Structure of PDB 5wpb Chain A Binding Site BS04

Receptor Information
>5wpb Chain A (length=101) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRY
INGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNK
F
Ligand information
Ligand IDB8P
InChIInChI=1S/C17H15N3O3/c21-16(22)9-8-15-17(23-11-12-5-3-4-10-18-12)20-14-7-2-1-6-13(14)19-15/h1-7,10H,8-9,11H2,(H,21,22)
InChIKeyTXJSUZJFIYIMRT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2c(c1)nc(c(n2)OCc3ccccn3)CCC(=O)O
ACDLabs 12.01c21ccccc1nc(CCC(=O)O)c(n2)OCc3ccccn3
CACTVS 3.385OC(=O)CCc1nc2ccccc2nc1OCc3ccccn3
FormulaC17 H15 N3 O3
Name3-{3-[(pyridin-2-yl)methoxy]quinoxalin-2-yl}propanoic acid
ChEMBLCHEMBL4095967
DrugBank
ZINC
PDB chain5wpb Chain A Residue 1304 [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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PDB5wpb Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		W1143 G1154 R1155 S1175 D1178 W1182 Y1184 Y1189
Binding residue
(residue number reindexed from 1)		W37 G48 R49 S69 D72 W76 Y78 Y83
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.57,IC50=270uM
BindingDB: IC50=270000nM
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding

View graph for
Molecular Function
External links
PDB RCSB:5wpb, PDBe:5wpb, PDBj:5wpb
PDBsum5wpb
PubMed29019676
UniProtQ9UBN7|HDAC6_HUMAN Histone deacetylase 6 (Gene Name=HDAC6)

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