Structure of PDB 5isy Chain C Binding Site BS02

Receptor Information
>5isy Chain C (length=249) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DRIIEKDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGE
PVWLVQQQRRHDMGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCG
HEMYPSKTEWAMLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNG
VHTVLAGFVEVGETLEQAVAREVMEQSGIKVKNLRYVTSQPWPFPQSLMT
AFMAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAM
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain5isy Chain C Residue 302 [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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PDB5isy Structural basis of prokaryotic NAD-RNA decapping by NudC
Resolution2.354 Å
Binding residue
(original residue number in PDB)		F160 W194 M201 V240 A241
Binding residue
(residue number reindexed from 1)		F158 W192 M199 V238 A239
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.1.-
3.6.1.22: NAD(+) diphosphatase.
Gene Ontology
Molecular Function
GO:0000210 NAD+ diphosphatase activity
GO:0000287 magnesium ion binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0035529 NADH pyrophosphatase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0110153 RNA NAD-cap (NMN-forming) hydrolase activity
Biological Process
GO:0006402 mRNA catabolic process
GO:0006734 NADH metabolic process
GO:0006742 NADP catabolic process
GO:0019677 NAD catabolic process
GO:0048255 mRNA stabilization
GO:0110155 NAD-cap decapping

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5isy, PDBe:5isy, PDBj:5isy
PDBsum5isy
PubMed27561816
UniProtP32664|NUDC_ECOLI NAD-capped RNA hydrolase NudC (Gene Name=nudC)

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