Structure of PDB 2b4y Chain D Binding Site BS02

Receptor Information
>2b4y Chain D (length=262) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFYWRKWQAQDLATPLA
FAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQ
NIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAP
EPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELA
HCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQ
GPCGTTLPEALA
Ligand information
Ligand IDAPR
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-KEOHHSTQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)C(O)C4O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(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
CACTVS 3.341Nc1ncnc2n(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
FormulaC15 H23 N5 O14 P2
NameADENOSINE-5-DIPHOSPHORIBOSE
ChEMBLCHEMBL1231026
DrugBank
ZINCZINC000017654550
PDB chain2b4y Chain D Residue 4002 [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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PDB2b4y Crystal Structure of Human Sirtuin homolog 5 in complex with NAD
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G58 A59 G60 E64 F70 Q140 H158 G249 T250 S251 N275 T276 E277 P292 C293
Binding residue
(residue number reindexed from 1)		G23 A24 G25 E29 F35 Q100 H118 G209 T210 S211 N235 T236 E237 P252 C253
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) P68 T69 F70 N141 D143 H158
Catalytic site (residue number reindexed from 1) P33 T34 F35 N101 D103 H118
Enzyme Commision number 2.3.1.-
Gene Ontology
Molecular Function
GO:0036054 protein-malonyllysine demalonylase activity
GO:0036055 protein-succinyllysine desuccinylase activity
GO:0070403 NAD+ binding

View graph for
Molecular Function
External links
PDB RCSB:2b4y, PDBe:2b4y, PDBj:2b4y
PDBsum2b4y
PubMed
UniProtQ9NXA8|SIR5_HUMAN NAD-dependent protein deacylase sirtuin-5, mitochondrial (Gene Name=SIRT5)

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