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 IDYMDB00119
NameD-Ribose 5-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionD-Ribose 5-phosphate, also known as D-ribose-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. D-Ribose 5-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). D-Ribose 5-phosphate exists in all living species, ranging from bacteria to humans.
Structure
Thumb
Synonyms
  • D-Ribose 5-phosphate
  • D-Ribose 5-phosphic acid
  • D-ribose-5-P
  • D-ribose-5-phosphate
  • D-ribose-5-phosphorate
  • D-ribose-5-phosphoric acid
  • ribose-5-P
  • Ribose-5-phosphate
  • ribose-5-phosphorate
  • ribose-5-phosphoric acid
  • ribose-5P
  • D-Ribose 5'-phosphate
  • Ribose 5-phosphate
  • D-Ribose 5'-phosphoric acid
  • Ribose 5-phosphoric acid
  • D-Ribose 5-phosphoric acid
  • Ribose-5-phosphoric acid, (D-ribose)-isomer
  • Ribose phosphate
  • Ribose-5-phosphoric acid, (D-ribofuranose)-isomer
  • Ribose-5-phosphoric acid, monobarium salt, (D-ribose)-isomer
  • Ribose 5-monophosphate
  • Ribose-5-phosphoric acid, monosodium salt, (D-ribose)-isomer
CAS number3615-55-2
WeightAverage: 230.1098
Monoisotopic: 230.01915384
InChI KeyKTVPXOYAKDPRHY-SOOFDHNKSA-N
InChIInChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5?/m1/s1
IUPAC Name{[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC NameD-ribofuranose 5-phosphate
Chemical FormulaC5H11O8P
SMILES[H]OC1([H])O[C@]([H])(C([H])([H])OP(=O)(O[H])O[H])[C@@]([H])(O[H])[C@@]1([H])O[H]
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
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • 1,2-diol
  • Secondary alcohol
  • Hemiacetal
  • Polyol
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • 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 Solubility33.6 g/LALOGPS
logP-2.1ALOGPS
logP-2.4ChemAxon
logS-0.84ALOGPS
pKa (Strongest Acidic)1.22ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area136.68 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity40.83 m³·mol⁻¹ChemAxon
Polarizability18.21 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
Histidine BiosynthesisPW002418 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
Pentose phosphate pathwayec00030 Map00030
Purine metabolismec00230 Map00230
SMPDB Reactions
D-Ribose 5-phosphate + Adenosine triphosphateAdenosine monophosphate + hydron + Phosphoribosyl pyrophosphate
D-ribulose 5-phosphateD-Ribose 5-phosphate
D-Ribose 5-phosphateD-ribulose 5-phosphate
Xylulose 5-phosphate + D-Ribose 5-phosphate → L-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
Xylulose 5-phosphate + D-Ribose 5-phosphateD-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-014j-1942000000-8c3468eabd202324a3aeJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-0fr2-1943000000-b5d1468f33c224a23bd3JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)splash10-00di-9532000000-693524b08b2ccd6179c5JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)splash10-00di-9421000000-dbcd94d0a73f35716059JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-014j-1942000000-8c3468eabd202324a3aeJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0fr2-1943000000-b5d1468f33c224a23bd3JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9532000000-693524b08b2ccd6179c5JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9421000000-dbcd94d0a73f35716059JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9320000000-9b5fdcbd0e9ea3ece549JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-06vi-9164100000-2305f99f73e0c553d514JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0002-9320000000-7f3d980d223a6b9f5f3fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0002-9000000000-a5df0614f5cbd8b55405JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-056r-0090700000-ea86961dacc666b5fc7dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0002-9100000000-6cbb3e84820a37a47fbbJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-004i-0090000000-10949588537786dbae1eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0a4i-0000900000-10d8b4fd09ed514cc12eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-002b-9000000000-49264a7584727750bd70JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0002-9100000000-6cbb3e84820a37a47fbbJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-004i-0090000000-10949588537786dbae1eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0a4i-0000900000-10d8b4fd09ed514cc12eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-002b-9000000000-340deaecb0169ce2acd3JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-1790000000-a3ced14cd6c2537c6d8fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-5940000000-8bcb763477232ce1dd2cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00y1-9300000000-ff5bd2489969fca00eb7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-7190000000-184075252146923d2684JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-917b1eb059131caa49acJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-579393c266ea056c9e74JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
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
  • Graille, M., Meyer, P., Leulliot, N., Sorel, I., Janin, J., Van Tilbeurgh, H., Quevillon-Cheruel, S. (2005). "Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archaeal and bacterial enzymes." Biochimie 87:763-769.16054529
  • 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
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID52742
HMDB IDHMDB01548
Pubchem Compound ID77982
Kegg IDC00117
ChemSpider ID388313
FOODB IDFDB001615
WikipediaRibose_5-phosphate
BioCyc IDRIBOSE-5P

Enzymes

General function:
Involved in catalytic activity
Specific function:
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
Gene Name:
TKL2
Uniprot ID:
P33315
Molecular weight:
75028.79688
Reactions
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate → D-ribose 5-phosphate + D-xylulose 5-phosphate.
General function:
Involved in catalytic activity
Specific function:
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
Gene Name:
TKL1
Uniprot ID:
P23254
Molecular weight:
73805.0
Reactions
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate → D-ribose 5-phosphate + D-xylulose 5-phosphate.
General function:
Involved in magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS5
Uniprot ID:
Q12265
Molecular weight:
53504.19922
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS2
Uniprot ID:
P38620
Molecular weight:
34764.60156
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS1
Uniprot ID:
P32895
Molecular weight:
47047.0
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS3
Uniprot ID:
P38689
Molecular weight:
35123.30078
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in hydrolase activity
Specific function:
ADP-ribose + H(2)O = AMP + D-ribose 5- phosphate
Gene Name:
YSA1
Uniprot ID:
Q01976
Molecular weight:
26086.80078
Reactions
ADP-ribose + H(2)O → AMP + D-ribose 5-phosphate.
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.
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 magnesium ion binding
Specific function:
5-phosphoribose 1-diphosphate synthase involved in nucleotide, histidine, and tryptophan biosynthesis. Active in heteromultimeric complexes with other 5-phosphoribose 1- diphosphate synthases (PRS2, PRS3, PRS4 and PRS5)
Gene Name:
PRS4
Uniprot ID:
P38063
Molecular weight:
35845.69922
Reactions
ATP + D-ribose 5-phosphate → AMP + 5-phospho-alpha-D-ribose 1-diphosphate.