You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

alpha-D-ribose 5-phosphate (YMDB00650)

Identification
YMDB IDYMDB00650
Namealpha-D-ribose 5-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionD-Ribose 5-phosphate, also known as R-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 eukaryotes, ranging from yeast to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 5-O-phosphono-alpha-D-ribofuranose
  • alpha-D-ribose 5-phosphate
  • arabinose-5-P
  • arabinose-5P
  • D-Arabinose 5-phosphate
  • d-ribose 5-phosphate
  • d-ribose-5-phosphate
  • ribose 5-phosphate
  • 5-O-Phosphono-a-D-ribofuranose
  • 5-O-Phosphono-α-D-ribofuranose
  • a-D-Ribose 5-phosphate
  • a-D-Ribose 5-phosphoric acid
  • alpha-D-Ribose 5-phosphoric acid
  • Α-D-ribose 5-phosphate
  • Α-D-ribose 5-phosphoric acid
  • D-Ribose 5-phosphoric acid
  • D-Ribofuranose 5-phosphate
  • R-5-p
  • Ribose 5-(dihydrogen phosphate)
  • Ribose 5-monophosphate
  • alpha-D-Ribose-5-phosphate
  • Α-D-ribose-5-phosphate
CAS number4300-28-1
WeightAverage: 230.1098
Monoisotopic: 230.01915384
InChI KeyKTVPXOYAKDPRHY-AIHAYLRMSA-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,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Nameα-D-ribose 5-phosphate
Chemical FormulaC5H11O8P
SMILESO[C@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
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
Polarizability18.25 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 ReactionsNot Available
KEGG Reactions
Cytidine monophosphate + water → Cytosine + alpha-D-ribose 5-phosphate
Ribose 1-phosphate ↔ alpha-D-ribose 5-phosphate
Adenosine triphosphate + alpha-D-ribose 5-phosphate ↔ Adenosine monophosphate + hydron + Phosphoribosyl pyrophosphate
Adenosine triphosphate + D-Ribose → alpha-D-ribose 5-phosphate + hydron + ADP
alpha-D-ribose 5-phosphate ↔ D-ribulose 5-phosphate
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 (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0159-1900000000-c7b876b70c54c880bdf3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01c1-9600000000-649e860a529bc7f5b4f8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-053s-9000000000-f9d938955d2446665511JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004j-9040000000-9ee7ba6767ffa3f356dbJSpectraViewer
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 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
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D 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
  • 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:Not Available
External Links:
ResourceLink
CHEBI ID18189
HMDB IDHMDB11734
Pubchem Compound ID230
Kegg IDC00117
ChemSpider ID25946122
FOODB IDFDB001615
WikipediaRibose_5-phosphate
BioCyc IDARABINOSE-5P

Enzymes

Protein Details
1. Phosphoglucomutase-2
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
This enzyme participates in both the breakdown and synthesis of glucose. Can also act on mannose
Gene Name:
PGM2
Uniprot ID:
P37012
Molecular weight:
63088.0
Reactions
Alpha-D-glucose 1-phosphate → alpha-D-glucose 6-phosphate.
Protein Details
2. Phosphoglucomutase-1
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
This enzyme participates in both the breakdown and synthesis of glucose. Can also act on mannose
Gene Name:
PGM1
Uniprot ID:
P33401
Molecular weight:
63111.30078
Reactions
Alpha-D-glucose 1-phosphate → alpha-D-glucose 6-phosphate.
Protein Details
3. Transketolase 2
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.
Protein Details
4. Transketolase 1
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.
Protein Details
5. Ribose-phosphate pyrophosphokinase 5
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.
Protein Details
6. Ribose-phosphate pyrophosphokinase 2
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.
Protein Details
7. Ribose-phosphate pyrophosphokinase 1
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.
Protein Details
8. Ribose-phosphate pyrophosphokinase 3
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.
Protein Details
9. tRNA pseudouridine synthase 1
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine at positions 27 and 28 in the anticodon stem and loop of transfer RNAs; at positions 34 and 36 of intron-containing precursor tRNA(Ile) and at position 35 in the intron-containing tRNA(Tyr)
Gene Name:
PUS1
Uniprot ID:
Q12211
Molecular weight:
62142.0
Reactions
tRNA uridine → tRNA pseudouridine.
Protein Details
10. tRNA pseudouridine synthase 4
General function:
Involved in RNA processing
Specific function:
Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
Gene Name:
PUS4
Uniprot ID:
P48567
Molecular weight:
45273.10156
Reactions
tRNA uridine → tRNA pseudouridine.
Protein Details
11. tRNA pseudouridine synthase 2
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS2
Uniprot ID:
P53167
Molecular weight:
41874.80078
Reactions
tRNA uridine → tRNA pseudouridine.
Protein Details
12. tRNA pseudouridine synthase 3
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridines at positions 38 and 39 in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS3
Uniprot ID:
P31115
Molecular weight:
50888.30078
Reactions
tRNA uridine → tRNA pseudouridine.
Protein Details
13. 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.
Protein Details
14. Ribose-5-phosphate isomerase
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.
Protein Details
15. Ribose-phosphate pyrophosphokinase 4
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.