Structure of PDB 6hsh Chain A Binding Site BS02

Receptor Information
>6hsh Chain A (length=404) Species: 6183 (Schistosoma mansoni) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVGIVYGDQYRQLCCSSPKFGDRYALVMDLINAYKLIPELSRVPPLQWDS
PSRMYEAVTAFHSTEYVDALKKLQMLHCEEKELTADDELLMDSFSLNYDC
PGFPSVFDYSLAAVQGSLAAASALICRHCEVVINWGGGWHHAKRSEASGF
CYLNDIVLAIHRLVSSTQTRVLYVDLDLHHGDGVEEAFWYSPRVVTFSVH
HASPGFFPGTGTWNIFLNGAGRGRFSAFNLPLEEGINDLDWSNAIGPILD
SLNIVIQPSYVVVQCGADCLATDPHRIFRLTNFYPCSLSGYLYAIKKILS
WKVPTLILGGGGYNFPDTARLWTRVTALTIEEVKGKKMTISPEIPEHSYF
SRYGPDFELDIDYFPHESHNDSIQKHHRRILEQLRNYADLNKLIYDYDQV
YQLY
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 chain6hsh Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6hsh Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants.
Resolution1.545 Å
Binding residue
(original residue number in PDB)		D100 H142 G150 F151 D186 H188 F216 Y341
Binding residue
(residue number reindexed from 1)		D99 H141 G149 F150 D177 H179 F207 Y313
Annotation score1
Binding affinityMOAD: Kd=28.4nM
PDBbind-CN: -logKd/Ki=7.55,Kd=28.4nM
BindingDB: Kd=28nM,IC50=303nM
Enzymatic activity
Enzyme Commision number 3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity
GO:0046872 metal ion binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006338 chromatin remodeling
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6hsh, PDBe:6hsh, PDBj:6hsh
PDBsum6hsh
PubMed30347148
UniProtA5H660

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