 2 (HDAC1, 2) inhibitors.
Resolution1.66 Å
Binding residue
(original residue number in PDB)		M35 R39 F114 L144 H145 H146 G154 F155 C156 D181 H183 L276 G305 G306 Y308
Binding residue
(residue number reindexed from 1)		M24 R28 F103 L133 H134 H135 G143 F144 C145 D170 H172 L265 G294 G295 Y297
Annotation score1
Binding affinityMOAD: Ki=0.346uM
PDBbind-CN: -logKd/Ki=6.46,Ki=0.346uM
BindingDB: IC50=62nM
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:5iwg, PDBe:5iwg, PDBj:5iwg
PDBsum5iwg
PubMed27377864
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

[Back to BioLiP]