Structure of PDB 7u3m Chain A Binding Site BS01

Receptor Information
>7u3m Chain A (length=640) 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
VQSSYWSSFKHLAQSETNDIVWPEPLKRMPASVRTVVVPPPGVELTLPKN
CQHSISESTAKEVQRIRDKHFDLTDQNILRSLGNIISVLDRMMRSDEVCN
GCVVVSDLSVSVQCALQHALTEPAERVLVVYVGDGELPVKTNDGKVFLVQ
ICTKETEDKCVNRLTLCLREGESLTAGFMQALLGLILPVAYEFNPALVLG
IVEETTRLMRVWGHMTCLIQGLARGRMLTLLQGYDKDLLELTVSALSGAS
ISPLGPLRAPKPEDVEMMEKQRQRLQERWGLLRCTVSESW
Ligand information
Ligand IDL8C
InChIInChI=1S/C13H19N3O2/c1-15-6-8-16(9-7-15)10-11-2-4-12(5-3-11)13(17)14-18/h2-5,18H,6-10H2,1H3,(H,14,17)
InChIKeyVMDZCGSWWDTUMR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 2.0.7		CN1CCN(CC1)Cc2ccc(cc2)C(=O)NO
ACDLabs 12.01ONC(=O)c1ccc(cc1)CN1CCN(C)CC1
FormulaC13 H19 N3 O2
NameN-hydroxy-4-[(4-methylpiperazin-1-yl)methyl]benzamide
ChEMBLCHEMBL5203383
DrugBank
ZINC
PDB chain7u3m Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7u3m Identification of histone deacetylase 10 (HDAC10) inhibitors that modulate autophagy in transformed cells.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		H137 F146 H176 W205 D267 E274 Y307
Binding residue
(residue number reindexed from 1)		H137 F146 H176 W205 D267 E274 Y307
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7u3m, PDBe:7u3m, PDBj:7u3m
PDBsum7u3m
PubMed35306288
UniProtF1QCV2|HDA10_DANRE Polyamine deacetylase HDAC10 (Gene Name=hdac10)

[Back to BioLiP]