Structure of PDB 5yqm Chain A Binding Site BS02

Receptor Information
>5yqm Chain A (length=295) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GASGSERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPS
TGLYDNLEPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRL
LKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEY
PLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKV
DLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGGMDFDS
KKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Ligand information
Ligand IDA2X
InChIInChI=1S/C20H19N3OS2/c1-14-12-15(2)22-20(21-14)25-13-19(24)23-16-8-10-18(11-9-16)26-17-6-4-3-5-7-17/h3-12H,13H2,1-2H3,(H,23,24)
InChIKeyKOUOSAPHOUALKH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc(C)nc(SCC(=O)Nc2ccc(Sc3ccccc3)cc2)n1
OpenEye OEToolkits 2.0.6Cc1cc(nc(n1)SCC(=O)Nc2ccc(cc2)Sc3ccccc3)C
FormulaC20 H19 N3 O S2
Name2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-(4-phenylsulfanylphenyl)ethanamide
ChEMBLCHEMBL4476189
DrugBank
ZINC
PDB chain5yqm 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5yqm X-ray crystal structure guided discovery of new selective, substrate-mimicking sirtuin 2 inhibitors that exhibit activities against non-small cell lung cancer cells.
Resolution1.735 Å
Binding residue
(original residue number in PDB)		I93 F96 F119 F131 A135 L138 Y139 P140 F143 D170 F190 I232 F234
Binding residue
(residue number reindexed from 1)		I43 F46 F65 F77 A81 L84 Y85 P86 F89 D116 F136 I178 F180
Annotation score1
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 N114 D116 H133
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:5yqm, PDBe:5yqm, PDBj:5yqm
PDBsum5yqm
PubMed29957526
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

[Back to BioLiP]