Structure of PDB 5kh7 Chain A Binding Site BS04

Receptor Information
>5kh7 Chain A (length=100) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYIN
GHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFG
Ligand information
Ligand ID6T7
InChIInChI=1S/C12H11N3O3/c16-11-4-3-10(9-2-1-6-13-8-9)14-15(11)7-5-12(17)18/h1-4,6,8H,5,7H2,(H,17,18)
InChIKeyFPHNPEYKDLCEEE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)CCN1N=C(C=CC1=O)c2cccnc2
OpenEye OEToolkits 2.0.5c1cc(cnc1)C2=NN(C(=O)C=C2)CCC(=O)O
FormulaC12 H11 N3 O3
Name3-(6-oxidanylidene-3-pyridin-3-yl-pyridazin-1-yl)propanoic acid
ChEMBLCHEMBL4084541
DrugBank
ZINCZINC000061957849
PDB chain5kh7 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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PDB5kh7 Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		W1143 R1155 W1182 Y1184 Y1189
Binding residue
(residue number reindexed from 1)		W35 R47 W74 Y76 Y81
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.66,Kd=220uM
BindingDB: Kd=210000nM,IC50=350000nM
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:5kh7, PDBe:5kh7, PDBj:5kh7
PDBsum5kh7
PubMed29019676
UniProtQ9UBN7|HDAC6_HUMAN Histone deacetylase 6 (Gene Name=HDAC6)

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