Record Information
Version2.0
Creation Date2012-05-31 13:55:08 -0600
Update Date2015-09-16 14:50:11 -0600
Secondary Accession Numbers
  • ECMDB02033
Identification
Name:D-Ribose-5-phosphate
DescriptionD-ribose-5-phosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Ribose 5-phosphate is both a product and an intermediate of the pentose phosphate pathway. The last step of the oxidative reactions in the pentose phosphate pathway is the production of ribulose-5-phosphate. Ribulose-5-phosphate can reversibly isomerize to ribose-5-phosphate. Ribulose-5-phosphate can alternatively undergo a series of isomerizations as well as transaldolations and transketolations that result in the production of other pentoses phosphates as well as fructose 6-phosphate and glyceraldehyde-3-phosphate (both intermediates in glycolysis). The enzyme ribose-phosphate diphosphokinase converts ribose-5-phosphate into phosphoribosyl pyrophosphate. (WikiPedia)
Structure
Thumb
Synonyms:
  • α-D-ribose-5-phosphate
  • α-D-ribose-5-phosphoric acid
  • a-D-Ribose-5-phosphate
  • a-D-Ribose-5-phosphoric acid
  • Alpha-D-Ribose-5-phosphate
  • alpha-D-Ribose-5-phosphoric acid
  • D-Ribose 5'-phosphate
  • D-Ribose 5'-phosphoric acid
  • D-Ribose 5-phosphate
  • D-Ribose 5-phosphoric acid
  • D-ribose-5-P
  • D-Ribose-5-phosphorate
  • D-Ribose-5-phosphoric acid
  • R5P
  • Ribose 5-phosphate
  • Ribose 5-phosphoric acid
  • Ribose-5-P
  • Ribose-5-phosphate
  • Ribose-5-phosphorate
  • Ribose-5-phosphoric acid
  • Ribose-5P
  • α-D-Ribose-5-phosphate
  • α-D-Ribose-5-phosphoric acid
Chemical Formula:C5H11O8P
Weight:Average: 230.1098
Monoisotopic: 230.01915384
InChI Key:KTVPXOYAKDPRHY-SOOFDHNKSA-N
InChI:InChI=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
CAS number:4151-19-3
IUPAC Name:{[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name:D-ribofuranose 5-phosphate
SMILES:OC1O[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
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
LogP:-2.919PhysProp
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
Reactions:
D-Ribose-5-phosphate <> D-Ribulose 5-phosphate
D-Ribose-5-phosphate + Xylulose 5-phosphate <> D-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
Ribose-1-phosphate <> D-Ribose-5-phosphate
Adenosine diphosphate ribose + Water <> Adenosine monophosphate +2 Hydrogen ion + D-Ribose-5-phosphate
Water + D-Ribose-5-phosphate > Phosphate + Ribose
Adenosine triphosphate + D-Ribose-5-phosphate <> Adenosine monophosphate + Hydrogen ion + Phosphoribosyl pyrophosphate
Adenosine monophosphate + Water <> Adenine + D-Ribose-5-phosphate
Adenosine triphosphate + Ribose <> ADP + Hydrogen ion + D-Ribose-5-phosphate
Adenosine triphosphate + D-Ribose-5-phosphate <> Adenosine monophosphate + Phosphoribosyl pyrophosphate
Adenosine triphosphate + Ribose <> ADP + D-Ribose-5-phosphate
Adenosine diphosphate ribose + Water <> Adenosine monophosphate + D-Ribose-5-phosphate
D-Ribose-5-phosphate <> D-Ribulose 5-phosphate
alpha-D-Ribose 1-phosphate + Ribose-1-phosphate <> D-Ribose-5-phosphate
Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate <> D-Ribose-5-phosphate + Xylulose 5-phosphate
Aminofructose 6-phosphate + D-Ribose-5-phosphate <> Iminoerythrose 4-phosphate + Sedoheptulose 7-phosphate
D-Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate <> D-Ribose-5-phosphate + Xylulose 5-phosphate
Water + Adenosine monophosphate > D-Ribose-5-phosphate + Adenine
Water + Nicotinamide ribotide <> Hydrogen ion + D-Ribose-5-phosphate + Niacinamide
D-ribose + Adenosine triphosphate > Hydrogen ion + D-Ribose-5-phosphate + ADP
Adenosine diphosphate ribose + Water > Hydrogen ion + Adenosine monophosphate + D-Ribose-5-phosphate
D-Ribose-5-phosphate + Uracil <> Water + Pseudouridine 5'-phosphate
Adenosine diphosphate ribose + Water > Adenosine monophosphate + D-Ribose-5-phosphate
Ribose-1-phosphate > D-Ribose-5-phosphate
Adenosine triphosphate + D-Ribose-5-phosphate > Adenosine monophosphate + Phosphoribosyl pyrophosphate
Pseudouridine 5'-phosphate + Water > Uracil + D-Ribose-5-phosphate

SMPDB Pathways:
PRPP BiosynthesisPW000909 ThumbThumb?image type=greyscaleThumb?image type=simple
Pentose PhosphatePW000893 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine ribonucleosides degradtionPW002024 ThumbThumb?image type=greyscaleThumb?image type=simple
Ribose DegradationPW002102 ThumbThumb?image type=greyscaleThumb?image type=simple
adenine and adenosine salvage IIIPW002072 ThumbThumb?image type=greyscaleThumb?image type=simple
purine ribonucleosides degradationPW002076 ThumbThumb?image type=greyscaleThumb?image type=simple
pyrimidine ribonucleosides degradationPW002104 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-014j-1942000000-8c3468eabd202324a3aeView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-0fr2-1943000000-b5d1468f33c224a23bd3View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)splash10-00di-9532000000-693524b08b2ccd6179c5View in 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-dbcd94d0a73f35716059View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-014j-1942000000-8c3468eabd202324a3aeView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0fr2-1943000000-b5d1468f33c224a23bd3View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9532000000-693524b08b2ccd6179c5View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-9421000000-dbcd94d0a73f35716059View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9320000000-9b5fdcbd0e9ea3ece549View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-06vi-9164100000-2305f99f73e0c553d514View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0002-9320000000-7f3d980d223a6b9f5f3fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0002-9000000000-a5df0614f5cbd8b55405View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-056r-0090700000-ea86961dacc666b5fc7dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0002-9100000000-6cbb3e84820a37a47fbbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-004i-0090000000-10949588537786dbae1eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negativesplash10-0a4i-0000900000-10d8b4fd09ed514cc12eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-002b-9000000000-49264a7584727750bd70View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0002-9100000000-6cbb3e84820a37a47fbbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-004i-0090000000-10949588537786dbae1eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0a4i-0000900000-10d8b4fd09ed514cc12eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-002b-9000000000-340deaecb0169ce2acd3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-1790000000-a3ced14cd6c2537c6d8fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-5940000000-8bcb763477232ce1dd2cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00y1-9300000000-ff5bd2489969fca00eb7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-7190000000-184075252146923d2684View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-917b1eb059131caa49acView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-579393c266ea056c9e74View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Nakayama Y, Kinoshita A, Tomita M: Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model. 2005 May 9;2(1):18. Pubmed: 15882454
  • Pilz RB, Willis RC, Boss GR: The influence of ribose 5-phosphate availability on purine synthesis of cultured human lymphoblasts and mitogen-stimulated lymphocytes. J Biol Chem. 1984 Mar 10;259(5):2927-35. Pubmed: 6699001
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID17797
HMDB IDHMDB01548
Pubchem Compound ID439167
Kegg IDC00117
ChemSpider ID388313
WikipediaD-ribose-5-P
BioCyc IDRIBOSE-5P
EcoCyc IDRIBOSE-5P

Enzymes

General function:
Involved in catalytic activity
Specific function:
Phosphotransfer between the C1 and C5 carbon atoms of pentose
Gene Name:
deoB
Uniprot ID:
P0A6K6
Molecular weight:
44370
Reactions
Alpha-D-ribose 1-phosphate = D-ribose 5-phosphate.
2-deoxy-alpha-D-ribose 1-phosphate = 2-deoxy-alpha-D-ribose 5-phosphate.
General function:
Involved in magnesium ion binding
Specific function:
ATP + D-ribose 5-phosphate = AMP + 5-phospho- alpha-D-ribose 1-diphosphate
Gene Name:
prs
Uniprot ID:
P0A717
Molecular weight:
34218
Reactions
ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in ribose-5-phosphate isomerase activity
Specific function:
D-ribose 5-phosphate = D-ribulose 5-phosphate
Gene Name:
rpiA
Uniprot ID:
P0A7Z0
Molecular weight:
22860
Reactions
D-ribose 5-phosphate = D-ribulose 5-phosphate.
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + D-ribose = ADP + D-ribose 5-phosphate
Gene Name:
rbsK
Uniprot ID:
P0A9J6
Molecular weight:
32290
Reactions
ATP + D-ribose = ADP + D-ribose 5-phosphate.
General function:
Involved in catalytic activity
Specific function:
Involved in regulation of AMP concentrations
Gene Name:
amn
Uniprot ID:
P0AE12
Molecular weight:
53994
Reactions
AMP + H(2)O = D-ribose 5-phosphate + adenine.
General function:
Involved in acid phosphatase activity
Specific function:
Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:
aphA
Uniprot ID:
P0AE22
Molecular weight:
26103
Reactions
A phosphate monoester + H(2)O = an alcohol + 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:
tktA
Uniprot ID:
P27302
Molecular weight:
72211
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:
tktB
Uniprot ID:
P33570
Molecular weight:
73042
Reactions
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate.
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
This enzyme participates in both the breakdown and synthesis of glucose
Gene Name:
pgm
Uniprot ID:
P36938
Molecular weight:
58361
Reactions
Alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.
General function:
Involved in carbohydrate metabolic process
Specific function:
In addition to its activity on D-ribose 5-phosphate it probably also has activity on D-allose 6-phosphate
Gene Name:
rpiB
Uniprot ID:
P37351
Molecular weight:
16073
Reactions
D-ribose 5-phosphate = D-ribulose 5-phosphate.
D-allose 6-phosphate = D-allulose 6-phosphate.
General function:
Involved in catalytic activity
Specific function:
Catalyzes the hydrolysis of sugar phosphate to sugar and inorganic phosphate. Has a wide substrate specificity catalyzing the hydrolysis of fructose-1-P most efficiently, but it remains uncertain if this is the real substrate in vivo
Gene Name:
supH
Uniprot ID:
P75792
Molecular weight:
30413
Reactions
Sugar phosphate + H(2)O = sugar + phosphate.
General function:
Involved in hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Specific function:
Acts on ADP-mannose and ADP-glucose as well as ADP- ribose. Prevents glycogen biosynthesis. The reaction catalyzed by this enzyme is a limiting step of the gluconeogenic process
Gene Name:
nudF
Uniprot ID:
Q93K97
Molecular weight:
23667
Reactions
ADP-ribose + H(2)O = AMP + D-ribose 5-phosphate.
General function:
Involved in hydrolase activity
Specific function:
Active on adenosine(5')triphospho(5')adenosine (Ap3A), ADP-ribose, NADH, adenosine(5')diphospho(5')adenosine (Ap2A)
Gene Name:
nudE
Uniprot ID:
P45799
Molecular weight:
21153
Reactions
ADP-ribose + H(2)O = AMP + D-ribose 5-phosphate.
General function:
Involved in catalytic activity
Specific function:
Specific function unknown
Gene Name:
yhfW
Uniprot ID:
P45549
Molecular weight:
44559

Transporters

General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368