Adenosine diphosphate ribose (ECMDB01178) (M2MDB000285)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (338)
Record Information
Version2.0
Creation Date2012-05-31 13:46:56 -0600
Update Date2015-06-03 15:53:48 -0600
Secondary Accession Numbers
  • ECMDB01178
Identification
Name:Adenosine diphosphate ribose
DescriptionAdenosine diphosphate ribose is a member of the chemical class known as Purine Ribonucleoside Diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety. Adenosine diphosphate ribose is a molecule formed into chains by the enzyme poly ADP ribose polymerase. It binds to and activates the TRPM2 ion channel (WikiPedia)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (Rib5)ppA
  • 5-(Adenosine 5'-pyrophosphoryl)-D-ribose
  • A5'pp5Rib
  • Adenosine 5'-diphosphoribose
  • Adenosine diphosphate ribose
  • Adenosine diphosphoric acid ribose
  • AdoPPRib
  • ADP Ribose
  • ADP-D-Ribose
  • ADP-Rib
  • ADP-Ribose
  • ADPribose
  • Ribose adenosine diphosphate
  • Ribose adenosine diphosphoric acid
  • [5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [hydroxy-[(3,4,5-trihydroxyoxolan-2-yl)methoxy]phosphoryl] hydrogen phosphate
  • [5-(6-Aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [hydroxy-[(3,4,5-trihydroxyoxolan-2-yl)methoxy]phosphoryl] hydrogen phosphoric acid
Chemical Formula:C15H23N5O14P2
Weight:Average: 559.3157
Monoisotopic: 559.071673493
InChI Key:SRNWOUGRCWSEMX-KEOHHSTQSA-N
InChI:InChI=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
CAS number:20762-30-5
IUPAC Name:[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(2R,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methoxy})phosphinic acid
Traditional IUPAC Name:{[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy[(2R,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methoxyphosphinic acid
SMILES:[H][C@@]1(O)O[C@]([H])(COP(O)(=O)OP(O)(=O)OC[C@@]2([H])O[C@@]([H])(N3C=NC4=C(N)N=CN=C34)[C@]([H])(O)[C@]2([H])O)[C@@]([H])(O)[C@@]1([H])O
Chemical Taxonomy
Description belongs to the class of organic compounds known as pterins and derivatives. These are polycyclic aromatic compounds containing a pterin moiety, which consist of a pteridine ring bearing a ketone and an amine group to form 2-aminopteridin-4(3H)-one.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPteridines and derivatives
Sub ClassPterins and derivatives
Direct ParentPterins and derivatives
Alternative Parents
Substituents
  • Pterin
  • Aminobenzoic acid
  • Aminobenzoic acid or derivatives
  • Benzoic acid or derivatives
  • Benzoic acid
  • Benzoyl
  • Aniline or substituted anilines
  • Phenylalkylamine
  • Aminopyrimidine
  • Pyrimidone
  • Aralkylamine
  • Secondary aliphatic/aromatic amine
  • Monocyclic benzene moiety
  • Pyrazine
  • Pyrimidine
  • Benzenoid
  • Heteroaromatic compound
  • Vinylogous amide
  • Amino acid or derivatives
  • Lactam
  • Amino acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Secondary amine
  • Azacycle
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organonitrogen compound
  • Amine
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Primary amine
  • Organic oxygen compound
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility3.61 g/LALOGPS
logP-1.8ALOGPS
logP-6.7ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area291.52 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity111.12 m³·mol⁻¹ChemAxon
Polarizability46.49 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Adenosine diphosphate ribose + Water <> Adenosine monophosphate +2 Hydrogen ion + D-Ribose-5-phosphate
Adenosine diphosphate ribose + Water <> Adenosine monophosphate + D-Ribose-5-phosphate
Water + NAD <> Hydrogen ion + Adenosine diphosphate ribose + Niacinamide
Adenosine diphosphate ribose + Water > Hydrogen ion + Adenosine monophosphate + D-Ribose-5-phosphate
Adenosine diphosphate ribose + Water > Adenosine monophosphate + D-Ribose-5-phosphate
Adenosine diphosphate ribose + Water <> Adenosine monophosphate +2 Hydrogen ion + D-Ribose-5-phosphate
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
26± 0 uMBW2511348 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L GlucoStationary Phase, glucose limitedBioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h37 oCPMID: 17379776
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_23) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0910030000-15bc114d0093122a9468View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0910000000-57bfcc225cdf516ed5abView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-1900000000-eb6f598a96eefc1ac9d3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a59-1701290000-09ca534c89e3f60461c6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-1910100000-2271592b903e18d9a380View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a7i-3900000000-22c2e6d08bb7730ff5f5View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16960
HMDB IDHMDB01178
Pubchem Compound ID192
Kegg IDC00301
ChemSpider ID187
WikipediaAdenosine_diphosphate_ribose
BioCyc IDADENOSINE_DIPHOSPHATE_RIBOSE
EcoCyc IDADENOSINE_DIPHOSPHATE_RIBOSE
Ligand ExpoAPR

Enzymes

Protein Details
1. ADP-ribose pyrophosphatase
General function:
Involved in hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Specific function:
Acts on ADP-mannose and ADP-glucose as well as ADP- ribose. Prevents glycogen biosynthesis. The reaction catalyzed by this enzyme is a limiting step of the gluconeogenic process
Gene Name:
nudF
Uniprot ID:
Q93K97
Molecular weight:
23667
Reactions
ADP-ribose + H(2)O = AMP + D-ribose 5-phosphate.
Protein Details
2. ADP compounds hydrolase nudE
General function:
Involved in hydrolase activity
Specific function:
Active on adenosine(5')triphospho(5')adenosine (Ap3A), ADP-ribose, NADH, adenosine(5')diphospho(5')adenosine (Ap2A)
Gene Name:
nudE
Uniprot ID:
P45799
Molecular weight:
21153
Reactions
ADP-ribose + H(2)O = AMP + D-ribose 5-phosphate.