Structure of PDB 5y2f Chain A Binding Site BS02

Receptor Information
>5y2f Chain A (length=297) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNYAAGLSPYADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTG
AGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLE
RVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDT
VVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADE
ASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADL
RIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEP
Ligand information
Ligand IDAR6
InChIInChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
InChIKeySRNWOUGRCWSEMX-ZQSHOCFMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)N
ACDLabs 12.01O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OP(=O)(O)OCC4OC(O)C(O)C4O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC15 H23 N5 O14 P2
Name[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE;
Adenosine-5-Diphosphoribose
ChEMBL
DrugBankDB02059
ZINCZINC000014880207
PDB chain5y2f Chain A Residue 401 [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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PDB5y2f Identification of a cellularly active SIRT6 allosteric activator.
Resolution2.53 Å
Binding residue
(original residue number in PDB)		G50 A51 G52 T55 D61 F62 R63 W69 Q111 H131 G212 T213 S214 I217 N238 L239 Q240 Y255 V256
Binding residue
(residue number reindexed from 1)		G50 A51 G52 T55 D61 F62 R63 W69 Q111 H131 G212 T213 S214 I217 N238 L239 Q240 Y255 V256
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) P60 D61 F62 R63 N112 D114 H131
Catalytic site (residue number reindexed from 1) P60 D61 F62 R63 N112 D114 H131
Enzyme Commision number 2.3.1.-
2.3.1.286: protein acetyllysine N-acetyltransferase.
2.4.2.-
Gene Ontology

View graph for
Molecular Function
External links
PDB RCSB:5y2f, PDBe:5y2f, PDBj:5y2f
PDBsum5y2f
PubMed30374165
UniProtQ8N6T7|SIR6_HUMAN NAD-dependent protein deacylase sirtuin-6 (Gene Name=SIRT6)

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