Deoxyribose (PAMDB000483)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000483
Identification
Name: Deoxyribose
Description:Deoxyribose is an aldopentose, a monosaccharide containing five carbon atoms, and including an aldehyde functional group. It is derived from the pentose sugar ribose by the replacement of the hydroxyl group at the 2 position with hydrogen, leading to the net loss of an oxygen atom, and has chemical formula C5H10O4. In deoxyribose, the carbon furthest from the attached carbon is stripped of the oxygen atom in what would be a hydroxyl group in ribose. The common base adenine (a purine derivative) coupled to deoxyribose is called deoxyadenosine. The 5-triphosphate derivative of adenosine, commonly called adenosine triphosphate (ATP) is an important energy transport molecule in cells. (Wikipedia)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 2'-Deoxy-D-ribose
  • 2-Deoxy-D-ribose
  • 2-Deoxyribose
  • Deoxyribose
Chemical Formula: C5H10O4
Average Molecular Weight: 134.1305
Monoisotopic Molecular Weight: 134.057908808
InChI Key: PDWIQYODPROSQH-WISUUJSJSA-N
InChI:InChI=1S/C5H10O4/c6-2-4-3(7)1-5(8)9-4/h3-8H,1-2H2/t3-,4+,5+/m1/s1
CAS number: 533-67-5
IUPAC Name:(2S,4R,5S)-5-(hydroxymethyl)oxolane-2,4-diol
Traditional IUPAC Name: 2-deoxyribose
SMILES:OC[C@@H]1O[C@H](O)C[C@H]1O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as monosaccharides. These are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Carbohydrates and carbohydrate conjugates
Sub ClassMonosaccharides
Direct Parent Monosaccharides
Alternative Parents
Substituents
  • Monosaccharide
  • Oxolane
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Solid
Charge:0
Melting point: 91 °C
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility1050.0 mg/mLALOGPS
logP-2.1ALOGPS
logP-1.4ChemAxon
logS0.89ALOGPS
pKa (Strongest Acidic)12.36ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.92 Å2ChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.45 m3·mol-1ChemAxon
Polarizability12.67 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Deoxyribose 5-phosphate + ADP <> Deoxyribose + Adenosine triphosphate
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kr-1900000000-90110d36692d2fa02034View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014r-5900000000-a2fc5c56decd9a9dd270View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-059b-9000000000-af78f6c0618e210b1719View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-2900000000-3fa7ba0b3105a4089704View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-067r-9500000000-3672c628038bf5b3bdc5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9000000000-a63ae9417695ec37c8acView in MoNA
References
References:
  • Chappel A, Scholem RD, Brown GK, Truscott RM, Cotton RG, Haan EA, Danks DM: Deoxyribose-5-phosphate aldolase deficiency--a harmless inborn error of metabolism. J Inherit Metab Dis. 1983;6(3):105-7. Pubmed: 6422138
  • Formichi P, Radi E, Battisti C, Tarquini E, Leonini A, Di Stefano A, Federico A: Human fibroblasts undergo oxidative stress-induced apoptosis without internucleosomal DNA fragmentation. J Cell Physiol. 2006 Aug;208(2):289-97. Pubmed: 16646085
  • Gutteridge JM, Quinlan GJ: Antioxidant protection against organic and inorganic oxygen radicals by normal human plasma: the important primary role for iron-binding and iron-oxidising proteins. Biochim Biophys Acta. 1992 Oct 20;1159(3):248-54. Pubmed: 1327159
  • Gutteridge JM, Quinlan GJ: Antioxidant protection against organic and inorganic oxygen radicals by normal human plasma: the important primary role for iron-binding and iron-oxidising proteins. Biochim Biophys Acta. 1993 Feb 13;1156(2):144-50. Pubmed: 8427873
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Lapenna D, Ciofani G, Festi D, Neri M, Pierdomenico SD, Giamberardino MA, Cuccurullo F: Antioxidant properties of ursodeoxycholic acid. Biochem Pharmacol. 2002 Dec 1;64(11):1661-7. Pubmed: 12429355
  • Truscott RJ, Halpern B, Hammond J, Hunt S, Cotton RG, Haan EA, Danks DM: Abnormal deoxyribose metabolites in the urine of a child with a possible new inborn error of metabolism. Biomed Mass Spectrom. 1979 Oct;6(10):453-9. Pubmed: 526564
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID28816
HMDB IDHMDB03224
Pubchem Compound ID10786
Kegg IDC01801
ChemSpider ID17216222
WikipediaDeoxyribose
BioCyc ID2-DEOXYRIBOSE
EcoCyc ID2-DEOXYRIBOSE

Enzymes

Protein Details
• Ribokinase
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + D-ribose = ADP + D-ribose 5-phosphate
Gene Name:
rbsK
Locus Tag:
PA1950
Molecular weight:
31.8 kDa
Reactions
ATP + D-ribose = ADP + D-ribose 5-phosphate.

Transporters