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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2015-04-16 17:35:57 UTC
HMDB IDHMDB00618
Secondary Accession Numbers
  • HMDB02033
  • HMDB02694
Metabolite Identification
Common NameD-Ribulose 5-phosphate
DescriptionD-Ribulose 5-phosphate is a metabolite in the Pentose phosphate pathway, Pentose and glucuronate interconversions, and in the Riboflavin metabolism (KEGG).
Structure
Thumb
Synonyms
  1. alpha-D-Ribose 5-phosphate
  2. D-Ribulose 5-phosphate
  3. Erythro-Pentulose 5-phosphate
  4. Ribulose 5-phosphate
  5. Ribulose phosphate
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
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
  • Oxolane
  • Secondary alcohol
  • Polyol
  • Hemiacetal
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Endoplasmic reticulum
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 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
Spectra
SpectraGC-MS
Biological Properties
Cellular Locations
  • Endoplasmic reticulum
Biofluid Locations
  • Blood
  • Cellular Cytoplasm
  • Saliva
Tissue Location
  • Prostate
Pathways
NameSMPDB LinkKEGG Link
Pentose Phosphate PathwaySMP00031map00030
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
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
BiofluidStatusValueAgeSexConditionReferenceDetails
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. [12881455 ]
Associated OMIM IDs
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022145
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC00199
BioCyc IDRIBULOSE-5P
BiGG ID34237
Wikipedia LinkRibulose 5-phosphate
NuGOwiki LinkHMDB00618
Metagene LinkHMDB00618
METLIN ID5591
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. [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. [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. [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(1):18. [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. [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. [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. [6199353 ]
  8. Schenk G, Duggleby RG, Nixon PF: Heterologous expression of human transketolase. Int J Biochem Cell Biol. 1998 Mar;30(3):369-78. [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. [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. [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. [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. [1463749 ]
  13. Gatsura VV: [Pentosephosphate cycle metabolites as energy-supplying anti-ischemic agents] Farmakol Toksikol. 1991 Jul-Aug;54(4):4-8. [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. [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. [15967507 ]
  16. Chalmers AH: Fresh substrate essential for transketolase assay. Clin Chem. 1993 Jun;39(6):1347-8. [7980725 ]
  17. Buttery JE, Chamberlain BR: Fresh vs frozen substrate for transketolase assay. Clin Chem. 1994 Sep;40(9):1786-7. [8070095 ]
  18. Takeuchi T, Nishino K, Itokawa Y: Improved determination of transketolase activity in erythrocytes. Clin Chem. 1984 May;30(5):658-61. [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. [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. [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. [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. [6699001 ]

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
General function:
Involved in ribose-5-phosphate isomerase activity
Specific function:
Not Available
Gene Name:
RPIA
Uniprot ID:
P49247
Molecular weight:
33268.72
Reactions
D-Ribose 5-phosphate → D-Ribulose 5-phosphatedetails
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
RPE
Uniprot ID:
Q53TV9
Molecular weight:
19537.4
General function:
Involved in catalytic activity
Specific function:
Catalyzes the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate.
Gene Name:
RPE
Uniprot ID:
Q96AT9
Molecular weight:
19537.385
Reactions
D-Ribulose 5-phosphate → Xylulose 5-phosphatedetails
General function:
Involved in catalytic activity
Specific function:
Plays an essential role in total transketolase activity and cell proliferation in cancer cells; after transfection with anti-TKTL1 siRNA, total transketolase activity dramatically decreases and proliferation was significantly inhibited in cancer cells. Plays a pivotal role in carcinogenesis.
Gene Name:
TKTL2
Uniprot ID:
Q9H0I9
Molecular weight:
67876.625
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
PGD
Uniprot ID:
A9Z1X1
Molecular weight:
32311.5