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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-05-22 15:34:10 UTC
HMDB IDHMDB0000618
Secondary Accession Numbers
  • HMDB0002033
  • HMDB0002694
  • HMDB00618
  • HMDB02033
  • HMDB02694
Metabolite Identification
Common NameD-Ribulose 5-phosphate
DescriptionD-Ribulose 5-phosphate is a metabolite in the following pathways: pentose phosphate pathway, pentose and glucuronate interconversions, and riboflavin metabolism (KEGG).
Structure
Data?1558539250
Synonyms
ValueSource
D-Erythro-pent-2-ulose 5-(dihydrogen phosphate)ChEBI
D-Erythro-pent-2-ulose 5-(dihydrogen phosphoric acid)Generator
D-Ribulose 5-phosphoric acidGenerator
Ribulose 5-phosphateHMDB
Ribulose 5-phosphate, (D)-isomerHMDB
Ribulose 5-phosphate, (L)-isomerHMDB
Chemical FormulaC5H11O8P
Average Molecular Weight230.1098
Monoisotopic Molecular Weight230.01915384
IUPAC Name{[(2R,3R)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional NameAra
CAS Registry Number4151-19-3
SMILES
OCC(=O)[C@H](O)[C@H](O)COP(O)(O)=O
InChI Identifier
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
InChI KeyFNZLKVNUWIIPSJ-UHNVWZDZSA-N
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
  • Acyloin
  • Beta-hydroxy ketone
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Alpha-hydroxy ketone
  • Ketone
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Alcohol
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility33.6 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
Polarizability17.95 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)splash10-0a4i-2936000000-adde71232cd79c7c92aaJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)splash10-0a4i-2947000000-ae4da5853e1b24392d1dJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4j-1935000000-dfb75754c9a7045f108fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0a4j-1935000000-31be2cabeeebc480c1b8JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0pba-1924000000-11aca642135096a8e378JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-014j-1943000000-34588179b9bd7796e907JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0pbj-2914000000-d91b422c677fd9231297JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0592-9800000000-d336b0e2eff1402939d8JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-029t-9327100000-10a5d90f15e25f16925cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004j-9010000000-49c14e85e3a3dee61721JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01q9-3790000000-6f5913e9948fa7667e41JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0btd-9710000000-3724bb9f611bbdc1fe11JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002r-9520000000-c36fdbcc1d3b19b2fafdJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-b67b8ea484aa4ddb40e3JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-82b17cf4f5a8c927fe64JSpectraViewer | MoNA
Biological Properties
Cellular Locations
  • Endoplasmic reticulum
Biospecimen Locations
  • Blood
  • Cellular Cytoplasm
  • Saliva
Tissue Locations
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1.86 +/- 0.79 uMChildren (1-13 years old)BothNormal details
BloodDetected and Quantified1.58 +/- 1.31 uMAdult (>18 years old)BothNormal details
Cellular CytoplasmDetected and Quantified0.148 uMAdult (>18 years old)BothNormal details
SalivaDetected and Quantified5.09 +/- 4.91 uMAdult (>18 years old)Male
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.818 +/- 1.58 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.818 +/- 1.58 uMAdult (>18 years old)Not Specified
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified4.70 +/- 2.86 uMAdult (>18 years old)FemaleNormal details
SalivaDetected and Quantified0.825 +/- 0.406 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.830 +/- 0.542 uMAdult (>18 years old)Not Specified
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.992 +/- 0.935 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.264 +/- 0.406 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.608 +/- 0.811 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.82 +/- 0.22 uMAdult (>18 years old)BothTransaldolase deficiency details
SalivaDetected and Quantified3.41 +/- 1.80 uMAdult (>18 years old)MaleAlzheimer's disease details
SalivaDetected and Quantified3.16 +/- 1.86 uMAdult (>18 years old)MaleFrontotemporal lobe dementia details
SalivaDetected and Quantified4.74 +/- 4.64 uMAdult (>18 years old)BothLewy body disease details
Associated Disorders and Diseases
Disease References
Transaldolase deficiency
  1. Huck JH, Struys EA, Verhoeven NM, Jakobs C, van der Knaap MS: Profiling of pentose phosphate pathway intermediates in blood spots by tandem mass spectrometry: application to transaldolase deficiency. Clin Chem. 2003 Aug;49(8):1375-80. [PubMed:12881455 ]
Alzheimer's disease
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Frontotemporal dementia
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Lewy body disease
  1. Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022145
KNApSAcK IDNot Available
Chemspider ID388327
KEGG Compound IDC00199
BioCyc IDRIBULOSE-5P
BiGG IDNot Available
Wikipedia LinkRibulose_5-phosphate
METLIN IDNot Available
PubChem Compound439184
PDB IDNot Available
ChEBI ID17363
References
Synthesis ReferenceWong, 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)
General References
  1. Shen BW, Perraud AL, Scharenberg A, Stoddard BL: The crystal structure and mutational analysis of human NUDT9. J Mol Biol. 2003 Sep 12;332(2):385-98. [PubMed:12948489 ]
  2. Verhoeven NM, Huck JH, Roos B, Struys EA, Salomons GS, Douwes AC, van der Knaap MS, Jakobs C: Transaldolase deficiency: liver cirrhosis associated with a new inborn error in the pentose phosphate pathway. Am J Hum Genet. 2001 May;68(5):1086-92. Epub 2001 Mar 27. [PubMed:11283793 ]
  3. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  4. 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;2:18. [PubMed:15882454 ]
  5. Lachant NA, Zerez CR, Tanaka KR: Pyrimidine nucleotides impair phosphoribosylpyrophosphate (PRPP) synthetase subunit aggregation by sequestering magnesium. A mechanism for the decreased PRPP synthetase activity in hereditary erythrocyte pyrimidine 5'-nucleotidase deficiency. Biochim Biophys Acta. 1989 Jan 19;994(1):81-8. [PubMed:2535789 ]
  6. Huck JH, Struys EA, Verhoeven NM, Jakobs C, van der Knaap MS: Profiling of pentose phosphate pathway intermediates in blood spots by tandem mass spectrometry: application to transaldolase deficiency. Clin Chem. 2003 Aug;49(8):1375-80. [PubMed:12881455 ]
  7. Boss GR: Decreased phosphoribosylpyrophosphate as the basis for decreased purine synthesis during amino acid starvation of human lymphoblasts. J Biol Chem. 1984 Mar 10;259(5):2936-41. [PubMed:6199353 ]
  8. Schenk G, Duggleby RG, Nixon PF: Heterologous expression of human transketolase. Int J Biochem Cell Biol. 1998 Mar;30(3):369-78. [PubMed:9611778 ]
  9. Cornwell MM, Tsuruo T, Gottesman MM, Pastan I: ATP-binding properties of P glycoprotein from multidrug-resistant KB cells. FASEB J. 1987 Jul;1(1):51-4. [PubMed:2886389 ]
  10. Boer P, Sperling O: Role of cellular ribose-5-phosphate content in the regulation of 5-phosphoribosyl-1-pyrophosphate and de novo purine synthesis in a human hepatoma cell line. Metabolism. 1995 Nov;44(11):1469-74. [PubMed:7476336 ]
  11. Delplanque J, Delpierre G, Opperdoes FR, Van Schaftingen E: Tissue distribution and evolution of fructosamine 3-kinase and fructosamine 3-kinase-related protein. J Biol Chem. 2004 Nov 5;279(45):46606-13. Epub 2004 Aug 25. [PubMed:15331600 ]
  12. Berthon HA, Kuchel PW, Nixon PF: High control coefficient of transketolase in the nonoxidative pentose phosphate pathway of human erythrocytes: NMR, antibody, and computer simulation studies. Biochemistry. 1992 Dec 29;31(51):12792-8. [PubMed:1463749 ]
  13. Gatsura VV: [Pentosephosphate cycle metabolites as energy-supplying anti-ischemic agents]. Farmakol Toksikol. 1991 Jul-Aug;54(4):4-8. [PubMed:1786823 ]
  14. Parry RJ, Burns MR, Skae PN, Hoyt JC, Pal B: Carbocyclic analogues of D-ribose-5-phosphate: synthesis and behavior with 5-phosphoribosyl alpha-1-pyrophosphate synthetases. Bioorg Med Chem. 1996 Jul;4(7):1077-88. [PubMed:8831979 ]
  15. Song EK, Park HJ, Kim JS, Lee HH, Kim UH, Han MK: A novel fluorometric assay for ADP-ribose pyrophosphatase activity. J Biochem Biophys Methods. 2005 Jun 30;63(3):161-9. [PubMed:15967507 ]
  16. Chalmers AH: Fresh substrate essential for transketolase assay. Clin Chem. 1993 Jun;39(6):1347-8. [PubMed:7980725 ]
  17. Buttery JE, Chamberlain BR: Fresh vs frozen substrate for transketolase assay. Clin Chem. 1994 Sep;40(9):1786-7. [PubMed:8070095 ]
  18. Takeuchi T, Nishino K, Itokawa Y: Improved determination of transketolase activity in erythrocytes. Clin Chem. 1984 May;30(5):658-61. [PubMed:6713626 ]
  19. Kakuta Y, Tahara M, Maetani S, Yao M, Tanaka I, Kimura M: Crystal structure of the regulatory subunit of archaeal initiation factor 2B (aIF2B) from hyperthermophilic archaeon Pyrococcus horikoshii OT3: a proposed structure of the regulatory subcomplex of eukaryotic IF2B. Biochem Biophys Res Commun. 2004 Jul 2;319(3):725-32. [PubMed:15184043 ]
  20. Mocali A, Paoletti F: Transketolase from human leukocytes. Isolation, properties and induction of polyclonal antibodies. Eur J Biochem. 1989 Mar 1;180(1):213-9. [PubMed:2495942 ]
  21. Nordenberg J, Aviram R, Beery E, Stenzel KH, Novogrodsky A: Inhibition of 6-phosphogluconate dehydrogenase by glucose 1,6-diphosphate in human normal and malignant colon extracts. Cancer Lett. 1984 Jun;23(2):193-9. [PubMed:6234985 ]
  22. 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 ]

Only showing the first 10 proteins. There are 15 proteins in total.

Enzymes

General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:
PRPS1L1
Uniprot ID:
P21108
Molecular weight:
34838.915
General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes with similar activities ADP-ribose ADP-mannose, ADP-glucose, 8-oxo-GDP and 8-oxo-dGDP. Can also hydrolyze other nucleotide sugars with low activity.
Gene Name:
NUDT5
Uniprot ID:
Q9UKK9
Molecular weight:
24327.41
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:
PRPS1
Uniprot ID:
P60891
Molecular weight:
12324.195
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
Gene Name:
PRPS2
Uniprot ID:
P11908
Molecular weight:
35054.06
General function:
Involved in catalytic activity
Specific function:
Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate (By similarity).
Gene Name:
TKTL1
Uniprot ID:
P51854
Molecular weight:
59302.195
General function:
Involved in catalytic activity
Specific function:
Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.
Gene Name:
TKT
Uniprot ID:
P29401
Molecular weight:
67876.95
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH (By similarity).
Gene Name:
PGD
Uniprot ID:
P52209
Molecular weight:
53139.56
Reactions
6-Phosphogluconic acid + NADP → D-Ribulose 5-phosphate + CO(2) + NADPHdetails
6-Phosphogluconic acid + NADP → D-Ribulose 5-phosphate + Carbon dioxide + NADPH + Hydrogen Iondetails
General function:
Involved in ribokinase activity
Specific function:
Not Available
Gene Name:
RBKS
Uniprot ID:
Q9H477
Molecular weight:
34142.685
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
This enzyme participates in both the breakdown and synthesis of glucose.
Gene Name:
PGM1
Uniprot ID:
P36871
Molecular weight:
63789.985
General function:
Involved in intramolecular transferase activity, phosphotransferases
Specific function:
Interconverts GlcNAc-6-P and GlcNAc-1-P.
Gene Name:
PGM3
Uniprot ID:
O95394
Molecular weight:
62940.905

Only showing the first 10 proteins. There are 15 proteins in total.