Structure of PDB 5cb5 Chain M Binding Site BS01

Receptor Information
>5cb5 Chain M (length=173) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTRIHVVQGDITKLAVDVIVNAAAPSLMGGGGVAGAIHRAAGPALLDACL
KVRQQQGDCPTGHAVITLAGDLPAKAVVHTVGPVWRGGEQNEDQLLQDAY
LNSLRLVAANSYTSVAFPAISTGVYGYPRAAAAEIAVKTVSEFITRHALP
EQVYFVCYDEENAHLYERLLTQQ
Ligand information
Ligand IDZOD
InChIInChI=1S/C17H25N5O15P2/c1-6(23)34-13-11(25)8(36-17(13)27)3-33-39(30,31)37-38(28,29)32-2-7-10(24)12(26)16(35-7)22-5-21-9-14(18)19-4-20-15(9)22/h4-5,7-8,10-13,16-17,24-27H,2-3H2,1H3,(H,28,29)(H,30,31)(H2,18,19,20)/t7-,8-,10-,11-,12-,13-,16-,17-/m1/s1
InChIKeyBFNOPXRXIQJDHO-QJWJOKBXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC(=O)O[C@@H]1[C@@H]([C@H](O[C@H]1O)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O
ACDLabs 12.01CC(=O)OC1C(O)OC(C1O)COP(OP(O)(=O)OCC4OC(n2cnc3c(N)ncnc23)C(O)C4O)(=O)O
OpenEye OEToolkits 1.9.2CC(=O)OC1C(C(OC1O)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O
CACTVS 3.385CC(=O)O[CH]1[CH](O)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH]1O
CACTVS 3.385CC(=O)O[C@H]1[C@H](O)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@H]1O
FormulaC17 H25 N5 O15 P2
Name[(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanoate
ChEMBL
DrugBank
ZINCZINC000096095472
PDB chain5cb5 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

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PDB5cb5 Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D11 I12 A23 A25 G30 G31 G32 G33 V34 A120 S122 T123 G124 V125 Y126 Y159
Binding residue
(residue number reindexed from 1)		D10 I11 A22 A24 G29 G30 G31 G32 V33 A119 S121 T122 G123 V124 Y125 Y158
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:5cb5, PDBe:5cb5, PDBj:5cb5
PDBsum5cb5
PubMed26481419
UniProtP0A8D6|YMDB_ECOLI O-acetyl-ADP-ribose deacetylase (Gene Name=ymdB)

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