Structure of PDB 6cee Chain A Binding Site BS04

Receptor Information
>6cee 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]
SPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYI
NGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKF
Ligand information
Ligand IDEYM
InChIInChI=1S/C12H12N2O3/c1-14-10-5-3-2-4-8(10)13-9(12(14)17)6-7-11(15)16/h2-5H,6-7H2,1H3,(H,15,16)
InChIKeyJIXBAXULUJSRDR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=O)C(=Nc2ccccc12)CCC(O)=O
ACDLabs 12.01c2ccc1c(N=C(C(=O)N1C)CCC(O)=O)c2
OpenEye OEToolkits 2.0.6CN1c2ccccc2N=C(C1=O)CCC(=O)O
FormulaC12 H12 N2 O3
Name3-(4-methyl-3-oxo-3,4-dihydroquinoxalin-2-yl)propanoic acid
ChEMBLCHEMBL4068652
DrugBank
ZINCZINC000001674125
PDB chain6cee Chain A Residue 1304 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6cee Identification and Structure-Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		W1143 G1154 R1155 W1182 Y1184 Y1189
Binding residue
(residue number reindexed from 1)		W36 G47 R48 W75 Y77 Y82
Annotation score1
Binding affinityMOAD: ic50=65uM
PDBbind-CN: -logKd/Ki=4.19,IC50=65uM
BindingDB: IC50=65000nM
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:6cee, PDBe:6cee, PDBj:6cee
PDBsum6cee
PubMed29741882
UniProtQ9UBN7|HDAC6_HUMAN Histone deacetylase 6 (Gene Name=HDAC6)

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