Record Information
Version2.0
Creation Date2012-05-31 14:06:36 -0600
Update Date2015-09-13 12:56:14 -0600
Secondary Accession Numbers
  • ECMDB04148
Identification
Name:D-Ribulose 5-phosphate
Description:D-Ribulose 5-phosphate is a metabolite in the Pentose phosphate pathway. It is also involved in pentose and glucuronate interconversions, and in Riboflavin metabolism (KEGG)
Structure
Thumb
Synonyms:
  • a-D-Ribose 5-phosphate
  • a-D-Ribose 5-phosphoric acid
  • Alpha-D-Ribose 5-phosphate
  • alpha-D-Ribose 5-phosphoric acid
  • D-Ribulose 5-phosphate
  • D-Ribulose 5-phosphoric acid
  • D-Ribulose-5-P
  • Erythro-Pentulose 5-phosphate
  • erythro-Pentulose 5-phosphoric acid
  • Ribulose 5-phosphate
  • Ribulose 5-phosphoric acid
  • Ribulose phosphate
  • Ribulose phosphoric acid
  • Ribulose-5-P
  • Ribulose-5P
  • Ru5P
  • α-D-Ribose 5-phosphate
  • α-D-Ribose 5-phosphoric acid
Chemical Formula:C5H11O8P
Weight:Average: 230.1098
Monoisotopic: 230.01915384
InChI Key:FNZLKVNUWIIPSJ-UHNVWZDZSA-N
InChI:InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5+/m1/s1
CAS number:4151-19-3
IUPAC Name:{[(2R,3R)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional IUPAC Name:Ara
SMILES:OCC(=O)[C@H](O)[C@H](O)COP(O)(O)=O
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.
KingdomOrganic compounds
Super ClassOrganooxygen compounds
ClassCarbohydrates and carbohydrate conjugates
Sub ClassMonosaccharides
Direct ParentMonosaccharide phosphates
Alternative Parents
Substituents
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Beta-hydroxy ketone
  • Beta-ketoaldehyde
  • Acyloin
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Polyol
  • Ketone
  • 1,2-diol
  • Hydrocarbon derivative
  • Primary alcohol
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility26.1 g/LALOGPS
logP-1.8ALOGPS
logP-2.8ChemAxon
logS-0.95ALOGPS
pKa (Strongest Acidic)1.48ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area144.52 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity42.47 m³·mol⁻¹ChemAxon
Polarizability17.86 ųChemAxon
Number of Rings0ChemAxon
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-Ribulose 5-phosphate <> D-Arabinose 5-phosphate
D-Ribulose 5-phosphate <> Xylulose 5-phosphate
6-Phosphogluconic acid + NADP <> Carbon dioxide + NADPH + D-Ribulose 5-phosphate + Hydrogen ion
D-Ribulose 5-phosphate <> 3,4-Dihydroxy-2-butanone-4-P + Formic acid + Hydrogen ion
Adenosine triphosphate + D-Ribulose 5-phosphate + D-Ribulose 5-phosphate <> ADP + D-Ribulose 1,5-bisphosphate
NAD(P)<sup>+</sup> + 6-Phosphogluconic acid > NAD(P)H + D-Ribulose 5-phosphate + Carbon dioxide
D-Arabinose 5-phosphate <> D-Ribulose 5-phosphate
D-Ribulose 5-phosphate > Hydrogen ion + 3,4-Dihydroxy-2-butanone-4-P + Formic acid
D-Ribose-5-phosphate <> D-Ribulose 5-phosphate
D-Ribulose 5-phosphate <> Xylulose 5-phosphate
6-Phosphogluconic acid + NADP > D-Ribulose 5-phosphate + Carbon dioxide + NADPH
D-Arabinose 5-phosphate > D-Ribulose 5-phosphate
D-Arabinose 5-phosphate > D-Ribulose 5-phosphate
Adenosine triphosphate + D-Ribulose 5-phosphate > ADP + D-Ribulose 1,5-bisphosphate
D-Ribulose 5-phosphate > Formic acid + 1-Deoxy-L-glycero-tetrulose 4-phosphate
D-Ribulose 5-phosphate > Xylulose 5-phosphate
D-Ribose-5-phosphate > D-Ribulose 5-phosphate
D-Ribose-5-phosphate > D-Ribulose 5-phosphate
D-Arabinose 5-phosphate <> D-Ribulose 5-phosphate
Adenosine triphosphate + L-Ribulose + D-Ribulose <> ADP + L-Ribulose 5-phosphate + D-Ribulose 5-phosphate
6-Phosphogluconic acid + NADP > D-Ribulose 5-phosphate + Carbon dioxide + NADPH + NADPH
D-Ribulose 5-phosphate <> Xylulose 5-phosphate + Xylulose 5-phosphate
D-Ribulose 5-phosphate <> D-Ribose-5-phosphate
D-Ribulose 5-phosphate > D-Arabinose 5-phosphate

SMPDB Pathways:
Flavin biosynthesisPW001971 ThumbThumb?image type=greyscaleThumb?image type=simple
Glutathione metabolismPW000833 ThumbThumb?image type=greyscaleThumb?image type=simple
Lipopolysaccharide biosynthesisPW000831 ThumbThumb?image type=greyscaleThumb?image type=simple
Pentose PhosphatePW000893 ThumbThumb?image type=greyscaleThumb?image type=simple
ketogluconate metabolismPW002003 ThumbThumb?image type=greyscaleThumb?image type=simple
lipopolysaccharide biosynthesis IIPW001905 ThumbThumb?image type=greyscaleThumb?image type=simple
lipopolysaccharide biosynthesis IIIPW002059 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
78± 0 uMBW2511348 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L GlucoStationary Phase, glucose limitedBioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h37 oCPMID: 17379776
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-MS (1 MEOX; 5 TMS)splash10-0a4i-2936000000-adde71232cd79c7c92aaView in MoNA
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)splash10-0a4i-2947000000-ae4da5853e1b24392d1dView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4j-1935000000-dfb75754c9a7045f108fView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4j-1935000000-31be2cabeeebc480c1b8View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0pba-1924000000-11aca642135096a8e378View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-014j-1943000000-34588179b9bd7796e907View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0pbj-2914000000-d91b422c677fd9231297View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0592-9800000000-d336b0e2eff1402939d8View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-029t-9327100000-10a5d90f15e25f16925cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004j-9010000000-49c14e85e3a3dee61721View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01q9-3790000000-6f5913e9948fa7667e41View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0btd-9710000000-3724bb9f611bbdc1fe11View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002r-9520000000-c36fdbcc1d3b19b2fafdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-b67b8ea484aa4ddb40e3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-82b17cf4f5a8c927fe64View in MoNA
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
  • Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
  • 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
Synthesis Reference:Wong, Chi-Huey; McCurry, Stephen D.; Whitesides, George M. Practical enzymic syntheses of ribulose 1,5 bisphosphate and ribose 5-phosphate. Journal of the American Chemical Society (1980), 102(27), 7938-9.
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID17797
HMDB IDHMDB00618
Pubchem Compound ID439167
Kegg IDC00199
ChemSpider ID388327
WikipediaRibulose 5-phosphate
BioCyc IDRIBULOSE-5P
EcoCyc IDRIBULOSE-5P
Ligand Expo5RP

Enzymes

General function:
Involved in oxidation-reduction process
Specific function:
Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH
Gene Name:
gnd
Uniprot ID:
P00350
Molecular weight:
51481
Reactions
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH.
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + L(or D)-ribulose = ADP + L(or D)- ribulose 5-phosphate
Gene Name:
araB
Uniprot ID:
P08204
Molecular weight:
61089
Reactions
ATP + L(or D)-ribulose = ADP + L(or D)-ribulose 5-phosphate.
General function:
Involved in 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
Specific function:
Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
Gene Name:
ribB
Uniprot ID:
P0A7J0
Molecular weight:
23353
Reactions
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate.
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 ATP binding
Specific function:
ATP + D-ribulose 5-phosphate = ADP + D- ribulose 1,5-bisphosphate
Gene Name:
prkB
Uniprot ID:
P0AEX5
Molecular weight:
32344
Reactions
ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate.
General function:
Involved in catalytic activity
Specific function:
D-ribulose 5-phosphate = D-xylulose 5- phosphate
Gene Name:
rpe
Uniprot ID:
P0AG07
Molecular weight:
24554
Reactions
D-ribulose 5-phosphate = D-xylulose 5-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 protein binding
Specific function:
Catalyzes the interconversion of D-arabinose 5-phosphate and D-ribulose 5-phosphate
Gene Name:
kdsD
Uniprot ID:
P45395
Molecular weight:
35196
Reactions
D-arabinose 5-phosphate = D-ribulose 5-phosphate.
General function:
Involved in catalytic activity
Specific function:
Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP)
Gene Name:
ispD
Uniprot ID:
Q46893
Molecular weight:
25737
Reactions
CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol.
General function:
Involved in catalytic activity
Specific function:
Specific function unknown
Gene Name:
gutQ
Uniprot ID:
P17115
Molecular weight:
34031
Reactions
D-arabinose 5-phosphate = D-ribulose 5-phosphate.
General function:
Involved in catalytic activity
Specific function:
Probable pentose-5-phosphate 3-epimerase
Gene Name:
sgcE
Uniprot ID:
P39362
Molecular weight:
23214