You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.
Identification
YMDB IDYMDB00948
NameD-ribulose 5-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionD-Ribulose 5-phosphate 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. D-Ribulose 5-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
Synonyms
  • alpha-D-Ribose 5-phosphate
  • D-Ribulose 5-phosphate
  • D-Ribulose 5-phosphic acid
  • erythro-Pentulose 5-phosphate
  • Ribulose 5-phosphate
  • Ribulose phosphate
  • D-Erythro-pent-2-ulose 5-(dihydrogen phosphate)
  • D-Erythro-pent-2-ulose 5-(dihydrogen phosphoric acid)
  • D-Ribulose 5-phosphoric acid
  • Ribulose 5-phosphate, (D)-isomer
  • Ribulose 5-phosphate, (L)-isomer
CAS number4151-19-3
WeightAverage: 230.1098
Monoisotopic: 230.01915384
InChI KeyFNZLKVNUWIIPSJ-UHNVWZDZSA-N
InChIInChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5+/m1/s1
IUPAC Name{[(2R,3R)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional IUPAC NameAra
Chemical FormulaC5H11O8P
SMILESOCC(=O)[C@H](O)[C@H](O)COP(O)(O)=O
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
  • Pentose-5-phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Acyloin
  • Beta-hydroxy ketone
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Alpha-hydroxy ketone
  • Ketone
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Alcohol
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility26.1 g/LALOGPS
logP-1.8ALOGPS
logP-2.8ChemAxon
logS-0.95ALOGPS
pKa (Strongest Acidic)1.48ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area144.52 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity42.47 m³·mol⁻¹ChemAxon
Polarizability17.95 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Riboflavin metabolismPW002443 ThumbThumb?image type=greyscaleThumb?image type=simple
RiboneogenesisPW002511 ThumbThumb?image type=greyscaleThumb?image type=simple
xylitol degradationPW002433 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Methane metabolismec00680 Map00680
Pentose and glucuronate interconversionsec00040 Map00040
Pentose phosphate pathwayec00030 Map00030
Riboflavin metabolismec00740 Map00740
Vitamin B6 metabolismec00750 Map00750
SMPDB Reactions
Xylulose 5-phosphateD-ribulose 5-phosphate
Xylulose 5-phosphateD-ribulose 5-phosphate
D-ribulose 5-phosphateD-Ribose 5-phosphate
D-Ribose 5-phosphateD-ribulose 5-phosphate
D-ribulose 5-phosphateFormic acid + 2-Hydroxy-3-oxobutyl phosphate
KEGG Reactions
D-ribulose 5-phosphateFormic acid + 2-Hydroxy-3-oxobutyl phosphate + hydron
6-Phosphogluconic acid + NADPCarbon dioxide + NADPH + D-ribulose 5-phosphate
alpha-D-ribose 5-phosphateD-ribulose 5-phosphate
D-ribulose 5-phosphateXylulose 5-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)splash10-0a4i-2936000000-adde71232cd79c7c92aaJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)splash10-0a4i-2947000000-ae4da5853e1b24392d1dJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4j-1935000000-dfb75754c9a7045f108fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4j-1935000000-31be2cabeeebc480c1b8JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0pba-1924000000-11aca642135096a8e378JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-014j-1943000000-34588179b9bd7796e907JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0pbj-2914000000-d91b422c677fd9231297JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0592-9800000000-d336b0e2eff1402939d8JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-029t-9327100000-10a5d90f15e25f16925cJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004j-9010000000-49c14e85e3a3dee61721JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 10V, positivesplash10-00ec-0970000000-6e833fd34cda3327e6aeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 15V, positivesplash10-007o-0930000000-72bf0b63618d4b200421JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 17V, positivesplash10-007o-0920000000-fe7037f21876801587ecJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 20V, positivesplash10-007o-0910000000-5dacb5e16b8a32f079c0JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 23V, positivesplash10-007o-0900000000-1d35981b82e13d258d9dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 25V, positivesplash10-00ec-0900000000-23938808d1a77a77203dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 27V, positivesplash10-00dl-0900000000-abc2b8be05c39eef69e6JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 3V, positivesplash10-00di-0190000000-f09b49c51cfa01814ef3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 4V, positivesplash10-00di-0490000000-acd1f6a33bd147e29ac3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 5V, positivesplash10-00ec-0980000000-e8070ccdca137f841520JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 7V, positivesplash10-007o-0940000000-0e8aaff469756dafc2eeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 8V, positivesplash10-000x-0920000000-bef5b5a1a6528a057748JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 9V, positivesplash10-000x-0910000000-7a57ccc066185b618224JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 11V, positivesplash10-007o-0900000000-0412a8fa5b22fb04ec87JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 12V, positivesplash10-007o-0900000000-e655723668ec0397d76eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 14V, positivesplash10-00dl-0900000000-4d7aa68ec0ea7a05fe8bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 18V, positivesplash10-00di-1900000000-ef58c4a909999b72f8faJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 22V, positivesplash10-0229-4900000000-6c4c40d2771cf3aec25fJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01q9-3790000000-6f5913e9948fa7667e41JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0btd-9710000000-3724bb9f611bbdc1fe11JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002r-9520000000-c36fdbcc1d3b19b2fafdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-b67b8ea484aa4ddb40e3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-82b17cf4f5a8c927fe64JSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • 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
  • Kondo, H., Nakamura, Y., Dong, Y. X., Nikawa, J., Sueda, S. (2004). "Pyridoxine biosynthesis in yeast: participation of ribose 5-phosphate ketol-isomerase." Biochem J 379:65-70.14690456
  • Vaseghi, S., Baumeister, A., Rizzi, M., Reuss, M. (1999). "In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae." Metab Eng 1:128-140.10935926
  • Senac, T., Hahn-Hagerdal, B. (1990). "Intermediary Metabolite Concentrations in Xylulose- and Glucose-Fermenting Saccharomyces cerevisiae Cells." Appl Environ Microbiol 56:120-126.16348083
  • Jin, C., Barrientos, A., Tzagoloff, A. (2003). "Yeast dihydroxybutanone phosphate synthase, an enzyme of the riboflavin biosynthetic pathway, has a second unrelated function in expression of mitochondrial respiration." J Biol Chem 278:14698-14703.12595523
  • Bar, J., Naumann, M., Reuter, R., Kopperschlager, G. (1996). "Improved purification of ribulose 5-phosphate 3-epimerase from Saccharomyces cerevisiae and characterization of the enzyme." Bioseparation 6:233-241.9032985
  • Reuter, R., Naumann, M., Bar, J., Miosga, T., Kopperschlager, G. (1998). "Ribose-5-phosphate isomerase from Saccharomyces cerevisiae: purification and molecular analysis of the enzyme." Bioseparation 7:107-115.9763699
Synthesis Reference:Wong, Chi-Huey; McCurry, Stephen D.; Whitesides, George M. Practical enzymic syntheses of ribulose 1,5 bisphosphate and ribose 5-phosphate. Journal of the American Chemical Society (1980), 102(27), 7938-9.
External Links:
ResourceLink
CHEBI ID17363
HMDB IDHMDB00618
Pubchem Compound ID439167
Kegg IDC00199
ChemSpider ID23106877
FOODB IDFDB022145
WikipediaRibulose 5-phosphate
BioCyc IDRIBULOSE-5P

Enzymes

General function:
Involved in ribose-5-phosphate isomerase activity
Specific function:
D-ribose 5-phosphate = D-ribulose 5-phosphate
Gene Name:
RKI1
Uniprot ID:
Q12189
Molecular weight:
28257.80078
Reactions
D-ribose 5-phosphate → D-ribulose 5-phosphate.
General function:
Involved in 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
Specific function:
Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
Gene Name:
RIB3
Uniprot ID:
Q99258
Molecular weight:
22567.40039
Reactions
D-ribulose 5-phosphate → formate + L-3,4-dihydroxybutan-2-one 4-phosphate.
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH
Gene Name:
GND1
Uniprot ID:
P38720
Molecular weight:
53542.69922
Reactions
6-phospho-D-gluconate + NADP(+) → D-ribulose 5-phosphate + CO(2) + NADPH.
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH
Gene Name:
GND2
Uniprot ID:
P53319
Molecular weight:
53922.30078
Reactions
6-phospho-D-gluconate + NADP(+) → D-ribulose 5-phosphate + CO(2) + NADPH.
General function:
Involved in catalytic activity
Specific function:
Involved in the protective response to oxidative stress
Gene Name:
RPE1
Uniprot ID:
P46969
Molecular weight:
25966.90039
Reactions
D-ribulose 5-phosphate → D-xylulose 5-phosphate.