Structure of PDB 5cms Chain M Binding Site BS01

Receptor Information
>5cms Chain M (length=172) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRIHVVQGDITKLAVDVIVNAANPSLMGGGGVDGAIHRAAGPALLDACLK
VRQQQGDCPTGHAVITLAGDLPAKAVVHTVGPVWRGGEQNEDQLLQDAYL
NSLRLVAANSYTSVAFPAISTGVAGYPRAAAAEIAVKTVSEFITRHALPE
QVYFVCYDEENAHLYERLLTQQ
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 chain5cms Chain M Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5cms Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase
Resolution2.98 Å
Binding residue
(original residue number in PDB)		D11 I12 V34 A120 S122 T123 G124 V125 A126 Y159
Binding residue
(residue number reindexed from 1)		D9 I10 V32 A118 S120 T121 G122 V123 A124 Y157
Annotation score5
Enzymatic activity
Enzyme Commision number 3.1.1.106: O-acetyl-ADP-ribose deacetylase.
Gene Ontology
Molecular Function
GO:0001883 purine nucleoside binding
GO:0008428 ribonuclease inhibitor activity
GO:0016787 hydrolase activity
GO:0019213 deacetylase activity
GO:0019899 enzyme binding
GO:0060698 endoribonuclease inhibitor activity
GO:0061463 O-acetyl-ADP-ribose deacetylase activity
Biological Process
GO:0042278 purine nucleoside metabolic process
GO:0046677 response to antibiotic
GO:0060701 negative regulation of ribonuclease activity
GO:1900231 regulation of single-species biofilm formation on inanimate substrate

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5cms, PDBe:5cms, PDBj:5cms
PDBsum5cms
PubMed26481419
UniProtP0A8D6|YMDB_ECOLI O-acetyl-ADP-ribose deacetylase (Gene Name=ymdB)

[Back to BioLiP]