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
Description:Adenosine 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
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
DescriptionThis compound belongs to the class of chemical entities known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPurine nucleotides
Direct ParentPurine nucleotide sugars
Alternative Parents
Substituents
  • Purine nucleotide sugar
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Primary aromatic amine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Tetrahydrofuran
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Secondary alcohol
  • Hemiacetal
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Alcohol
  • Amine
  • Primary amine
  • Organonitrogen compound
  • Organopnictogen compound
  • Organooxygen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
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:
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 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
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

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.
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.