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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-09-14 00:03:55 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
StatusExpected but not Quantified
Origin
  • Endogenous
Biofunction
  • Component of nicotinate and nicotinamide metabolism
  • Component of purine metabolism
  • Second messenger
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
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 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count9ChemAxon
Refractivity111.12 m3·mol-1ChemAxon
Polarizability46.75 Å3ChemAxon
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-MSNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
Biofluid LocationsNot Available
Tissue Location
  • Prostate
Pathways
Adenylosuccinate Lyase DeficiencyPw000076Pw000076 greyscalePw000076 simpleNot Available
Azathioprine PathwayPw000266Pw000266 greyscalePw000266 simpleNot Available
Glutamate MetabolismPw000003Pw000003 greyscalePw000003 simpleMap00250
Gout or Kelley-Seegmiller SyndromePw000077Pw000077 greyscalePw000077 simpleNot Available
HomocarnosinosisPw000071Pw000071 greyscalePw000071 simpleNot Available
Displaying entries 6 - 10 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
NuGOwiki LinkHMDB0001178
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