Structure of PDB 5td7 Chain A Binding Site BS02

Receptor Information
>5td7 Chain A (length=626) 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
VVLEGGFNLTSLGQSVCQTVHSLLGDPTPRISGLGTACDSALESIQNVRN
VQSSYWSSFKHLAQSVRTVVVPPPGVELTLPKNCQHSISESTAKEVQRIR
DKHFDLTDQNILRSLGNIISVLDRMMRSDEVCNGCVVVSDLSVSVQCALQ
HALTEPAERVLVVYVGDGELPVKTNDGKVFLVQICTKETEDKCVNRLTLC
LREGESLTAGFMQALLGLILPVAYEFNPALVLGIVEETAAKTRLMRVWGH
MTCLIQGLARGRMLTLLQGYDKDLLELTVSALSGASISPLGPLRAPKPED
VEMMEKQRQRLQERWGLLRCTVSESW
Ligand information
Ligand IDFKS
InChIInChI=1S/C10H21F3N2O2/c11-10(12,13)9(16,17)5-2-1-3-7-15-8-4-6-14/h15-17H,1-8,14H2
InChIKeyIVRAKANOVJJYCX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C(CCC(C(F)(F)F)(O)O)CCNCCCN
CACTVS 3.385NCCCNCCCCCC(O)(O)C(F)(F)F
ACDLabs 12.01C(N)CCNCCCCCC(C(F)(F)F)(O)O
FormulaC10 H21 F3 N2 O2
Name7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol
ChEMBL
DrugBank
ZINCZINC000263620577
PDB chain5td7 Chain A Residue 711 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5td7 Histone deacetylase 10 structure and molecular function as a polyamine deacetylase.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		D94 P134 H136 H137 G145 F146 D174 H176 W205 E274 E304 G305 F307
Binding residue
(residue number reindexed from 1)		D94 P134 H136 H137 G145 F146 D174 H176 W205 E274 E304 G305 F307
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.77,IC50=1.7uM
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:5td7, PDBe:5td7, PDBj:5td7
PDBsum5td7
PubMed28516954
UniProtF1QCV2|HDA10_DANRE Polyamine deacetylase HDAC10 (Gene Name=hdac10)

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