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D-Ribose 5-phosphate (YMDB00119)

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
MOLSDFPDBSMILESInChI
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-monophosphate
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 triphosphate → Adenosine monophosphate + hydron + Phosphoribosyl pyrophosphate
D-ribulose 5-phosphate → D-Ribose 5-phosphate
D-Ribose 5-phosphate ↔ D-ribulose 5-phosphate
Xylulose 5-phosphate + D-Ribose 5-phosphate → L-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
Xylulose 5-phosphate + D-Ribose 5-phosphate → D-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
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:
  • 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

Protein Details
1. 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
2. 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
3. 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
4. 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
5. 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
6. 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
7. ADP-ribose pyrophosphatase
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.
Protein Details
8. 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
9. 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
10. 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.