2-deoxy-D-ribofuranose 1-phosphate (YMDB00663)

Identification
YMDB IDYMDB00663
Name2-deoxy-D-ribofuranose 1-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionDeoxyribose 1-phosphate belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Deoxyribose 1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Deoxyribose 1-phosphate exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2-deoxy-1-O-phosphono-D-erythro-pentofuranose
  • 2-deoxy-1-O-phosphono-D-ribofuranose
  • 2-deoxy-alpha-D-ribose 1-phosphate
  • 2-deoxy-alpha-delta-ribose 1-phosphate
  • 2-deoxy-d-erythro-pentofuranose 1-phosphate
  • 2-deoxy-d-ribose 1-phosphate
  • 2-deoxy-D-ribose-1-phosphate
  • 2-deoxy-delta-erythro-pentofuranose 1-phosphate
  • 2-deoxy-delta-ribose 1-phosphate
  • 2-deoxy-delta-ribose-1-phosphate
  • 2-deoxyribofuranose 1-phosphate
  • d-2-deoxy-ribofuranose 1-phosphate
  • delta-2-deoxy-ribofuranose 1-phosphate
  • deoxy-ribose 1-phosphate
  • Deoxyribose 1-phosphate
  • Deoxyribose 1-phosphic acid
  • Deoxyribose-1-phosphate
  • 2-Deoxy-D-ribose 1-phosphoric acid
  • Deoxyribose 1-phosphoric acid
  • 2-Deoxyribose 1-phosphate
  • 2-Deoxyribose 1-phosphate, (alpha-D-erythro)-isomer
  • 2-Deoxyribose 1-phosphate, (beta-D-erythro)-isomer
CAS number17210-42-3
WeightAverage: 214.1104
Monoisotopic: 214.024239218
InChI KeyKBDKAJNTYKVSEK-PYHARJCCSA-N
InChIInChI=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
IUPAC Name{[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid
Traditional IUPAC Namedeoxyribose-1-phosphate
Chemical FormulaC5H11O7P
SMILESOC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O
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
  • 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
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
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
phosphate + 2'-Deoxyuridine ↔ Uracil + 2-deoxy-D-ribofuranose 1-phosphate
phosphate + 2'-Deoxyadenosine ↔ 2-deoxy-D-ribofuranose 1-phosphate + Adenine
2'-Deoxyguanosine + phosphate ↔ 2-deoxy-D-ribofuranose 1-phosphate + Guanine
2'-Deoxyinosine + phosphate ↔ Hypoxanthine + 2-deoxy-D-ribofuranose 1-phosphate
phosphate + Thymidine ↔ Thymine + 2-deoxy-D-ribofuranose 1-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9100000000-0b83a26b67c41b7ca8c9JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0002-9120000000-ed5a733798dcf4d7c439JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kb-9430000000-ef11f7c98a651dbe59d7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-9400000000-5e3754bb21aff6c3ce06JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9300000000-615ca1fa907e42aa9c9dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fs-9260000000-5a7b6b1faaba56e1c97dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5f0b0b093f8d726f7076JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-b1cd1b026728c07d36bbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-3690000000-41b666017994305912b8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-9200000000-99440f284bdeb59e2f04JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052b-9000000000-f613851350f97d5430bcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fr-9080000000-e66a31856a5562cb0b9dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
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:Not Available
External Links:
ResourceLink
CHEBI ID28542
HMDB IDHMDB01351
Pubchem Compound ID5460448
Kegg IDC00672
ChemSpider ID24785157
FOODB IDFDB022571
Wikipedia IDNot Available
BioCyc IDDEOXY-RIBOSE-1P

Enzymes

Protein Details
1. Purine nucleoside phosphorylase
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:
PNP1
Uniprot ID:
Q05788
Molecular weight:
33754.60156
Reactions
Purine nucleoside + phosphate → purine + alpha-D-ribose 1-phosphate.