Deoxyribose 5-phosphate (ECMDB01031) (M2MDB000230)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)XML
Proteins (778)
Record Information
Version2.0
Creation Date2012-05-31 13:03:42 -0600
Update Date2015-10-15 16:13:48 -0600
Secondary Accession Numbers
  • ECMDB01031
Identification
Name:Deoxyribose 5-phosphate
DescriptionDeoxyribose 5-phosphate is a a metabolite in the pentose phosphate pathway. It can be generated from D-glyceraldehdye-3 phosphate via the enzyme 2-Deoxyribose 5-phosphate aldolase (DERA). Alternately Deoxyribose 5-phosphate can be converted to D-glyceraldehyde-3 phosphate that can then feed into the pentose phosphate pathway. Deoxyribose 5-phosphate can also be generated from 2-Deoxy-D-ribose via the enzyme Ribokinase (EC 2.7.1.15). It has been shown in a number of organisms that deoxynucleosides or deoxyriboses cause the induction of aldolases (such as DERA) involved in their catabolism, leading to the utilisation of the pentose moiety as carbon and energy source.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 2-Deoxy-a-D-ribose 5-phosphate
  • 2-Deoxy-a-D-ribose 5-phosphoric acid
  • 2-Deoxy-a-delta-ribose 5-phosphate
  • 2-Deoxy-a-delta-ribose 5-phosphoric acid
  • 2-Deoxy-a-δ-ribose 5-phosphate
  • 2-Deoxy-a-δ-ribose 5-phosphoric acid
  • 2-Deoxy-alpha-D-ribose 5-phosphate
  • 2-Deoxy-alpha-D-ribose 5-phosphoric acid
  • 2-Deoxy-alpha-delta-ribose 5-phosphate
  • 2-Deoxy-alpha-delta-ribose 5-phosphoric acid
  • 2-Deoxy-D-ribose 5-phosphate
  • 2-Deoxy-D-ribose 5-phosphoric acid
  • 2-Deoxy-D-ribose-5-phosphate
  • 2-Deoxy-D-ribose-5-phosphoric acid
  • 2-Deoxy-α-D-ribose 5-phosphate
  • 2-Deoxy-α-D-ribose 5-phosphoric acid
  • 2-Deoxy-α-δ-ribose 5-phosphate
  • 2-Deoxy-α-δ-ribose 5-phosphoric acid
  • 2-Deoxyribose 5-phosphate
  • 2-Deoxyribose 5-phosphoric acid
  • 2-Deoxyribose-5-p
  • 2-Deoxyribose-5-phosphate
  • 2-Deoxyribose-5-phosphoric acid
  • Deoxy-ribose-5p
  • Deoxyribose 5-phosphate
  • Deoxyribose 5-phosphoric acid
  • Deoxyribose-5-p
  • Deoxyribose-5-phosphate
  • Deoxyribose-5-phosphoric acid
  • DR5P
Chemical Formula:C5H11O7P
Weight:Average: 214.1104
Monoisotopic: 214.024239218
InChI Key:KKZFLSZAWCYPOC-VPENINKCSA-N
InChI:InChI=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
CAS number:102916-66-5
IUPAC Name:{[(2R,3S)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name:[(2R,3S)-3,5-dihydroxyoxolan-2-yl]methoxyphosphonic acid
SMILES:O[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
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Polarizability17.2 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Deoxyribose 5-phosphate <> Acetaldehyde + D-Glyceraldehyde 3-phosphate
Deoxyribose 1-phosphate <> Deoxyribose 5-phosphate
Deoxyribose 5-phosphate + ADP <> Deoxyribose + Adenosine triphosphate
2-deoxy-alpha-D-ribose 1-phosphate > Deoxyribose 5-phosphate
Deoxyribose 5-phosphate > D-Glyceraldehyde 3-phosphate + Acetaldehyde
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:
  • purine deoxyribonucleosides degradation PWY0-1297
  • pyrimidine deoxyribonucleosides degradation PWY0-1298
Concentrations
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-3970000000-cea24354ca1ecb0c0a48View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00kb-7910000000-15b8562df923ebe3a60dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9100000000-b43c0287c08e6bc1db46View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fr-7490000000-7a526ffdff192213b787View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-07ad0e8899ae08668c78View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-2a1b5224e4fe99513e45View in MoNA
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Method of preparing 2-deoxyribose 5-phosphate US Patent
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID16132
HMDB IDHMDB01031
Pubchem Compound ID635
Kegg IDC00673
ChemSpider ID25057464
Wikipedia IDNot Available
BioCyc IDDEOXY-RIBOSE-5P
EcoCyc IDDEOXY-RIBOSE-5P

Enzymes

Protein Details
1. Phosphopentomutase
General function:
Involved in catalytic activity
Specific function:
Phosphotransfer between the C1 and C5 carbon atoms of pentose
Gene Name:
deoB
Uniprot ID:
P0A6K6
Molecular weight:
44370
Reactions
Alpha-D-ribose 1-phosphate = D-ribose 5-phosphate.
2-deoxy-alpha-D-ribose 1-phosphate = 2-deoxy-alpha-D-ribose 5-phosphate.
Protein Details
2. Deoxyribose-phosphate aldolase
General function:
Involved in catalytic activity
Specific function:
2-deoxy-D-ribose 5-phosphate = D- glyceraldehyde 3-phosphate + acetaldehyde
Gene Name:
deoC
Uniprot ID:
P0A6L0
Molecular weight:
27733
Reactions
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde.
Protein Details
3. Ribokinase
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + D-ribose = ADP + D-ribose 5-phosphate
Gene Name:
rbsK
Uniprot ID:
P0A9J6
Molecular weight:
32290
Reactions
ATP + D-ribose = ADP + D-ribose 5-phosphate.