Structure of PDB 5mat Chain A Binding Site BS02

Receptor Information
>5mat Chain A (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSTGLYDN
LEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLK
DKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPL
SWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDL
LLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGG
MDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Ligand information
Ligand ID7KJ
InChIInChI=1S/C28H28N4O3S/c1-16-23(17(2)35-31-16)13-29-19-9-10-22-25(12-19)36-27-26(22)28(33)32(15-30-27)14-18-8-11-24(34-3)21-7-5-4-6-20(18)21/h4-8,11,15,19,29H,9-10,12-14H2,1-3H3/t19-/m1/s1
InChIKeyHBGRZTNWJBBJHU-LJQANCHMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c(c(on1)C)CN[C@@H]2CCc3c(sc4c3C(=O)N(C=N4)Cc5ccc(c6c5cccc6)OC)C2
OpenEye OEToolkits 2.0.6Cc1c(c(on1)C)CNC2CCc3c(sc4c3C(=O)N(C=N4)Cc5ccc(c6c5cccc6)OC)C2
CACTVS 3.385COc1ccc(CN2C=Nc3sc4C[CH](CCc4c3C2=O)NCc5c(C)onc5C)c6ccccc16
CACTVS 3.385COc1ccc(CN2C=Nc3sc4C[C@@H](CCc4c3C2=O)NCc5c(C)onc5C)c6ccccc16
FormulaC28 H28 N4 O3 S
Name(7~{R})-7-[(3,5-dimethyl-1,2-oxazol-4-yl)methylamino]-3-[(4-methoxynaphthalen-1-yl)methyl]-5,6,7,8-tetrahydro-[1]benzothiolo[2,3-d]pyrimidin-4-one
ChEMBL
DrugBank
ZINCZINC000584905376
PDB chain5mat 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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PDB5mat Thienopyrimidinone Based Sirtuin-2 (SIRT2)-Selective Inhibitors Bind in the Ligand Induced Selectivity Pocket.
Resolution2.069 Å
Binding residue
(original residue number in PDB)		I93 P94 F96 F119 A135 L138 Y139 F143 I169 F190 F235
Binding residue
(residue number reindexed from 1)		I39 P40 F42 F63 A79 L82 Y83 F87 I113 F134 F179
Annotation score1
Binding affinityMOAD: ic50=0.58uM
PDBbind-CN: -logKd/Ki=6.24,IC50=0.58uM
BindingDB: IC50=580nM
Enzymatic activity
Catalytic site (original residue number in PDB) P94 D95 F96 R97 N168 D170 H187
Catalytic site (residue number reindexed from 1) P40 D41 F42 R43 N112 D114 H131
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:5mat, PDBe:5mat, PDBj:5mat
PDBsum5mat
PubMed28135086
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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