Structure of PDB 3ewf Chain A Binding Site BS06

Receptor Information
>3ewf Chain A (length=364) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVAS
MEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAA
AIGGATITAAQCLIDGMCKVAINWSGGWHAAKKDEASGFCYLNDAVLGIL
RLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGD
VSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQ
LGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTAR
CWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQ
QILNYIKGNLKHVV
Ligand information
Ligand IDMCM
InChIInChI=1S/C10H9NO2/c1-6-4-10(12)13-9-5-7(11)2-3-8(6)9/h2-5H,11H2,1H3
InChIKeyGLNDAGDHSLMOKX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CC(=O)Oc2c1ccc(c2)N
CACTVS 3.341CC1=CC(=O)Oc2cc(N)ccc12
ACDLabs 10.04O=C2Oc1cc(ccc1C(=C2)C)N
FormulaC10 H9 N O2
Name7-AMINO-4-METHYL-CHROMEN-2-ONE;
7-AMINO-4-METHYLCOUMARIN
ChEMBLCHEMBL270672
DrugBankDB08168
ZINCZINC000000057949
PDB chain3ewf Chain J Residue 6 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ewf Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		K33 F152 P273
Binding residue
(residue number reindexed from 1)		K20 F139 P260
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0030544 Hsp70 protein binding
GO:0033558 protein lysine deacetylase activity
GO:0046872 metal ion binding
GO:0051879 Hsp90 protein binding
GO:0140297 DNA-binding transcription factor binding
GO:0160008 protein decrotonylase activity
GO:0160009 histone decrotonylase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006325 chromatin organization
GO:0007064 mitotic sister chromatid cohesion
GO:0031397 negative regulation of protein ubiquitination
GO:0031647 regulation of protein stability
GO:0032204 regulation of telomere maintenance
GO:0040029 epigenetic regulation of gene expression
Cellular Component
GO:0000118 histone deacetylase complex
GO:0000228 nuclear chromosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ewf, PDBe:3ewf, PDBj:3ewf
PDBsum3ewf
PubMed19053282
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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