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Identification
YMDB IDYMDB00253
NameD-Ribose
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionD-Ribose, also known as D-ribofuranoside or ribose, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Ribose is an extremely weak basic (essentially neutral) compound (based on its pKa). D-Ribose exists in all living species, ranging from bacteria to humans.
Structure
Thumb
Synonyms
  • Alpha-d-ribose
  • alpha-D-ribose-5
  • Alpha-delta-ribose
  • alpha-delta-ribose-5
  • D-(-)-ribose
  • D-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  • d-Ribose
  • delta-(-)-ribose
  • delta-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  • delta-Ribose
  • Ribose
  • (3R,4S,5R)-5-(Hydroxymethyl)tetrahydrofuran-2,3,4-triol
  • D-Ribofuranoside
  • D-​Ribofuranose
  • Ribofuranoside
  • Ribofuranose
CAS number50-69-1
WeightAverage: 150.1299
Monoisotopic: 150.05282343
InChI KeyHMFHBZSHGGEWLO-SOOFDHNKSA-N
InChIInChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1
IUPAC Name(3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional IUPAC NameD-ribofuranoside
Chemical FormulaC5H10O5
SMILES[H]OC([H])([H])[C@@]1([H])OC([H])(O[H])[C@]([H])(O[H])[C@]1([H])O[H]
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
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point95 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogP-2.32 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility1070 g/LALOGPS
logP-2.6ALOGPS
logP-2.3ChemAxon
logS0.85ALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.96 m³·mol⁻¹ChemAxon
Polarizability13.68 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic PropertiesNot Available
SMPDB Pathways
NAD metabolismPW002421 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pentose phosphate pathwayec00030 Map00030
SMPDB Reactions
Nicotinamide riboside + waterhydron + D-Ribose + Niacinamide
KEGG Reactions
Adenosine + waterD-Ribose + Adenine
water + GuanosineD-Ribose + Guanine
Adenosine triphosphate + D-Ribosealpha-D-ribose 5-phosphate + hydron + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Synthesis Reference:Park, Yong-Cheol; Choi, Jin-Ho; Bennett, George N.; Seo, Jin-Ho. Characterization of D-ribose biosynthesis in Bacillus subtilis JY200 deficient in transketolase gene. Journal of Biotechnology (2006), 121(4), 508-516.
External Links:
ResourceLink
CHEBI ID47013
HMDB IDHMDB00283
Pubchem Compound ID5779
Kegg IDC00121
ChemSpider ID5575
FOODB IDFDB011145
WikipediaRibose
BioCyc IDCPD-560

Enzymes

General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + D-ribose = ADP + D-ribose 5-phosphate
Gene Name:
RBK1
Uniprot ID:
P25332
Molecular weight:
36923.80078
Reactions
ATP + D-ribose → ADP + D-ribose 5-phosphate.
General function:
Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
Specific function:
Also acts on cytidine
Gene Name:
URH1
Uniprot ID:
Q04179
Molecular weight:
37960.0
Reactions
Uridine + H(2)O → D-ribose + uracil.