Structure of PDB 6wdv Chain A Binding Site BS01

Receptor Information
>6wdv Chain A (length=638) 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
VQSSYWSSFKHLAQSETDIVWPEPLKRMPASVRTVVVPPPGVELTLPKNC
QHSISESTAKEVQRIRDKHFLTDQNILRSLGNIISVLDRMMRSDEVCNGC
VVVSDLSVSVQCALQHALTEPAERVLVVYVGDGELPVKTNDGKVFLVQIC
TKETEDKCVNRLTLCLREGESLTAGFMQALLGLILPVAYEFNPALVLGIV
EETARLMRVWGHMTCLIQGLARGRMLTLLQGYDKDLLELTVSALSGASIS
PLGPLRAPKPEDVEMMEKQRQRLQERWGLLRCTVSESW
Ligand information
Ligand IDTWM
InChIInChI=1S/C19H21N3O2/c1-21(2)12-16-13-22(18-6-4-3-5-17(16)18)11-14-7-9-15(10-8-14)19(23)20-24/h3-10,13,24H,11-12H2,1-2H3,(H,20,23)
InChIKeyLYCCCRFBRDLGGA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(C)Cc1cn(Cc2ccc(cc2)C(=O)NO)c3ccccc13
ACDLabs 12.01c2n(c1ccccc1c2CN(C)C)Cc3ccc(C(NO)=O)cc3
OpenEye OEToolkits 2.0.7CN(C)Cc1cn(c2c1cccc2)Cc3ccc(cc3)C(=O)NO
FormulaC19 H21 N3 O2
Name4-({3-[(dimethylamino)methyl]-1H-indol-1-yl}methyl)-N-hydroxybenzamide
ChEMBLCHEMBL4066920
DrugBank
ZINC
PDB chain6wdv 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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PDB6wdv Structural Basis for the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		E24 H136 H137 F146 D174 H176 W205 D267 E274 Y307
Binding residue
(residue number reindexed from 1)		E24 H136 H137 F146 D174 H176 W205 D267 E274 Y307
Annotation score1
Binding affinityMOAD: ic50=5nM
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:6wdv, PDBe:6wdv, PDBj:6wdv
PDBsum6wdv
PubMed32659072
UniProtF1QCV2|HDA10_DANRE Polyamine deacetylase HDAC10 (Gene Name=hdac10)

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