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 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity42.47 m3·mol-1ChemAxon
Polarizability17.86 Å3ChemAxon
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 Pw001971Pw001971 greyscalePw001971 simple
Glutathione metabolismPW000833 Pw000833Pw000833 greyscalePw000833 simple
Lipopolysaccharide biosynthesisPW000831 Pw000831Pw000831 greyscalePw000831 simple
Pentose PhosphatePW000893 Pw000893Pw000893 greyscalePw000893 simple
ketogluconate metabolismPW002003 Pw002003Pw002003 greyscalePw002003 simple
lipopolysaccharide biosynthesis IIPW001905 Pw001905Pw001905 greyscalePw001905 simple
lipopolysaccharide biosynthesis IIIPW002059 Pw002059Pw002059 greyscalePw002059 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-MSNot Available
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0a4j-1935000000-dfb75754c9a7045f108fView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0a4j-1935000000-31be2cabeeebc480c1b8View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0pba-1924000000-11aca642135096a8e378View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-014j-1943000000-34588179b9bd7796e907View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOFsplash10-0pbj-2914000000-d91b422c677fd9231297View in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)Not Available
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