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Identification
YMDB IDYMDB00661
Name2-deoxy-D-ribose
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionDeoxyribose, more, precisely 2-deoxyribose, is a monosaccharide. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of an oxygen atom. Since the pentose sugars arabinose and ribose only differ by the stereochemistry at C2', 2-deoxyribose and 2-deoxyarabinose are equivalent, although the latter term is rarely used because ribose, not arabinose, is the precursor to deoxyribose. [Wikipedia]
Structure
Thumb
Synonyms
  • 2-Deoxy-alpha-D-ribose 1-phosphate
  • 2-Deoxy-D-arabinose
  • 2-Deoxy-D-erythro-pentose
  • 2-Deoxy-D-ribohexopyranose
  • 2-Deoxy-D-ribose
  • 2-Deoxy-D-ribose 1-phosphate
  • 2-Deoxypentose
  • 2-Deoxyribose
  • 2-Desoxy ribosoe
  • 2'-Deoxy-D-ribose
  • D-2-Deoxyribose
  • D-2-Desoxyribose
  • D-dRib
  • D-Erythro-Pentose, 2-deoxy-
  • D-Ribose, 2-deoxy-
  • deoxy-ribose 1-phosphate
  • Deoxyribose
  • Ribose, 2-deoxy-, D-
  • Thyminose
  • Aldehydo-2-deoxy-D-ribose
  • 2 Deoxyribose
CAS number533-67-5
WeightAverage: 134.1305
Monoisotopic: 134.057908808
InChI KeyASJSAQIRZKANQN-CRCLSJGQSA-N
InChIInChI=1S/C5H10O4/c6-2-1-4(8)5(9)3-7/h2,4-5,7-9H,1,3H2/t4-,5+/m0/s1
IUPAC Name(3S,4R)-3,4,5-trihydroxypentanal
Traditional IUPAC Namedeoxyribose
Chemical FormulaC5H10O4
SMILES[H]C([H])(C=O)[C@]([H])(O)[C@]([H])(O)CO
Chemical Taxonomy
Description belongs to the class of organic compounds known as beta-hydroxy aldehydes. These are organic compounds containing an aldehyde substituted with a hydroxy group on the second carbon atom.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentBeta-hydroxy aldehydes
Alternative Parents
Substituents
  • Beta-hydroxy aldehyde
  • Alpha-hydrogen aldehyde
  • Secondary alcohol
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point91 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility709 g/LALOGPS
logP-1.9ALOGPS
logP-2.2ChemAxon
logS0.72ALOGPS
pKa (Strongest Acidic)11.6ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.04 m³·mol⁻¹ChemAxon
Polarizability12.71 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pentose phosphate pathwayec00030 Map00030
Pyrimidine metabolismec00240 Map00240
SMPDB ReactionsNot Available
KEGG Reactions
Adenosine triphosphate + 2-deoxy-D-ribose2-deoxy-D-ribose 5-phosphate + hydron + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)splash10-0q29-1930000000-3b3b7534518a42b65f6cJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)splash10-0l6u-0920000000-e79f5da8378c43b427b1JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 4 TMS)splash10-014i-0759000000-9b44bab9c4e1abec9d88JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0229-9100000000-713dd41c8dce5aaa858bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kr-3900000000-6f94399f0f1d9b862e3eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0005-9200000000-ccb4dd4b156851d1ad09JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052g-9000000000-a9eae6d5f2c8ca4f88adJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-4900000000-5221aaf74ab7d833a28fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9200000000-d5db3a53add7b4afc509JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-0fc8a929da1442a26b40JSpectraViewer
References
References:
  • 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
  • Cirillo, V. P. (1968). "Relationship between sugar structure and competition for the sugar transport system in Bakers' yeast." J Bacteriol 95:603-611.5640385
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID28816
HMDB IDHMDB03224
Pubchem Compound ID10786
Kegg IDC00672
ChemSpider ID24765641
FOODB IDNot Available
WikipediaDeoxyribose
BioCyc IDCPD-7298

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.