Structure of PDB 1yc2 Chain E Binding Site BS02

Receptor Information
>1yc2 Chain E (length=250) Species: 2234 (Archaeoglobus fulgidus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEDEIRKAAEILAKSKHAVVFTGAGISAESGIPTFRGEDGLWRKYDPEEV
ASISGFKRNPRAFWEFSMEMKDKLFAEPNPAHYAIAELERMGIVKAVITQ
NIDMLHQRAGSRRVLELHGSMDKLDCLDCHETYDWSEFVEDFNKGEIPRC
RKCGSYYVKPRVVLFGEPLPQRTLFEAIEEAKHCDAFMVVGSSLVVYPAA
ELPYIAKKAGAKMIIVNAEPTMADPIFDVKIIGKAGEVLPKIVEEVKRLR
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 chain1yc2 Chain E Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1yc2 Mechanism of Sirtuin Inhibition by Nicotinamide: Altering the NAD(+) Cosubstrate Specificity of a Sir2 Enzyme.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G23 G25 E29 T34 F35 R36 G37 H118 F165 G191 S192 S193 N217 A218 E219 K234 A235
Binding residue
(residue number reindexed from 1)		G23 G25 E29 T34 F35 R36 G37 H118 F165 G191 S192 S193 N217 A218 E219 K234 A235
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) P33 T34 F35 R36 N101 D103 H118
Catalytic site (residue number reindexed from 1) P33 T34 F35 R36 N101 D103 H118
Enzyme Commision number 2.3.1.286: protein acetyllysine N-acetyltransferase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0017136 NAD-dependent histone deacetylase activity
GO:0034979 NAD-dependent protein lysine deacetylase activity
GO:0036054 protein-malonyllysine demalonylase activity
GO:0036055 protein-succinyllysine desuccinylase activity
GO:0046872 metal ion binding
GO:0051287 NAD binding
GO:0070403 NAD+ binding
Biological Process
GO:0006338 chromatin remodeling
GO:0006476 protein deacetylation
GO:0036049 peptidyl-lysine desuccinylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1yc2, PDBe:1yc2, PDBj:1yc2
PDBsum1yc2
PubMed15780941
UniProtO30124|NPD2_ARCFU NAD-dependent protein deacylase 2 (Gene Name=cobB2)

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