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Human Metabolome Database Version 3.5

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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 | 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 Comments
Blood Detected and Quantified
Article_icon
1.86 +/- 0.79 uM Children (1-13 year old) Both Normal Not Available
Blood Detected and Quantified
Article_icon
1.58 +/- 1.31 uM Adult (>18 years old) Both Normal Not Available
Cellular Cytoplasm Detected and Quantified
Article_icon
0.148 uM Adult (>18 years old) Both Normal Not Available
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Comments
Blood Detected and Quantified
Article_icon
0.82 +/- 0.22 uM Adult (>18 years old) Both Transaldolase deficiency Not Available
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
    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:
    • ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate [RN:R01049]
    Gene Name: PRPS1L1
    Uniprot ID: P21108 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: ADP-sugar pyrophosphatase
    Reactions:
    • ADP-ribose + H2O = AMP + D-ribose 5-phosphate [RN:R01054]
    Gene Name: NUDT5
    Uniprot ID: Q9UKK9 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Ribose-phosphate pyrophosphokinase 1
    Reactions:
    • ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate [RN:R01049]
    Gene Name: PRPS1
    Uniprot ID: P60891 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Ribose-phosphate pyrophosphokinase 2
    Reactions:
    • ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate [RN:R01049]
    Gene Name: PRPS2
    Uniprot ID: P11908 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Transketolase-like protein 1
    Reactions:
    • sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate [RN:R01641]
    Gene Name: TKTL1
    Uniprot ID: P51854 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Transketolase
    Reactions:
    • sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate [RN:R01641]
    Gene Name: TKT
    Uniprot ID: P29401 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: 6-phosphogluconate dehydrogenase, decarboxylating
    Reactions:
    • 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH [RN:R01528]
    Gene Name: PGD
    Uniprot ID: P52209 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Ribokinase
    Reactions:
    • ATP + D-ribose = ADP + D-ribose 5-phosphate [RN:R01051]
    Gene Name: RBKS
    Uniprot ID: Q9H477 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Phosphoglucomutase-1
    Reactions:
    • alpha-D-glucose 1-phosphate = D-glucose 6-phosphate [RN:R08639]
    Gene Name: PGM1
    Uniprot ID: P36871 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Phosphoacetylglucosamine mutase
    Reactions:
    • N-acetyl-alpha-D-glucosamine 1-phosphate = N-acetyl-D-glucosamine 6-phosphate [RN:R08193]
    Gene Name: PGM3
    Uniprot ID: O95394 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Ribose-5-phosphate isomerase
    Reactions:
    • D-ribose 5-phosphate = D-ribulose 5-phosphate [RN:R01056]
    Gene Name: RPIA
    Uniprot ID: P49247 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Putative uncharacterized protein RPE
    Reactions:
      Gene Name: RPE
      Uniprot ID: Q53TV9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Ribulose-phosphate 3-epimerase
      Reactions:
      • D-ribulose 5-phosphate = D-xylulose 5-phosphate [RN:R01529]
      Gene Name: RPE
      Uniprot ID: Q96AT9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Transketolase-like protein 2
      Reactions:
      • sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate [RN:R01641]
      Gene Name: TKTL2
      Uniprot ID: Q9H0I9 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Putative uncharacterized protein PGD
      Reactions:
        Gene Name: PGD
        Uniprot ID: A9Z1X1 Link_out
        Protein Sequence: FASTA
        Gene Sequence: FASTA