2-deoxy-D-ribose 5-phosphate (YMDB00662)

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
MOLSDFPDBSMILESInChI
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-ribose → 2-deoxy-D-ribose 5-phosphate + hydron + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9600000000-bdc9f54852e365293f11JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-006x-9185000000-bfea5991ff0a9475e0b9JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-3970000000-30d79004fa4e6fa5906dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00kb-7910000000-3de23781c803b806a189JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052b-9100000000-25bca847c2e30ed7e327JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fr-8490000000-6979c10cf3fafe02069dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-43a8b73209f01319d3c2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-16fc473b541d2a247dafJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-8910000000-7c465e8be120df2e083aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00r2-9200000000-4f0c0c2bf45b1986dd6aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9100000000-a91ae5a4e7423371ee52JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01r2-9030000000-5eb77e97817ae8e3e50fJSpectraViewer
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: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

Protein Details
1. Probable ribokinase
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.