Structure of PDB 5yql Chain A Binding Site BS01

Receptor Information
>5yql Chain A (length=296) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GASGSERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPS
TGLLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMR
LLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHE
YPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLK
VDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGGMDFD
SKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Ligand information
Ligand IDA2I
InChIInChI=1S/C21H21N3O2S/c1-15-11-16(2)23-21(22-15)27-14-20(25)24-18-8-6-7-17(12-18)13-26-19-9-4-3-5-10-19/h3-12H,13-14H2,1-2H3,(H,24,25)
InChIKeyUTHZHWWWTOWRMG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(nc(n1)SCC(=O)Nc2cccc(c2)COc3ccccc3)C
CACTVS 3.385Cc1cc(C)nc(SCC(=O)Nc2cccc(COc3ccccc3)c2)n1
FormulaC21 H21 N3 O2 S
Name2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-[3-(phenoxymethyl)phenyl]ethanamide
ChEMBLCHEMBL4079934
DrugBank
ZINC
PDB chain5yql Chain A Residue 1001 [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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PDB5yql X-ray crystal structure guided discovery of new selective, substrate-mimicking sirtuin 2 inhibitors that exhibit activities against non-small cell lung cancer cells.
Resolution1.601 Å
Binding residue
(original residue number in PDB)		F96 F119 F131 A135 L138 Y139 P140 F143 D170 F190 I232 F234
Binding residue
(residue number reindexed from 1)		F46 F66 F78 A82 L85 Y86 P87 F90 D117 F137 I179 F181
Annotation score1
Binding affinityMOAD: ic50=25.9uM
PDBbind-CN: -logKd/Ki=4.59,IC50=25.9uM
BindingDB: IC50=26303nM
Enzymatic activity
Catalytic site (original residue number in PDB) P94 D95 F96 R97 N168 D170 H187
Catalytic site (residue number reindexed from 1) P44 D45 F46 R47 N115 D117 H134
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:5yql, PDBe:5yql, PDBj:5yql
PDBsum5yql
PubMed29957526
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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