Structure of PDB 5y5n Chain A Binding Site BS02

Receptor Information
>5y5n Chain A (length=288) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GEADMDFLRNLFSQTLSLGSQKERLLDELTLEGVARYMQSERCRRVICLV
GAGISTSAGIPDFRSPHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFK
PTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSH
CVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFF
SCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAYRDV
AWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Ligand information
Ligand ID8NO
InChIInChI=1S/C21H20N2O2/c22-21(24)19-11-4-5-12-20(19)23-17-9-6-10-18(15-17)25-14-13-16-7-2-1-3-8-16/h1-12,15,23H,13-14H2,(H2,22,24)
InChIKeyVVRUXFPJOVUDCV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)CCOc2cccc(c2)Nc3ccccc3C(=O)N
CACTVS 3.385NC(=O)c1ccccc1Nc2cccc(OCCc3ccccc3)c2
FormulaC21 H20 N2 O2
Name2-[[3-(2-phenylethoxy)phenyl]amino]benzamide
ChEMBLCHEMBL2152613
DrugBank
ZINCZINC000095578829
PDB chain5y5n Chain A Residue 1002 [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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PDB5y5n Potent mechanism-based sirtuin-2-selective inhibition by anin situ-generated occupant of the substrate-binding site, "selectivity pocket" and NAD+-binding site.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F96 R97 F119 F131 A135 P140 F143 I169 F190 I232 V233
Binding residue
(residue number reindexed from 1)		F63 R64 F75 F87 A91 P96 F99 I125 F146 I188 V189
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.76,IC50=1.74uM
BindingDB: IC50=1000nM
Enzymatic activity
Catalytic site (original residue number in PDB) P94 D95 F96 R97 N168 D170 H187
Catalytic site (residue number reindexed from 1) P61 D62 F63 R64 N124 D126 H143
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:5y5n, PDBe:5y5n, PDBj:5y5n
PDBsum5y5n
PubMed28989670
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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