Structure of PDB 4rmh Chain A Binding Site BS03

Receptor Information
>4rmh Chain A (length=292) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYD
NKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKD
KGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLS
WMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLL
LVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGGMDFDSKKA
YRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Ligand information
Ligand ID3TE
InChIInChI=1S/C22H20N4OS2/c1-14-10-15(2)25-22(24-14)28-13-20(27)26-21-23-12-18(29-21)11-17-8-5-7-16-6-3-4-9-19(16)17/h3-10,12H,11,13H2,1-2H3,(H,23,26,27)
InChIKeyMENNDDDTIIZDDN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(Nc1ncc(s1)Cc3c2ccccc2ccc3)CSc4nc(cc(n4)C)C
OpenEye OEToolkits 1.7.6Cc1cc(nc(n1)SCC(=O)Nc2ncc(s2)Cc3cccc4c3cccc4)C
CACTVS 3.385Cc1cc(C)nc(SCC(=O)Nc2sc(Cc3cccc4ccccc34)cn2)n1
FormulaC22 H20 N4 O S2
Name2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide
ChEMBLCHEMBL3770903
DrugBank
ZINCZINC000000818861
PDB chain4rmh 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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PDB4rmh Selective Sirt2 inhibition by ligand-induced rearrangement of the active site.
Resolution1.42 Å
Binding residue
(original residue number in PDB)		F96 F119 F131 Y139 P140 F143 F190 I232 V233 F234
Binding residue
(residue number reindexed from 1)		F41 F62 F74 Y82 P83 F86 F133 I175 V176 F177
Annotation score1
Binding affinityBindingDB: IC50=>10000nM
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 N111 D113 H130
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:4rmh, PDBe:4rmh, PDBj:4rmh
PDBsum4rmh
PubMed25672491
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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