Structure of PDB 6xvg Chain A Binding Site BS01

Receptor Information
>6xvg 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]
DKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPD
FRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQ
NVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATG
RLCTVACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIR
PSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLG
LEIPAWDGPRVLERALPPLPRPPTPKLE
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 chain6xvg 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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PDB6xvg Binding site for activator MDL-801 on SIRT6.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
G52 A53 G54 T57 D63 F64 R65 Q113 H133 G214 T215 S216 I219 N240 L241 Q242 Y257 V258
Binding residue
(residue number reindexed from 1)
G39 A40 G41 T44 D50 F51 R52 Q100 H120 G194 T195 S196 I199 N220 L221 Q222 Y237 V238
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) P62 D63 F64 R65 N114 D116 H133
Catalytic site (residue number reindexed from 1) P49 D50 F51 R52 N101 D103 H120
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:6xvg, PDBe:6xvg, PDBj:6xvg
PDBsum6xvg
PubMed33649599
UniProtQ8N6T7|SIR6_HUMAN NAD-dependent protein deacylase sirtuin-6 (Gene Name=SIRT6)

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