Structure of PDB 5y0z Chain A Binding Site BS02

Receptor Information
>5y0z 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]
ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYD
NLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLL
KDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYP
LSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVD
LLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGGMDFDSKKAYRDV
AWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Ligand information
Ligand ID8K9
InChIInChI=1S/C30H44N2O3/c1-7-29(3,4)23-12-13-27(25(15-23)30(5,6)8-2)35-20-24(33)19-31-16-21-14-22(18-31)26-10-9-11-28(34)32(26)17-21/h9-13,15,21-22,24,33H,7-8,14,16-20H2,1-6H3/t21-,22+,24+/m0/s1
InChIKeyITCUJNFERKWPKY-WMTXJRDZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCC(C)(C)c1ccc(OC[C@H](O)CN2C[C@@H]3C[C@H](C2)C4=CC=CC(=O)N4C3)c(c1)C(C)(C)CC
OpenEye OEToolkits 2.0.6CCC(C)(C)c1ccc(c(c1)C(C)(C)CC)OCC(CN2CC3CC(C2)C4=CC=CC(=O)N4C3)O
CACTVS 3.385CCC(C)(C)c1ccc(OC[CH](O)CN2C[CH]3C[CH](C2)C4=CC=CC(=O)N4C3)c(c1)C(C)(C)CC
OpenEye OEToolkits 2.0.6CCC(C)(C)c1ccc(c(c1)C(C)(C)CC)OC[C@@H](CN2C[C@@H]3C[C@H](C2)C4=CC=CC(=O)N4C3)O
FormulaC30 H44 N2 O3
Name(1~{R},9~{S})-11-[(2~{R})-3-[2,4-bis(2-methylbutan-2-yl)phenoxy]-2-oxidanyl-propyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one
ChEMBL
DrugBank
ZINCZINC000217438197
PDB chain5y0z Chain A Residue 502 [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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PDB5y0z Identification of a novel small molecule that inhibits deacetylase but not defatty-acylase reaction catalysed by SIRT2.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		F96 R97 F119 Y139 P140 I169 H187 F190 V233 F235
Binding residue
(residue number reindexed from 1)		F41 R42 F64 Y84 P85 I114 H132 F135 V178 F180
Annotation score1
Binding affinityMOAD: ic50=0.46uM
PDBbind-CN: -logKd/Ki=6.34,IC50=0.46uM
Enzymatic activity
Catalytic site (original residue number in PDB) P94 D95 F96 R97 N168 D170 H187
Catalytic site (residue number reindexed from 1) P39 D40 F41 R42 N113 D115 H132
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:5y0z, PDBe:5y0z, PDBj:5y0z
PDBsum5y0z
PubMed29685974
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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