Structure of PDB 1w22 Chain B Binding Site BS05

Receptor Information
>1w22 Chain B (length=350) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASM
EEMATFHTDAYLQHLQKVSQEYGLGYDCPATEGIFDYAAAIGGATITAAQ
CLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILY
VDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRY
YSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPM
CSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILG
KTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLK
Ligand information
Ligand IDNHB
InChIInChI=1S/C17H15N3O4S2/c1-20(13-7-5-12(6-8-13)17(21)19-22)26(23,24)16-10-9-15(25-16)14-4-2-3-11-18-14/h2-11,22H,1H3,(H,19,21)
InChIKeyLFGYSFPVLMPUPE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN(c1ccc(cc1)C(=O)NO)[S](=O)(=O)c2sc(cc2)c3ccccn3
OpenEye OEToolkits 1.5.0CN(c1ccc(cc1)C(=O)NO)S(=O)(=O)c2ccc(s2)c3ccccn3
ACDLabs 10.04O=S(=O)(c2sc(c1ncccc1)cc2)N(c3ccc(C(=O)NO)cc3)C
FormulaC17 H15 N3 O4 S2
NameN-HYDROXY-4-(METHYL{[5-(2-PYRIDINYL)-2-THIENYL]SULFONYL}AMINO)BENZAMIDE
ChEMBL
DrugBankDB02917
ZINCZINC000005850198
PDB chain1w22 Chain B Residue 1378 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1w22 Crystal Structure of a Eukaryotic Zn-Dependent Histone Deacetylase,Human Hdac8,Complexed with a Hydroxamic Acid Inhibitor
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D101 H143 G151 F152 D178 H180 F208 Y306
Binding residue
(residue number reindexed from 1)		D77 H119 G127 F128 D154 H156 F184 Y282
Annotation score1
Binding affinityMOAD: ic50=175.5nM
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
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Cellular Component
External links
PDB RCSB:1w22, PDBe:1w22, PDBj:1w22
PDBsum1w22
PubMed15477595
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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