Structure of PDB 6uim Chain A Binding Site BS01

Receptor Information
>6uim Chain A (length=620) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AASGSALIFDEEMSRYKLLWTDPACEIEVPERLTVSYEALRTHGLAQRCK
AVPVRQATEQEILLAHSEEYLEAVKQTPGMNVEELMAFSKKYNDVYFHQN
IYHCAKLAAGATLQLVDSVMKREVRNGMALVRPPGHHSQRSAANGFCVFN
NVAFAALYAKKNYNLNRILIVDWDVHHGQGIQYCFEEDPSVLYFSWHRYE
HQSFWPNLPESDYSSVGKGKGSGFNINLPWNKVGMTNSDYLAAFFHVLLP
VAYEFDPELVIVSAGFDSAIGDPEGEMCALPEIFAHLTHLLMPLAAGKMC
VVLEGGYNLTSLGQSVCQTVHSLLGDPTPRISGLGTACDSALESIQNVRN
VQSSYWSSFKHLAQSVRTVVVPPPGVELTLPKNCQHSISESTAKEVQRIR
DKHFTDQNILRSLGNIISVLDRMMRSDEVCNGCVVVSDLSVSVQCALQHA
LTEPAERVLVVYVGDGELPVKTNDGKVFLVQICTKETEDKCVNRLTLCLR
EGESLTAGFMQALLGLILPVAYEFNPALVLGIVEETTRLMRVWGHMTCLI
QGLARGRMLTLLQGYDKDLLELTVSALSGASISPLGPRAPKPEDVEMMEK
QRQRLQERWGLLRCTVSESW
Ligand information
Ligand IDQ7Y
InChIInChI=1S/C10H22N2OS/c11-6-4-8-12-7-3-1-2-5-10(13)9-14/h12,14H,1-9,11H2
InChIKeyOOZNPNMKAJIVIZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCCCNCCCCCC(=O)CS
OpenEye OEToolkits 2.0.7C(CCC(=O)CS)CCNCCCN
ACDLabs 12.01C(C(CS)=O)CCCCNCCCN
FormulaC10 H22 N2 O S
Name7-[(3-aminopropyl)amino]-1-sulfanylheptan-2-one
ChEMBL
DrugBank
ZINC
PDB chain6uim 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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PDB6uim Binding ofN8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies for Blocking Polyamine Deacetylation.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		D94 H137 F146 D174 H176 W205 E274 Y307
Binding residue
(residue number reindexed from 1)		D94 H137 F146 D174 H176 W205 E274 Y307
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=6.74,IC50=180nM
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:6uim, PDBe:6uim, PDBj:6uim
PDBsum6uim
PubMed31746596
UniProtF1QCV2|HDA10_DANRE Polyamine deacetylase HDAC10 (Gene Name=hdac10)

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