Structure of PDB 6wbq Chain A Binding Site BS01

Receptor Information
>6wbq Chain A (length=634) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AASGSALIFDEEMSRYKLLWTDPECEIEVPERLTVSYEALRTHGLAQRCK
AVPVRQATEQEILLAHSEEYLEAVKQTPGMNVEELMAFSKKYNAVYFHQN
IYHCAKLAAGATLQLVDSVMKREVRNGMALVRPPGHHSQRSAANGFCVFN
NVAFAALYAKKNYNLNRILIVDWDVHHGQGIQYCFEEDPSVLYFSWHRYE
HQSFWPNLPESDYSSVGKGKGSGFNINLPWNKVGMTNSDYLAAFFHVLLP
VAYEFDPELVIVSAGFDSAIGDPEGEMCALPEIFAHLTHLLMPLAAGKMC
VVLEGGYNLTSLGQSVCQTVHSLLGDPTPRISGLGTACDSALESIQNVRN
VQSSYWSSFKHLAQDIVWPEPLKRMPASVRTVVVPPPGVELTLPKNCQHS
GDISESTAKEVQRIRDKHFLTDQNILRSLGNIISVLDRMMRSDEVCNGCV
VVSDLSVSVQCALQHALTEPAERVLVVYVGDGELPVKTNDGKVFLVQICT
KETEDKCVNRLTLCLREGESLTAGFMQALLGLILPVAYEFNPALVLGIVE
ETLMRVWGHMTCLIQGLARGRMLTLLQGYDKDLLELTVSALSGASISPLG
PRAPKPEDVEMMEKQRQRLQERWGLLRCTVSESW
Ligand information
Ligand IDN9W
InChIInChI=1S/C20H21N3O2/c1-22-11-10-19-17(13-22)16-4-2-3-5-18(16)23(19)12-14-6-8-15(9-7-14)20(24)21-25/h2-9,25H,10-13H2,1H3,(H,21,24)
InChIKeyGOVYBPLHWIEHEJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN1CCc2c(c3ccccc3n2Cc4ccc(cc4)C(=O)NO)C1
CACTVS 3.385CN1CCc2n(Cc3ccc(cc3)C(=O)NO)c4ccccc4c2C1
FormulaC20 H21 N3 O2
Name4-[(2-methyl-3,4-dihydro-1~{H}-pyrido[4,3-b]indol-5-yl)methyl]-~{N}-oxidanyl-benzamide
ChEMBLCHEMBL2018302
DrugBank
ZINCZINC000051951670
PDB chain6wbq Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6wbq Structural Basis for the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		E24 A94 H136 H137 G145 F146 D174 H176 W205 E274 Y307
Binding residue
(residue number reindexed from 1)		E24 A94 H136 H137 G145 F146 D174 H176 W205 E274 Y307
Annotation score1
Binding affinityMOAD: ic50=12nM
Enzymatic activity
Enzyme Commision number 3.5.1.48: acetylspermidine deacetylase.
3.5.1.62: acetylputrescine deacetylase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0019213 deacetylase activity
GO:0033558 protein lysine deacetylase activity
GO:0046872 metal ion binding
GO:0047609 acetylputrescine deacetylase activity
GO:0047611 acetylspermidine deacetylase activity
Biological Process
GO:0016236 macroautophagy
GO:0035825 homologous recombination
GO:0036269 swimming behavior
GO:0040029 epigenetic regulation of gene expression
GO:0090043 regulation of tubulin deacetylation
GO:0106047 polyamine deacetylation
GO:0106048 spermidine deacetylation
Cellular Component
GO:0005634 nucleus
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:6wbq, PDBe:6wbq, PDBj:6wbq
PDBsum6wbq
PubMed32659072
UniProtF1QCV2|HDA10_DANRE Polyamine deacetylase HDAC10 (Gene Name=hdac10)

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