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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-10-23 19:03:48 UTC
HMDB IDHMDB0001178
Secondary Accession Numbers
  • HMDB01178
Metabolite Identification
Common NameAdenosine diphosphate ribose
DescriptionAdenosine diphosphate ribose is a molecule formed into poly(ADP-ribose) or PAR chains by the enzyme poly ADP ribose polymerase or PARP. PARP is found in every cell nucleus. Its main role is to detect and signal single-strand DNA breaks (SSB) to the enzymatic machinery involved in the SSB repair. PARP activation is an immediate cellular response to metabolic, chemical, or radiation-induced DNA SSB damage. Once PARP detects a SSB, it binds to the DNA, and, after a structural change, begins the synthesis of a poly (ADP-ribose) chain (PAR) as a signal for the other DNA-repairing enzymes such as DNA ligase III (LigIII), DNA polymerase beta, and scaffolding proteins such as X-ray cross-complementing gene 1 (XRCC1). After repairing, the PAR chains are degraded via PAR glycohydrolase (PARG). ADP-ribose binds to and activates the TRPM2 ion channel. Adenosine diphosphate ribose is an intermediate in NAD metabolism. The enzyme NAD(P)+ nucleosidase [EC:3.2.2.6] catalyzes the production of this metabolite from nicotinamide adenine dinucleotide phosphate. This reaction is irreversible and occurs in the cytosol.
Structure
Thumb
Synonyms
ValueSource
(Rib5)ppaHMDB
5-(Adenosine 5'-pyrophosphoryl)-D-riboseHMDB
a5'pp5RIbHMDB
Adenosine 5'-diphosphoriboseHMDB
AdoPPRibHMDB
ADP RiboseHMDB
ADP-D-RiboseHMDB
ADP-RibHMDB
ADP-RiboseHMDB
ADPriboseHMDB
D-Ribofuranos-5-yl-ADPHMDB
Ribose adenosine diphosphateHMDB
[5-(6-Aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [hydroxy-[(3,4,5-trihydroxyoxolan-2-yl)methoxy]phosphoryl] hydrogen phosphateHMDB
Diphosphate ribose, adenosineMeSH
5'-Diphosphoribose, adenosineMeSH
Adenosine diphosphoriboseMeSH
Diphosphoribose, adenosineMeSH
Adenosine 5' diphosphoriboseMeSH
Ribose, ADPMeSH
Ribose, adenosine diphosphateMeSH
Chemical FormulaC15H23N5O14P2
Average Molecular Weight559.3157
Monoisotopic Molecular Weight559.071673493
IUPAC Name{[5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(3,4,5-trihydroxyoxolan-2-yl)methoxy]phosphoryl}oxy)phosphinic acid
Traditional Nameadp ribose
CAS Registry Number20762-30-5
SMILES
NC1=C2N=CN(C3OC(COP(O)(=O)OP(O)(=O)OCC4OC(O)C(O)C4O)C(O)C3O)C2=NC=N1
InChI Identifier
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)
InChI KeySRNWOUGRCWSEMX-UHFFFAOYSA-N
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
  • Oxolane
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Secondary alcohol
  • Hemiacetal
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Alcohol
  • Organic oxygen compound
  • Amine
  • Primary amine
  • Organonitrogen compound
  • Organopnictogen compound
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological Location:

  Subcellular:

  Organ and components:

Source:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Role

Biological role:

  Molecular messenger:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
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
Polarizability46.75 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-01r5-1196680000-fb6c20cc4fb54b50028eView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-01r5-2115904000-4597a65923641317c791View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0910130000-b9073b1bbcee0d4c7c6eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0910000000-4407a7719b31b18bb57bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-1900000000-9d6c2b567f9da9d1d1ceView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a59-1701390000-e958d4521e35989750e1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-1910100000-a653cbe7cba6b5fab234View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a7i-3900000000-c8a10ccf06e1cb8b548aView in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
Biofluid LocationsNot Available
Tissue Location
  • Prostate
Pathways
NameSMPDB/PathwhizKEGG
2-Hydroxyglutric Aciduria (D And L Form)Pw000212Pw000212 greyscalePw000212 simpleNot Available
4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase DeficiencyPw000070Pw000070 greyscalePw000070 simpleNot Available
AICA-RibosiduriaPw000082Pw000082 greyscalePw000082 simpleNot Available
Adenine phosphoribosyltransferase deficiency (APRT)Pw000511Pw000511 greyscalePw000511 simpleNot Available
Adenosine Deaminase DeficiencyPw000075Pw000075 greyscalePw000075 simpleNot Available
Displaying entries 1 - 5 of 24 in total
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022468
KNApSAcK IDNot Available
Chemspider ID187
KEGG Compound IDC00301
BioCyc IDADENOSINE_DIPHOSPHATE_RIBOSE
BiGG ID34547
Wikipedia LinkAdenosine_diphosphate_ribose
METLIN ID6059
PubChem Compound192
PDB IDNot Available
ChEBI ID16960
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Hardie WD, Wright PE, Bernard GR: Effects of intravenous amphotericin B infusion on hemodynamics and airway mechanics in awake sheep. Chest. 1991 Feb;99(2):457-62. [PubMed:1989809 ]
  2. Garcia-Szabo R, Kern DF, Malik AB: Pulmonary vascular response to thrombin: effects of thromboxane synthetase inhibition with OKY-046 and OKY-1581. Prostaglandins. 1984 Dec;28(6):851-66. [PubMed:6543018 ]
  3. Vela-Navarrete R, Escribano-Burgos M, Farre AL, Garcia-Cardoso J, Manzarbeitia F, Carrasco C: Serenoa repens treatment modifies bax/bcl-2 index expression and caspase-3 activity in prostatic tissue from patients with benign prostatic hyperplasia. J Urol. 2005 Feb;173(2):507-10. [PubMed:15643230 ]

Enzymes

General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes with similar activities ADP-ribose ADP-mannose, ADP-glucose, 8-oxo-GDP and 8-oxo-dGDP. Can also hydrolyze other nucleotide sugars with low activity.
Gene Name:
NUDT5
Uniprot ID:
Q9UKK9
Molecular weight:
24327.41
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes ADP-ribose (ADPR) to AMP and ribose 5'-phosphate.
Gene Name:
NUDT9
Uniprot ID:
Q9BW91
Molecular weight:
35448.725
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
General function:
Involved in NAD+ nucleosidase activity
Specific function:
Synthesizes cyclic ADP-ribose, a second messenger that elicits calcium release from intracellular stores. May be involved in pre-B-cell growth.
Gene Name:
BST1
Uniprot ID:
Q10588
Molecular weight:
35723.545
Reactions
NAD + Water → Adenosine diphosphate ribose + Niacinamidedetails
General function:
Involved in NAD+ nucleosidase activity
Specific function:
Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.
Gene Name:
CD38
Uniprot ID:
P28907
Molecular weight:
34328.145
Reactions
NAD + Water → Adenosine diphosphate ribose + Niacinamidedetails
General function:
Involved in ion channel activity
Specific function:
Nonselective, voltage-independent cation channel mediating sodium and calcium ion influx in response to oxidative stress. Extracellular calcium passes through the channel and acts from the intracellular side as a positive regulator in channel activation. Activated by ADP-ribose, nicotinamide adenine dinucleotide (NAD(+)), reactive nitrogen species and arachidonic acid. Inactivated by intracellular ATP. Confers susceptibility to cell death following oxidative stress. Isoform 2 does not seem to be regulated by ADPR. Has ADP-ribose pyrophosphatase activity.
Gene Name:
TRPM2
Uniprot ID:
O94759
Molecular weight:
171224.9
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the reverse reaction of mono-ADP-ribosylation.
Gene Name:
ADPRH
Uniprot ID:
P54922
Molecular weight:
39506.34
Reactions
Protein-N(omega)-(ADP-D-ribosyl)-L-arginine + Water → Adenosine diphosphate ribose + protein-L-argininedetails
ADP-Ribosyl-L-arginine + Water → Adenosine diphosphate ribose + L-Argininedetails
General function:
Not Available
Specific function:
Hydrolyzes ADP-ribose, IDP-ribose, CDP-glycerol, CDP-choline and CDP-ethanolamine, but not other non-reducing ADP-sugars or CDP-glucose. May be involved in immune cell signaling as suggested by the second-messenger role of ADP-ribose, which activates TRPM2 as a mediator of oxidative/nitrosative stress (By similarity).
Gene Name:
ADPRM
Uniprot ID:
Q3LIE5
Molecular weight:
39529.105
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails