Structure of PDB 6hsk Chain A Binding Site BS02

Receptor Information
>6hsk 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
AIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGIL
RLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGD
VSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQ
LGADTISGDRLGCFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTAR
CWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQ
QILNYIKGNLKHVV
Ligand information
Ligand IDGOK
InChIInChI=1S/C21H26N6O2/c1-26-14-17(18-4-2-3-5-19(18)26)11-22-10-15-6-8-27(9-7-15)21-23-12-16(13-24-21)20(28)25-29/h2-5,12-15,22,29H,6-11H2,1H3,(H,25,28)
InChIKeyPAWIYAYFNXQGAP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cn1cc(c2c1cccc2)CNCC3CCN(CC3)c4ncc(cn4)C(=O)NO
CACTVS 3.385Cn1cc(CNCC2CCN(CC2)c3ncc(cn3)C(=O)NO)c4ccccc14
FormulaC21 H26 N6 O2
Name2-[4-[[(1-methylindol-3-yl)methylamino]methyl]piperidin-1-yl]-~{N}-oxidanyl-pyrimidine-5-carboxamide
ChEMBLCHEMBL2105763
DrugBankDB12985
ZINCZINC000035836133
PDB chain6hsk Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6hsk Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants.
Resolution2.096 Å
Binding residue
(original residue number in PDB)		H142 H143 G151 F152 D178 H180 G206 F208 P209 Y306
Binding residue
(residue number reindexed from 1)		H129 H130 G138 F139 D165 H167 G193 F195 P196 Y293
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.03,IC50=93nM
BindingDB: IC50=64nM,Ki=24nM,Kd=23nM
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:6hsk, PDBe:6hsk, PDBj:6hsk
PDBsum6hsk
PubMed30347148
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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