Showing metabocard for Adenosine diphosphate ribose (BMDB0001178)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (10) Show 10 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:42:06 UTC
Update Date2020-05-21 16:28:55 UTC
BMDB IDBMDB0001178
Secondary Accession Numbers
  • BMDB01178
Metabolite Identification
Common NameAdenosine diphosphate ribose
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
ValueSource
Adenosine diphosphoric acid riboseGenerator
(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, adenosineHMDB
5'-Diphosphoribose, adenosineHMDB
Adenosine diphosphoriboseHMDB
Diphosphoribose, adenosineHMDB
Adenosine 5' diphosphoriboseHMDB
Ribose, ADPHMDB
Ribose, adenosine diphosphateHMDB
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
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
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • 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
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biospecimen Locations
  • Placenta
  • Prostate Tissue
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
PlacentaExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Prostate TissueExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0001178
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022468
KNApSAcK IDNot Available
Chemspider ID187
KEGG Compound IDC00301
BioCyc IDNot Available
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 ReferencesNot Available

Enzymes

Enzyme Details
1. ADP-ribose glycohydrolase ARH3
General function:
Posttranslational modification, protein turnover, chaperones
Specific function:
ADP-ribose glycohydrolase that preferentially hydrolyzes the scissile alpha-O-linkage attached to the anomeric C1'' position of ADP-ribose and acts on different substrates, such as proteins ADP-ribosylated on serine, free poly(ADP-ribose) and O-acetyl-ADP-D-ribose. Specifically acts as a serine mono-ADP-ribosylhydrolase by mediating the removal of mono-ADP-ribose attached to serine residues on proteins, thereby playing a key role in DNA damage response. Serine ADP-ribosylation of proteins constitutes the primary form of ADP-ribosylation of proteins in response to DNA damage. Does not hydrolyze ADP-ribosyl-arginine, -cysteine, -diphthamide, or -asparagine bonds. Also able to degrade protein free poly(ADP-ribose), which is synthesized in response to DNA damage: free poly(ADP-ribose) acts as a potent cell death signal and its degradation by ADPRHL2 protects cells from poly(ADP-ribose)-dependent cell death, a process named parthanatos. Also hydrolyzes free poly(ADP-ribose) in mitochondria. Specifically digests O-acetyl-ADP-D-ribose, a product of deacetylation reactions catalyzed by sirtuins. Specifically degrades 1''-O-acetyl-ADP-D-ribose isomer, rather than 2''-O-acetyl-ADP-D-ribose or 3''-O-acetyl-ADP-D-ribose isomers.
Gene Name:
ADPRS
Uniprot ID:
Q3SYV9
Molecular weight:
39221.0
Enzyme Details
2. Manganese-dependent ADP-ribose/CDP-alcohol diphosphatase
General function:
Involved in ADP-ribose diphosphatase activity
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:
A7YY53
Molecular weight:
39235.0
Enzyme Details
3. [Protein ADP-ribosylarginine] hydrolase
General function:
Posttranslational modification, protein turnover, chaperones
Specific function:
Specifically acts as a arginine mono-ADP-ribosylhydrolase by mediating the removal of mono-ADP-ribose attached to arginine residues on proteins.
Gene Name:
ADPRH
Uniprot ID:
Q32KR8
Molecular weight:
39152.0
Enzyme Details
4. Poly(ADP-ribose) glycohydrolase
General function:
Involved in poly(ADP-ribose) glycohydrolase activity
Specific function:
Poly(ADP-ribose) glycohydrolase that degrades poly(ADP-ribose) by hydrolyzing the ribose-ribose bonds present in poly(ADP-ribose) (PubMed:15658938). PARG acts both as an endo- and exoglycosidase, releasing poly(ADP-ribose) of different length as well as ADP-ribose monomers. It is however unable to cleave the ester bond between the terminal ADP-ribose and ADP-ribosylated residues, leaving proteins that are mono-ADP-ribosylated. Poly(ADP-ribose) is synthesized after DNA damage is only present transiently and is rapidly degraded by PARG. Required to prevent detrimental accumulation of poly(ADP-ribose) upon prolonged replicative stress, while it is not required for recovery from transient replicative stress. Required for retinoid acid-dependent gene transactivation, probably by removing poly(ADP-ribose) from histone demethylase KDM4D, allowing chromatin derepression at RAR-dependent gene promoters. Involved in the synthesis of ATP in the nucleus, together with PARP1, NMNAT1 and NUDT5. Nuclear ATP generation is required for extensive chromatin remodeling events that are energy-consuming (By similarity).
Gene Name:
PARG
Uniprot ID:
O02776
Molecular weight:
110837.0
Enzyme Details
5. tRNA 2'-phosphotransferase 1
General function:
Translation, ribosomal structure and biogenesis
Specific function:
Catalyzes the last step of tRNA splicing, the transfer of the splice junction 2'-phosphate from ligated tRNA to NAD to produce ADP-ribose 1''-2'' cyclic phosphate.
Gene Name:
TRPT1
Uniprot ID:
Q3ZBM7
Molecular weight:
27791.0
Enzyme Details
6. N-acetyl-D-glucosamine kinase
General function:
Carbohydrate transport and metabolism
Specific function:
Converts endogenous N-acetylglucosamine (GlcNAc), a major component of complex carbohydrates, from lysosomal degradation or nutritional sources into GlcNAc 6-phosphate. Involved in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway. Also has ManNAc kinase activity (By similarity).
Gene Name:
NAGK
Uniprot ID:
Q3SZM9
Molecular weight:
37268.0
Reactions
3 N-Acetyl-D-Glucosamine 6-Phosphate + 3 Adenosine diphosphate ribose →3 Chitin +3 Adenosine triphosphatedetails
Enzyme Details
7. Glutamate-cysteine ligase catalytic subunit
General function:
Involved in ADP binding
Specific function:
Not Available
Gene Name:
GCLC
Uniprot ID:
Q32S38
Molecular weight:
69023.0
Reactions
L-Glutamic acid + Adenosine triphosphate + L-Cysteine → Gamma-Glutamylcysteine + Adenosine diphosphate ribose + Hydrogen phosphatedetails
Enzyme Details
8. Glutamate--cysteine ligase regulatory subunit
General function:
Not Available
Specific function:
Not Available
Gene Name:
GCLM
Uniprot ID:
Q2T9Y6
Molecular weight:
30533.0
Reactions
L-Glutamic acid + Adenosine triphosphate + L-Cysteine → Gamma-Glutamylcysteine + Adenosine diphosphate ribose + Hydrogen phosphatedetails
Enzyme Details
9. Nudix hydrolase 5
General function:
Not Available
Specific function:
Not Available
Gene Name:
NUDT5
Uniprot ID:
F1MMR8
Molecular weight:
18648.0
Reactions
Adenosine diphosphate ribose + Water → Adenosine monophosphate + D-Ribose 5-phosphatedetails
Enzyme Details
10. Bone marrow stromal cell antigen 1
General function:
Not Available
Specific function:
Not Available
Gene Name:
BST1
Uniprot ID:
F1MLP3
Molecular weight:
35144.0
Reactions
Niacinamide + Hydrogen phosphate + Adenosine diphosphate ribose → NADP + Waterdetails
Niacinamide + Adenosine diphosphate ribose → NAD + Waterdetails