Adenosine diphosphate ribose (YMDB00360)

Identification
YMDB IDYMDB00360
NameAdenosine diphosphate ribose
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionAdenosine diphosphate ribose, also known as ADP-rib or ribose adenosine diphosphate, 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. Adenosine diphosphate ribose exists in all eukaryotes, ranging from yeast to plants to humans. Based on a literature review a small amount of articles have been published on Adenosine diphosphate ribose.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (Rib5)ppA
  • [5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [hydroxy-[(3,4,5-trihydroxyoxolan-2-yl)methoxy]phosphoryl] hydrogen phosphate
  • 5-(Adenosine 5'-pyrophosphoryl)-D-ribose
  • A5'pp5Rib
  • Adenosine 5'-diphosphoribose
  • Adenosine diphosphate ribose
  • AdoPPRib
  • ADP Ribose
  • ADP-D-ribose
  • ADP-Rib
  • ADP-ribose
  • ADPribose
  • Ribose adenosine diphosphate
  • Adenosine diphosphoric acid ribose
  • D-Ribofuranos-5-yl-ADP
  • Diphosphate ribose, adenosine
  • 5'-Diphosphoribose, adenosine
  • Adenosine diphosphoribose
  • Diphosphoribose, adenosine
  • Adenosine 5' diphosphoribose
  • Ribose, ADP
  • Ribose, adenosine diphosphate
CAS number20762-30-5
WeightAverage: 559.3157
Monoisotopic: 559.071673493
InChI KeySRNWOUGRCWSEMX-UHFFFAOYSA-N
InChIInChI=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)
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 IUPAC Nameadp ribose
Chemical FormulaC15H23N5O14P2
SMILES[H]OC1([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C2([H])OC([H])(N3C([H])=NC4=C3N=C([H])N=C4N([H])[H])C([H])(O[H])C2([H])O[H])C([H])(O[H])C1([H])O[H]
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine nucleotide sugars
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
  • Pyrimidine
  • Alkyl phosphate
  • Imidolactam
  • Phosphoric acid ester
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Secondary alcohol
  • Hemiacetal
  • Organoheterocyclic compound
  • Polyol
  • Azacycle
  • Oxacycle
  • Organic oxide
  • Amine
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
Biological Properties
Cellular Locations
  • nucleus
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG Pathways
Purine metabolismec00230 Map00230
SMPDB ReactionsNot Available
KEGG Reactions
NAD + water → hydron + Niacinamide + Adenosine diphosphate ribose
NAD + water ↔ hydron + Niacinamide + Adenosine diphosphate ribose
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-01r5-1196680000-fb6c20cc4fb54b50028eJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-01r5-2115904000-4597a65923641317c791JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ("Adenosine diphosphate ribose,1TMS,#1" TMS) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0910130000-b9073b1bbcee0d4c7c6eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0910000000-4407a7719b31b18bb57bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-1900000000-9d6c2b567f9da9d1d1ceJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a59-1701390000-e958d4521e35989750e1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-1910100000-a653cbe7cba6b5fab234JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a7i-3900000000-c8a10ccf06e1cb8b548aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0000090000-36723dbc3777092ad5f2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0faa-2853950000-c2c9d5c0b802214dc6ccJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-2921100000-97be795a8dc0bb3af64eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0000290000-f9ecd49245b2df56a8deJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ar0-1221970000-04d99933f777218ddd3cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a6v-5932310000-f0d589f4eccb4121906eJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID16960
HMDB IDHMDB01178
Pubchem Compound ID192
Kegg IDC00301
ChemSpider ID187
FOODB IDFDB022468
WikipediaAdenosine_diphosphate_ribose
BioCyc IDADENOSINE_DIPHOSPHATE_RIBOSE

Enzymes

Protein Details
1. ADP-ribose 1''-phosphate phosphatase
General function:
Involved in phosphatase activity
Specific function:
Highly specific phosphatase involved in the metabolism of ADP-ribose 1''-phosphate (Appr1p) which is produced as a consequence of tRNA splicing
Gene Name:
POA1
Uniprot ID:
P38218
Molecular weight:
19937.59961
Reactions
ADP-ribose 1''-phosphate + H(2)O → ADP-ribose + phosphate.
Protein Details
2. Probable ADP-ribose 1''-phosphate phosphatase YML087W
General function:
Involved in phosphatase activity
Specific function:
Highly specific phosphatase involved in the metabolism of ADP-ribose 1''-phosphate (Appr1p) which is produced as a consequence of tRNA splicing
Gene Name:
Not Available
Uniprot ID:
Q04299
Molecular weight:
32067.0
Reactions
ADP-ribose 1''-phosphate + H(2)O → ADP-ribose + phosphate.
Protein Details
3. ADP-ribose pyrophosphatase
General function:
Involved in hydrolase activity
Specific function:
ADP-ribose + H(2)O = AMP + D-ribose 5- phosphate
Gene Name:
YSA1
Uniprot ID:
Q01976
Molecular weight:
26086.80078
Reactions
ADP-ribose + H(2)O → AMP + D-ribose 5-phosphate.