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Identification
YMDB IDYMDB00662
Name2-deoxy-D-ribose 5-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionDeoxyribose 5-phosphate, also known as 2-deoxyribose-5-p, belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. Deoxyribose 5-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Deoxyribose 5-phosphate exists in all eukaryotes, ranging from yeast to humans.
Structure
Thumb
Synonyms
  • 2-deoxy-5-O-phosphono-D-erythro-pentose
  • 2-deoxy-alpha-D-ribose 5-phosphate
  • 2-deoxy-alpha-delta-ribose 5-phosphate
  • 2-Deoxy-D-ribose 5-phosphate
  • 2-deoxy-d-ribose-5-phosphate
  • 2-deoxyribose 5-phosphate
  • 2-deoxyribose-5-p
  • 2-deoxyribose-5-phosphate
  • deoxy-ribose-5p
  • Deoxyribose 5-phosphate
  • Deoxyribose 5-phosphic acid
  • deoxyribose-5-p
  • deoxyribose-5-phosphate
  • Deoxyribose 5-phosphoric acid
CAS number102916-66-5
WeightAverage: 214.1104
Monoisotopic: 214.024239218
InChI KeyKKZFLSZAWCYPOC-VPENINKCSA-N
InChIInChI=1S/C5H11O7P/c6-3-1-5(7)12-4(3)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1
IUPAC Name{[(2R,3S,5R)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Namedeoxyribose-5-phosphate
Chemical FormulaC5H11O7P
SMILESO[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1
Chemical Taxonomy
Description belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentose phosphates
Alternative Parents
Substituents
  • Pentose phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxide
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility37.5 g/LALOGPS
logP-2.1ALOGPS
logP-1.5ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area116.45 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity39.32 m³·mol⁻¹ChemAxon
Polarizability17.46 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG Pathways
Pentose phosphate pathwayec00030 Map00030
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
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
Synthesis Reference:Method of preparing 2-deoxyribose 5-phosphate US Patent #7270992
External Links:
ResourceLink
CHEBI ID16132
HMDB IDHMDB01031
Pubchem Compound ID635
Kegg IDC00673
ChemSpider ID25057464
FOODB IDFDB022380
Wikipedia IDNot Available
BioCyc IDDEOXY-RIBOSE-5P

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.