Human Metabolome Database Version 3.5

Showing metabocard for D-Ribulose 5-phosphate (HMDB00618)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:08:57 -0700
HMDB ID HMDB00618
Secondary Accession Numbers
  • HMDB02033
  • HMDB02694
Metabolite Identification
Common Name D-Ribulose 5-phosphate
Description D-Ribulose 5-phosphate is a metabolite in the Pentose phosphate pathway, Pentose and glucuronate interconversions, and in the Riboflavin metabolism (KEGG).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
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 Formula C5H11O8P
Average Molecular Weight 230.1098
Monoisotopic Molecular Weight 230.01915384
IUPAC Name {[(2S,3R,4S)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name [(2S,3R,4S)-3,4,5-trihydroxyoxolan-2-yl]methoxyphosphonic acid
CAS Registry Number 4151-19-3
SMILES OC1O[C@@H](COP(O)(O)=O)[C@H](O)[C@@H]1O
InChI Identifier 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?/m0/s1
InChI Key KTVPXOYAKDPRHY-OWMBCFKOSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Carbohydrates and Carbohydrate Conjugates
Class Monosaccharides
Sub Class Pentoses
Other Descriptors
  • Aliphatic Heteromonocyclic Compounds
  • D-ribose 5-phosphate(ChEBI)
  • Monosaccharide Phosphates
Substituents
  • 1,2 Diol
  • Hemiacetal
  • Organic Hypophosphite
  • Organic Phosphite
  • Oxolane
  • Phosphoric Acid Ester
  • Secondary Alcohol
Direct Parent Pentoses
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction Not Available
Application Not Available
Cellular locations
  • Endoplasmic reticulum
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 33.6 g/L ALOGPS
LogP -2.07 ALOGPS
LogP -2.4 ChemAxon
LogS -0.84 ALOGPS
pKa (strongest acidic) 1.22 ChemAxon
pKa (strongest basic) -3.7 ChemAxon
Hydrogen Acceptor Count 7 ChemAxon
Hydrogen Donor Count 5 ChemAxon
Polar Surface Area 136.68 A2 ChemAxon
Rotatable Bond Count 3 ChemAxon
Refractivity 40.83 ChemAxon
Polarizability 18.23 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -2 ChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations
  • Endoplasmic reticulum
Biofluid Locations
  • Blood
  • Cellular Cytoplasm
Tissue Location
  • Prostate
Pathways
Name SMPDB Link KEGG Link
Pentose Phosphate Pathway SMP00031 map00030 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
1.86 +/- 0.79 uM Children (1-13 year old) Both Normal
Blood Detected and Quantified
1.58 +/- 1.31 uM Adult (>18 years old) Both Normal
Cellular Cytoplasm Detected and Quantified
0.148 uM Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 0.82 +/- 0.22 uM Adult (>18 years old) Both Transaldolase deficiency
Associated Disorders and Diseases
Disease References
Transaldolase deficiency
  • 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 Link_out
      Associated OMIM IDs
      • 606003 Link_out (Transaldolase deficiency)
      DrugBank ID Not Available
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB022145
      KNApSAcK ID Not Available
      Chemspider ID Not Available
      KEGG Compound ID C00117 Link_out
      BioCyc ID RIBULOSE-5P Link_out
      BiGG ID 34237 Link_out
      Wikipedia Link Ribulose 5-phosphate Link_out
      NuGOwiki Link HMDB00618 Link_out
      Metagene Link HMDB00618 Link_out
      METLIN ID 5591 Link_out
      PubChem Compound 53477706 Link_out
      PDB ID Not Available
      ChEBI ID 17797 Link_out
      References
      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)
      General References
      1. 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 Link_out
      2. 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 Link_out
      3. Schenk G, Duggleby RG, Nixon PF: Heterologous expression of human transketolase. Int J Biochem Cell Biol. 1998 Mar;30(3):369-78. Pubmed: 9611778 Link_out
      4. 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 Link_out
      5. 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 Link_out
      6. 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 Link_out
      7. 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 Link_out
      8. 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 Link_out
      9. Gatsura VV: [Pentosephosphate cycle metabolites as energy-supplying anti-ischemic agents] Farmakol Toksikol. 1991 Jul-Aug;54(4):4-8. Pubmed: 1786823 Link_out
      10. 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 Link_out
      11. 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 Link_out
      12. 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 Link_out
      13. 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 Link_out
      14. Chalmers AH: Fresh substrate essential for transketolase assay. Clin Chem. 1993 Jun;39(6):1347-8. Pubmed: 7980725 Link_out
      15. Buttery JE, Chamberlain BR: Fresh vs frozen substrate for transketolase assay. Clin Chem. 1994 Sep;40(9):1786-7. Pubmed: 8070095 Link_out
      16. Takeuchi T, Nishino K, Itokawa Y: Improved determination of transketolase activity in erythrocytes. Clin Chem. 1984 May;30(5):658-61. Pubmed: 6713626 Link_out
      17. 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 Link_out
      18. 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 Link_out
      19. 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 Link_out
      20. 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 Link_out
      21. 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 Link_out
      22. 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. Pubmed: 19212411 Link_out

      Enzymes
      Name: Ribose-phosphate pyrophosphokinase 3
      Reactions: Not Available
      Gene Name: PRPS1L1
      Uniprot ID: P21108 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: ADP-sugar pyrophosphatase
      Reactions: Not Available
      Gene Name: NUDT5
      Uniprot ID: Q9UKK9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Ribose-phosphate pyrophosphokinase 1
      Reactions: Not Available
      Gene Name: PRPS1
      Uniprot ID: P60891 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Ribose-phosphate pyrophosphokinase 2
      Reactions: Not Available
      Gene Name: PRPS2
      Uniprot ID: P11908 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Transketolase-like protein 1
      Reactions: Not Available
      Gene Name: TKTL1
      Uniprot ID: P51854 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Transketolase
      Reactions: Not Available
      Gene Name: TKT
      Uniprot ID: P29401 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: 6-phosphogluconate dehydrogenase, decarboxylating
      Reactions:
      6-Phosphogluconic acid + NADP unknown D-Ribulose 5-phosphate + CO(2) + NADPH details
      6-Phosphogluconic acid + NADP unknown D-Ribulose 5-phosphate + Carbon dioxide + NADPH + Hydrogen Ion details
      Gene Name: PGD
      Uniprot ID: P52209 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Ribokinase
      Reactions: Not Available
      Gene Name: RBKS
      Uniprot ID: Q9H477 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Phosphoglucomutase-1
      Reactions: Not Available
      Gene Name: PGM1
      Uniprot ID: P36871 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Phosphoacetylglucosamine mutase
      Reactions: Not Available
      Gene Name: PGM3
      Uniprot ID: O95394 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Ribose-5-phosphate isomerase
      Reactions:
      D-Ribose 5-phosphate unknown D-Ribulose 5-phosphate details
      Gene Name: RPIA
      Uniprot ID: P49247 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Putative uncharacterized protein RPE
      Reactions: Not Available
      Gene Name: RPE
      Uniprot ID: Q53TV9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Ribulose-phosphate 3-epimerase
      Reactions:
      D-Ribulose 5-phosphate unknown Xylulose 5-phosphate details
      Gene Name: RPE
      Uniprot ID: Q96AT9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Transketolase-like protein 2
      Reactions: Not Available
      Gene Name: TKTL2
      Uniprot ID: Q9H0I9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Putative uncharacterized protein PGD
      Reactions: Not Available
      Gene Name: PGD
      Uniprot ID: A9Z1X1 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA