Structure of PDB 6nr0 Chain A Binding Site BS03

Receptor Information
>6nr0 Chain A (length=289) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYD
NLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLL
KDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYP
LSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVD
LLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQGGGMDFDSKKAYR
DVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ
Ligand information
Ligand IDKXG
InChIInChI=1S/C15H23N5O13P2S/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(31-14)1-29-34(25,26)33-35(27,28)30-2-6-9(22)11(24)15(36)32-6/h3-6,8-11,14-15,21-24,36H,1-2H2,(H,25,26)(H,27,28)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
InChIKeyAIFODOLMLYAQQN-KEOHHSTQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OCC4[C@H]([C@H]([C@H](O4)S)O)O)O)O)N
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)S)O)O)O)O)N
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H](S)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](S)[CH](O)[CH]4O)[CH](O)[CH]3O
ACDLabs 12.01C2(C(C(C(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)S)O)O)O2)O)O)n4c3c(c(ncn3)N)nc4
FormulaC15 H23 N5 O13 P2 S
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-sulfanyl-oxolan-2-yl]methyl hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain6nr0 Chain A Residue 403 [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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PDB6nr0 A Glycoconjugated SIRT2 Inhibitor with Aqueous Solubility Allows Structure-Based Design of SIRT2 Inhibitors.
Resolution2.45 Å
Binding residue
(original residue number in PDB)
G84 G86 D95 F96 R97 Q167 H187 F235 G261 T262 S263 N286 K287 E288 E323 C324
Binding residue
(residue number reindexed from 1)
G29 G31 D40 F41 R42 Q112 H132 F180 G206 T207 S208 N231 K232 E233 E257 C258
Annotation score3
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 N113 D115 H132
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:6nr0, PDBe:6nr0, PDBj:6nr0
PDBsum6nr0
PubMed31373792
UniProtQ8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)

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