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Showing metabocard for Ribose 1-phosphate (HMDB0001489)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (5) Show 5 proteinsXML
enzymes (5) Show 5 proteins
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-02-26 21:23:25 UTC
HMDB IDHMDB0001489
Secondary Accession Numbers
  • HMDB01489
Metabolite Identification
Common NameRibose 1-phosphate
DescriptionRibose 1-phosphate, also known as D-ribose-1P, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Ribose 1-phosphate is a drug. Ribose 1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Ribose 1-phosphate is an intermediate in the metabolism of Pyrimidine and the metabolism of Nicotinate and nicotinamide. Ribose 1-phosphate exists in all living species, ranging from bacteria to humans. Within humans, ribose 1-phosphate participates in a number of enzymatic reactions. In particular, guanine and ribose 1-phosphate can be biosynthesized from guanosine; which is mediated by the enzyme purine nucleoside phosphorylase. In addition, xanthine and ribose 1-phosphate can be biosynthesized from xanthosine; which is catalyzed by the enzyme purine nucleoside phosphorylase. As a result of this purine pathway, guanosine is converted into xanthosine, thus overcoming the lack of guanosine deaminase in mammals. In humans, ribose 1-phosphate is involved in the metabolic disorder called the mitochondrial dna depletion syndrome pathway. Outside of the human body, ribose 1-phosphate has been detected, but not quantified in, several different foods, such as apricots, sesbania flowers, italian sweet red peppers, lupines, and olives. This could make ribose 1-phosphate a potential biomarker for the consumption of these foods. It is a substrate for Uridine phosphorylase 2, Phosphoglucomutase, Purine nucleoside phosphorylase and Uridine phosphorylase 1. The activated ribose moiety in Ribose 1-phosphate which stems from the catabolism of purine nucleosides can be transferred to uracil and, in the presence of ATP, used for the synthesis of pyrimidine nucleotides; therefore, purine nucleosides can act as ribose donors for the salvage of pyrimidine bases. The presence of guanase, which irreversibly converts guanine to xanthine, affects the overall process of guanosine transformation. Ribose 1-phosphate can be formed from guanosine through the action of purine nucleoside phosphorylase. Ribose 1-phosphate can also act as a ribose donor in the synthesis of xanthosine as catalyzed by the same enzyme (purine nucleoside phosphorylase).
Structure
Data?1582752205
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
1-O-Phosphono-alpha-D-ribofuranoseChEBI
1-Phospho-alpha-D-ribofuranoseChEBI
D-Ribose 1-phosphateChEBI
1-O-Phosphono-a-D-ribofuranoseGenerator
1-O-Phosphono-α-D-ribofuranoseGenerator
1-Phospho-a-D-ribofuranoseGenerator
1-Phospho-α-D-ribofuranoseGenerator
D-Ribose 1-phosphoric acidGenerator
Ribose 1-phosphoric acidGenerator
1-O-Phosphono-D-ribofuranoseHMDB
a-D-Ribofuranose 1-(dihydrogen phosphate)HMDB
a-D-Ribose 1-phosphateHMDB
alpha-D-Ribofuranose 1-(dihydrogen phosphate)HMDB
alpha-D-Ribofuranose 1-phosphateHMDB
alpha-D-Ribose 1-phosphateHMDB
D-Ribofuranose 1-(dihydrogen phosphate)HMDB
D-Ribofuranose 1-phosphateHMDB
D-Ribose-1-phosphateHMDB
D-Ribose-1PHMDB
Ribofuranose 1-phosphateHMDB
Ribose 1-phosphate, (beta-D)-isomerHMDB
Ribose 1-phosphate, (alpha-D)-isomerHMDB
Chemical FormulaC5H11O8P
Average Molecular Weight230.1098
Monoisotopic Molecular Weight230.01915384
IUPAC Name{[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid
Traditional Nameribose 1-phosphate
CAS Registry Number14075-00-4
SMILES
OC[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
InChI KeyYXJDFQJKERBOBM-TXICZTDVSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

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 Solubility35.2 g/LALOGPS
logP-2ALOGPS
logP-2.4ChemAxon
logS-0.82ALOGPS
pKa (Strongest Acidic)1.16ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area136.68 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity40.83 m³·mol⁻¹ChemAxon
Polarizability18.17 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9110000000-add01bb15cc1fd9e2e29Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-014i-2931000000-fe633c386d1b3ab9db9aSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-0090000000-e2c9f6f60320b17dd479Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-01t9-9250000000-029c27941ed85100b53cSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9000000000-311ca08c80d0a6c765daSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9000000000-36d97c26c72c69ab56c6Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9000000000-08796c6cb24ecefd9abfSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-9230000000-bf825c0a48e8f3fb1db5Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-9330000000-af34500034734754addaSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9000000000-ea509fab4675ba638745Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9180000000-4449ca89ca00716d8cefSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9110000000-c74e6f3e6a87ec4b57fbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-81a191a3e73e8031cb23Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Cellular Cytoplasm
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Cellular CytoplasmDetected and Quantified60 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03101
Phenol Explorer Compound IDNot Available
FooDB IDFDB022650
KNApSAcK IDNot Available
Chemspider ID388373
KEGG Compound IDC00620
BioCyc IDRIBOSE-1P
BiGG ID34994
Wikipedia LinkNot Available
METLIN ID6273
PubChem Compound439236
PDB IDNot Available
ChEBI ID16300
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceTochikura, Tatsurokuro; Sakai, Takuo; Ogata, Koichi. Ribose 1-phosphate production by fermentation. Jpn. Tokkyo Koho (1969), 3 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Nakayama Y, Kinoshita A, Tomita M: Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model. 2005 May 9;2:18. [PubMed:15882454 ]
  2. Giorgelli F, Bottai C, Mascia L, Scolozzi C, Camici M, Ipata PL: Recycling of alpha-D-ribose 1-phosphate for nucleoside interconversion. Biochim Biophys Acta. 1997 Apr 17;1335(1-2):6-22. [PubMed:9133638 ]

Enzymes

Enzyme Details
1. Phosphoglucomutase-1
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
This enzyme participates in both the breakdown and synthesis of glucose.
Gene Name:
PGM1
Uniprot ID:
P36871
Molecular weight:
63789.985
Reactions
Ribose 1-phosphate → D-Ribose 5-phosphatedetails
Enzyme Details
2. Phosphoglucomutase-2
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
Catalyzes the conversion of the nucleoside breakdown products ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. May also catalyze the interconversion of glucose-1-phosphate and glucose-6-phosphate. Has low glucose 1,6-bisphosphate synthase activity.
Gene Name:
PGM2
Uniprot ID:
Q96G03
Molecular weight:
68282.765
Reactions
Ribose 1-phosphate → D-Ribose 5-phosphatedetails
Enzyme Details
3. Purine nucleoside phosphorylase
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:
PNP
Uniprot ID:
P00491
Molecular weight:
32117.69
Reactions
Nebularine + Phosphate → Purine + Ribose 1-phosphatedetails
Adenosine + Phosphate → Adenine + Ribose 1-phosphatedetails
Inosine + Phosphate → Hypoxanthine + Ribose 1-phosphatedetails
Guanosine + Phosphate → Guanine + Ribose 1-phosphatedetails
Nicotinamide riboside + Phosphate → Niacinamide + Ribose 1-phosphatedetails
Nicotinate D-ribonucleoside + Phosphate → Nicotinic acid + Ribose 1-phosphate + Hydrogen Iondetails
Xanthosine + Phosphate → Xanthine + Ribose 1-phosphatedetails
Enzyme Details
4. Uridine phosphorylase 1
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
UPP1
Uniprot ID:
Q16831
Molecular weight:
33934.005
Reactions
Uridine + Phosphate → Uracil + Ribose 1-phosphatedetails
Fluorouracil + Ribose 1-phosphate → 5-Fluorouridine + Phosphatedetails
Enzyme Details
5. Uridine phosphorylase 2
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis. Shows substrate specificity and accept uridine, deoxyuridine, and thymidine as well as the two pyrimidine nucleoside analogs 5-fluorouridine and 5-fluoro-2(')-deoxyuridine as substrates.
Gene Name:
UPP2
Uniprot ID:
O95045
Molecular weight:
41601.795
Reactions
Uridine + Phosphate → Uracil + Ribose 1-phosphatedetails
Fluorouracil + Ribose 1-phosphate → 5-Fluorouridine + Phosphatedetails