Structure of PDB 5dy5 Chain A Binding Site BS02

Receptor Information
>5dy5 Chain A (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTG
LYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFM
RLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRH
EYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFL
KVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSGMIMGLGGG
MDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Ligand information
Ligand ID5GR
InChIInChI=1S/C28H27N7O2S2/c1-19-11-20(2)31-28(30-19)38-18-26(36)32-27-29-14-25(39-27)13-22-9-6-10-24(12-22)37-17-23-16-35(34-33-23)15-21-7-4-3-5-8-21/h3-12,14,16H,13,15,17-18H2,1-2H3,(H,29,32,36)
InChIKeyYWLNYZXFIAFWSF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1cc(nc(n1)SCC(=O)Nc2ncc(s2)Cc3cccc(c3)OCc4cn(nn4)Cc5ccccc5)C
CACTVS 3.385Cc1cc(C)nc(SCC(=O)Nc2sc(Cc3cccc(OCc4cn(Cc5ccccc5)nn4)c3)cn2)n1
ACDLabs 12.01C(C(=O)Nc1ncc(s1)Cc2cc(ccc2)OCc3nnn(c3)Cc4ccccc4)Sc5nc(C)cc(C)n5
FormulaC28 H27 N7 O2 S2
NameN-(5-{3-[(1-benzyl-1H-1,2,3-triazol-4-yl)methoxy]benzyl}-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide
ChEMBLCHEMBL4228286
DrugBank
ZINCZINC000263621310
PDB chain5dy5 Chain A Residue 402 [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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PDB5dy5 Structure-Based Development of an Affinity Probe for Sirtuin 2.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		I93 F96 R97 F119 F131 A135 L138 Y139 P140 F143 D170 H187 F190 I232 V233 F234 F235
Binding residue
(residue number reindexed from 1)		I41 F44 R45 F67 F79 A83 L86 Y87 P88 F91 D118 H135 F138 I180 V181 F182 F183
Annotation score1
Binding affinityMOAD: ic50=0.163uM
PDBbind-CN: -logKd/Ki=6.79,IC50=0.163uM
BindingDB: IC50=160nM
Enzymatic activity
Catalytic site (original residue number in PDB) P94 D95 F96 R97 N168 D170 H187
Catalytic site (residue number reindexed from 1) P42 D43 F44 R45 N116 D118 H135
Enzyme Commision number 2.3.1.-
2.3.1.286: protein acetyllysine N-acetyltransferase.
Gene Ontology
Molecular Function
GO:0017136 NAD-dependent histone deacetylase activity
GO:0051287 NAD binding
GO:0070403 NAD+ binding

View graph for
Molecular Function
External links
PDB RCSB:5dy5, PDBe:5dy5, PDBj:5dy5
PDBsum5dy5
PubMed26748890
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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