P. aeruginosa Metabolome Database: Adenosine diphosphate ribose (PAMDB000285)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB000285

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

🔍MOL SDF PDB SMILES InChI View Structure

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

Average Molecular Weight:

559.3157

Monoisotopic Molecular Weight:

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

Taxonomy Description

This compound belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine nucleotide sugars

Direct Parent

Purine nucleotide sugars

Alternative Parents

Substituents

Purine nucleotide sugar
Purine ribonucleoside diphosphate
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
6-aminopurine
Purine
Imidazopyrimidine
Monoalkyl phosphate
Aminopyrimidine
Imidolactam
Alkyl phosphate
Pyrimidine
Primary aromatic amine
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
N-substituted imidazole
Monosaccharide
Saccharide
Heteroaromatic compound
Oxolane
Imidazole
Azole
Secondary alcohol
Polyol
Hemiacetal
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	3.61 mg/mL	ALOGPS
logP	-1.8	ALOGPS
logP	-6.7	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	291.52 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	111.12 m³·mol^-1	ChemAxon
Polarizability	46.49 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

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

Pathways:

Purine metabolism pae00230

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0910030000-15bc114d0093122a9468	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0910000000-57bfcc225cdf516ed5ab	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-1900000000-eb6f598a96eefc1ac9d3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a59-1701290000-09ca534c89e3f60461c6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-1910100000-2271592b903e18d9a380	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a7i-3900000000-22c2e6d08bb7730ff5f5	View 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

Links

External Links:

Resource	Link
CHEBI ID	16960
HMDB ID	HMDB01178
Pubchem Compound ID	192
Kegg ID	C00301
ChemSpider ID	187
Wikipedia	Adenosine_diphosphate_ribose
BioCyc ID	ADENOSINE_DIPHOSPHATE_RIBOSE
EcoCyc ID	ADENOSINE_DIPHOSPHATE_RIBOSE
Ligand Expo	APR

Adenosine diphosphate ribose (PAMDB000285)

Structure for Adenosine diphosphate ribose (PAMDB000285)