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
Description:D-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
DescriptionThis compound 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
Polarizability18.35 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
Water + D-Ribose-5-phosphate > Phosphate + Ribose
Adenosine monophosphate + Water <> Adenine + 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
Ribose-1-phosphate <> D-Ribose-5-phosphate
Adenosine triphosphate + D-Ribose-5-phosphate <> Hydrogen ion + Phosphoribosyl pyrophosphate + Adenosine monophosphate
D-Ribose-5-phosphate <> D-Ribulose 5-phosphate
D-ribose + Adenosine triphosphate > Hydrogen ion + D-Ribose-5-phosphate + ADP
Adenosine diphosphate ribose + Water > Hydrogen ion + Adenosine monophosphate + 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
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
1020± 0 uMK12 NCM3722Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glycerolMid-Log PhaseShake flask and filter culture37 oCPMID: 19561621
686± 0 uMK12 NCM3722Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L acetateMid-Log PhaseShake flask and filter culture37 oCPMID: 19561621
1320± 0 uMK12 NCM3722Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucoseMid-Log PhaseShake flask and filter culture37 oCPMID: 19561621
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
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