Record Information
Version2.0
Creation Date2012-05-31 13:50:34 -0600
Update Date2015-06-03 15:53:57 -0600
Secondary Accession Numbers
  • ECMDB01351
Identification
Name:Deoxyribose 1-phosphate
Description:Deoxyribose 1-phosphate is an intermediate in the metabolism of Pyrimidine. It is a substrate for Purine nucleoside phosphorylase and Thymidine phosphorylase.
Structure
Thumb
Synonyms:
  • 2-Deoxy-a-D-ribose 1-phosphate
  • 2-Deoxy-a-D-ribose 1-phosphoric acid
  • 2-Deoxy-a-delta-ribose 1-phosphate
  • 2-Deoxy-a-delta-ribose 1-phosphoric acid
  • 2-Deoxy-a-δ-ribose 1-phosphate
  • 2-Deoxy-a-δ-ribose 1-phosphoric acid
  • 2-Deoxy-alpha-D-ribose 1-phosphate
  • 2-Deoxy-alpha-D-ribose 1-phosphoric acid
  • 2-Deoxy-alpha-delta-ribose 1-phosphate
  • 2-Deoxy-alpha-delta-ribose 1-phosphoric acid
  • 2-Deoxy-D-erythro-pentofuranose 1-phosphate
  • 2-Deoxy-D-erythro-pentofuranose 1-phosphoric acid
  • 2-Deoxy-D-ribose 1-phosphate
  • 2-Deoxy-D-ribose 1-phosphoric acid
  • 2-Deoxy-D-ribose-1-phosphate
  • 2-Deoxy-D-ribose-1-phosphoric acid
  • 2-Deoxy-delta-erythro-pentofuranose 1-phosphate
  • 2-Deoxy-delta-erythro-pentofuranose 1-phosphoric acid
  • 2-Deoxy-delta-ribose 1-phosphate
  • 2-Deoxy-delta-ribose 1-phosphoric acid
  • 2-Deoxy-delta-ribose-1-phosphate
  • 2-Deoxy-delta-ribose-1-phosphoric acid
  • 2-Deoxy-α-D-ribose 1-phosphate
  • 2-Deoxy-α-D-ribose 1-phosphoric acid
  • 2-Deoxy-α-δ-ribose 1-phosphate
  • 2-Deoxy-α-δ-ribose 1-phosphoric acid
  • 2-Deoxy-δ-erythro-pentofuranose 1-phosphate
  • 2-Deoxy-δ-erythro-pentofuranose 1-phosphoric acid
  • 2-Deoxy-δ-ribose 1-phosphate
  • 2-Deoxy-δ-ribose 1-phosphoric acid
  • 2-Deoxy-δ-ribose-1-phosphate
  • 2-Deoxy-δ-ribose-1-phosphoric acid
  • 2-Deoxyribofuranose 1-phosphate
  • 2-Deoxyribofuranose 1-phosphoric acid
  • D-2-Deoxy-ribofuranose 1-phosphate
  • D-2-Deoxy-ribofuranose 1-phosphoric acid
  • Delta-2-Deoxy-ribofuranose 1-phosphate
  • delta-2-Deoxy-ribofuranose 1-phosphoric acid
  • Deoxy-D-ribose 1-phosphate
  • Deoxy-D-ribose 1-phosphoric acid
  • Deoxyribose 1-phosphate
  • Deoxyribose 1-phosphoric acid
  • Deoxyribose-1-phosphate
  • Deoxyribose-1-phosphoric acid
  • DR1P
  • δ-2-Deoxy-ribofuranose 1-phosphate
  • δ-2-Deoxy-ribofuranose 1-phosphoric acid
Chemical Formula:C5H11O7P
Weight:Average: 214.1104
Monoisotopic: 214.024239218
InChI Key:KBDKAJNTYKVSEK-PYHARJCCSA-N
InChI:InChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5?/m0/s1
CAS number:17210-42-3
IUPAC Name:{[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid
Traditional IUPAC Name:deoxyribose-1-phosphate
SMILES:OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O
Chemical Taxonomy
DescriptionThis compound 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
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • 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 Solubility37.6 g/LALOGPS
logP-2.1ALOGPS
logP-1.5ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)1.37ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area116.45 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity39.32 m³·mol⁻¹ChemAxon
Polarizability17.21 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
purine deoxyribonucleosides degradationPW002077 ThumbThumb?image type=greyscaleThumb?image type=simple
pyrimidine deoxyribonucleosides degradationPW002063 ThumbThumb?image type=greyscaleThumb?image type=simple
salvage pathways of pyrimidine deoxyribonucleotidesPW002061 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • purine deoxyribonucleosides degradation PWY0-1297
  • pyrimidine deoxyribonucleosides degradation PWY0-1298
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9100000000-0b83a26b67c41b7ca8c9View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0002-9120000000-ed5a733798dcf4d7c439View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kb-9430000000-ef11f7c98a651dbe59d7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-9400000000-5e3754bb21aff6c3ce06View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9300000000-615ca1fa907e42aa9c9dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fs-9260000000-5a7b6b1faaba56e1c97dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5f0b0b093f8d726f7076View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-b1cd1b026728c07d36bbView in MoNA
References
References:
  • Holmberg I, Stal P, Hamberg M: Quantitative determination of 8-hydroxy-2'-deoxyguanosine in human urine by isotope dilution mass spectrometry: normal levels in hemochromatosis. Free Radic Biol Med. 1999 Jan;26(1-2):129-35. Pubmed: 9890648
  • 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:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID28542
HMDB IDHMDB01351
Pubchem Compound ID439287
Kegg IDC00672
ChemSpider ID388420
Wikipedia IDNot Available
BioCyc IDDEOXY-D-RIBOSE-1-PHOSPHATE
EcoCyc IDDEOXY-D-RIBOSE-1-PHOSPHATE

Enzymes

General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis
Gene Name:
deoA
Uniprot ID:
P07650
Molecular weight:
47207
Reactions
Thymidine + phosphate = thymine + 2-deoxy-alpha-D-ribose 1-phosphate.
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.
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules
Gene Name:
deoD
Uniprot ID:
P0ABP8
Molecular weight:
25950
Reactions
Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1- phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis
Gene Name:
udp
Uniprot ID:
P12758
Molecular weight:
27159
Reactions
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
The nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the nucleoside molecule, with the formation of the corresponding free bases and pentose-1-phosphate. This protein can degrade all purine nucleosides except adenosine and deoxyadenosine
Gene Name:
xapA
Uniprot ID:
P45563
Molecular weight:
29834