Structure of PDB 4rmi Chain A Binding Site BS03

Receptor Information
>4rmi Chain A (length=278) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGFEI
SYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDT
LERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKC
EDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFAS
LISKAPLSTPRLLINKEKAGQSDPFLGGGMDFDSKKAYRDVAWLGECDQG
CLALAELLGWKKELEDLVRREHASIDAQ
Ligand information
Ligand ID3TK
InChIInChI=1S/C18H18N4OS2/c1-12-8-13(2)21-18(20-12)24-11-16(23)22-17-19-10-15(25-17)9-14-6-4-3-5-7-14/h3-8,10H,9,11H2,1-2H3,(H,19,22,23)
InChIKeyLHMBJRUBDQYYSV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc(C)nc(SCC(=O)Nc2sc(Cc3ccccc3)cn2)n1
OpenEye OEToolkits 1.7.6Cc1cc(nc(n1)SCC(=O)Nc2ncc(s2)Cc3ccccc3)C
ACDLabs 12.01O=C(Nc1ncc(s1)Cc2ccccc2)CSc3nc(cc(n3)C)C
FormulaC18 H18 N4 O S2
NameN-(5-benzyl-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide
ChEMBLCHEMBL3769988
DrugBank
ZINCZINC000000818843
PDB chain4rmi 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]
PDB4rmi Selective Sirt2 inhibition by ligand-induced rearrangement of the active site.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		F96 F119 F131 A135 Y139 P140 F143 D170 F190 I232
Binding residue
(residue number reindexed from 1)		F41 F48 F60 A64 Y68 P69 F72 D99 F119 I161
Annotation score1
Binding affinityBindingDB: IC50=3750nM
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 N97 D99 H116
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:4rmi, PDBe:4rmi, PDBj:4rmi
PDBsum4rmi
PubMed25672491
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

[Back to BioLiP]