Structure of PDB 5yqn Chain A Binding Site BS02

Receptor Information
>5yqn 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]
GASGSERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPS
TPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLL
LRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKE
KIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMG
TSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGGMDFDSKKAYRDV
AWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Ligand information
Ligand IDL55
InChIInChI=1S/C26H26N6O3S/c1-17-10-18(2)29-26(28-17)36-16-24(33)30-21-7-4-6-19(11-21)15-35-23-9-5-8-22(12-23)31-25(34)20-13-27-32(3)14-20/h4-14H,15-16H2,1-3H3,(H,30,33)(H,31,34)
InChIKeySLKIFBBCZNLTHR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(nc(n1)SCC(=O)Nc2cccc(c2)COc3cccc(c3)NC(=O)c4cnn(c4)C)C
CACTVS 3.385Cn1cc(cn1)C(=O)Nc2cccc(OCc3cccc(NC(=O)CSc4nc(C)cc(C)n4)c3)c2
FormulaC26 H26 N6 O3 S
NameN-[3-[[3-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]phenyl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide
ChEMBLCHEMBL4159477
DrugBank
ZINC
PDB chain5yqn 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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PDB5yqn X-ray crystal structure guided discovery of new selective, substrate-mimicking sirtuin 2 inhibitors that exhibit activities against non-small cell lung cancer cells.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		F96 R97 F119 L138 Y139 P140 F143 H187 F190 V233 F235
Binding residue
(residue number reindexed from 1)		F46 R47 F58 L77 Y78 P79 F82 H126 F129 V172 F174
Annotation score1
Binding affinityMOAD: ic50=93.7uM
PDBbind-CN: -logKd/Ki=4.03,IC50=93.7uM
BindingDB: IC50=93700nM
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 N107 D109 H126
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:5yqn, PDBe:5yqn, PDBj:5yqn
PDBsum5yqn
PubMed29957526
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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