Human Metabolome Database Version 3.5

Showing metabocard for D-Ribose (HMDB00283)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-05-29 13:25:21 -0600
HMDB ID HMDB00283
Secondary Accession Numbers None
Metabolite Identification
Common Name D-Ribose
Description D-ribose is commonly referred to simply as ribose, a five-carbon sugar found in all living cells. Ribose is not an essential nutrient because it can be synthesized by almost every tissue in the body from other substances, such as glucose. It is vital for life as a component of DNA, RNA, ATP, ADP, and AMP. In nature, small amounts of ribose can be found in ripe fruits and vegetables. Brewer's yeast, which has a high concentration of RNA, is another rich source of ribose. D-ribose is also a component of many so-called energy drinks and antiaging products available on the market today. Ribose is a structural component of ATP, which is the primary energy source for exercising muscle. The adenosine component is an adenine base attached to the five-carbon sugar ribose. ATP provides energy to working muscles by releasing a phosphate group, hence becoming ADP, which in turn may release a phosphate group, then becoming AMP. During intense muscular activity, the total amount of ATP available is quickly depleted. In an effort to correct this imbalance, AMP is broken down in the muscle and secreted from the cell. Once the breakdown products of AMP are released from the cell, the energy potential (TAN pool) of the muscle is reduced and ATP must then be reformed using ribose. Ribose helps restore the level of adenine nucleotides by bypassing the rate-limiting step in the de novo (oxidative pentose phosphate) pathway, which regenerates 5-phosphoribosyl-l-pyrophosphate (PRPP), the essential precursor for ATP. If ribose is not readily available to a cell, glucose may be converted to ribose. Ribose supplementation has been shown to increase the rate of ATP resynthesis following intense exercise. The use of ribose in men with severe coronary artery disease resulted in improved exercise tolerance. Hence, there is interest in the potential of ribose supplements to boost muscular performance in athletic activities. (PMID: 17618002 Link_out, Curr Sports Med Rep. 2007 Jul;6(4):254-7.).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. alpha-D-Ribose
  2. alpha-D-Ribose-5
  3. alpha-delta-Ribose
  4. alpha-delta-Ribose-5
  5. D-(-)-Ribose
  6. D-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  7. D-Ribose
  8. delta-(-)-Ribose
  9. delta-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  10. delta-Ribose
  11. Ribose
Chemical Formula C5H10O5
Average Molecular Weight 150.1299
Monoisotopic Molecular Weight 150.05282343
IUPAC Name (3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional IUPAC Name D-ribofuranose
CAS Registry Number 50-69-1
SMILES OC[C@H]1OC(O)[C@H](O)[C@@H]1O
InChI Identifier InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1
InChI Key HMFHBZSHGGEWLO-SOOFDHNKSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Carbohydrates and Carbohydrate Conjugates
Class Monosaccharides
Sub Class Pentoses
Other Descriptors
  • Aliphatic Heteromonocyclic Compounds
  • L-arabinose(ChEBI)
Substituents
  • 1,2 Diol
  • Hemiacetal
  • Oxolane
  • Primary Alcohol
  • Secondary Alcohol
Direct Parent Pentoses
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Second messenger
Application Not Available
Cellular locations
  • Extracellular
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 95 °C Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP -2.32 HANSCH,C ET AL. (1995)
Predicted Properties
Property Value Source
Water Solubility 1070 g/L ALOGPS
LogP -2.65 ALOGPS
LogP -2.3 ChemAxon
LogS 0.85 ALOGPS
pKa (strongest acidic) 11.31 ChemAxon
pKa (strongest basic) -3 ChemAxon
Hydrogen Acceptor Count 5 ChemAxon
Hydrogen Donor Count 4 ChemAxon
Polar Surface Area 90.15 A2 ChemAxon
Rotatable Bond Count 1 ChemAxon
Refractivity 29.96 ChemAxon
Polarizability 13.68 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
Gas-MS Spectrum
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies )
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • Skeletal Muscle
  • Fibroblasts
  • Neuron
  • Pancreas
  • Placenta
  • Testes
  • Kidney
  • Epidermis
  • Prostate
  • Adrenal Gland
  • Lung
  • Platelet
  • Spleen
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
2.3 (0.0-5.0) uM Adult (>18 years old) Both Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
2.5 (0.0 - 5.0) uM Adolescent (13-18 years old) Both Normal
Urine Detected and Quantified
2.5 (0.0 - 5.0) umol/mmol creatinine Adolescent (13-18 years old) Both Normal
Urine Detected and Quantified
3.0 (2.6-4.4) umol/mmol creatinine Adult (>18 years old) Both Normal
  • Geigy Scient...
Urine Detected and Quantified
6.35 +/- 4.59 umol/mmol creatinine Infant (0-1 year old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 2.4 (0.0-5.0) uM Adult (>18 years old) Both Ribose-5-phosphate isomerase deficiency
Cerebrospinal Fluid (CSF) Detected and Quantified 90.0 (47.0 - 146.0) uM Adolescent (13-18 years old) Both Ribose-5-phosphate isomerase deficiency
Urine Detected and Quantified 50.0 (5.0 - 102.0) umol/mmol creatinine Adolescent (13-18 years old) Both Ribose-5-Phosphate Isomerase Deficiency
Associated Disorders and Diseases
Disease References
Ribose-5-phosphate isomerase deficiency
  • Huck JH, Verhoeven NM, Struys EA, Salomons GS, Jakobs C, van der Knaap MS: Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy. Am J Hum Genet. 2004 Apr;74(4):745-51. Epub 2004 Feb 25. Pubmed: 14988808 Link_out
      Associated OMIM IDs
      • 608611 Link_out (Ribose-5-phosphate isomerase deficiency)
      DrugBank ID Not Available
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB011145
      KNApSAcK ID C00034198 Link_out
      Chemspider ID 5575 Link_out
      KEGG Compound ID C00121 Link_out
      BioCyc ID CPD-560 Link_out
      BiGG ID 33936 Link_out
      Wikipedia Link Ribose Link_out
      NuGOwiki Link HMDB00283 Link_out
      Metagene Link HMDB00283 Link_out
      METLIN ID 313 Link_out
      PubChem Compound 5779 Link_out
      PDB ID 1GQT Link_out
      ChEBI ID 16988 Link_out
      References
      Synthesis Reference Park, Yong-Cheol; Choi, Jin-Ho; Bennett, George N.; Seo, Jin-Ho. Characterization of D-ribose biosynthesis in Bacillus subtilis JY200 deficient in transketolase gene. Journal of Biotechnology (2006), 121(4), 508-516.
      Material Safety Data Sheet (MSDS) Download (PDF)
      General References
      1. Drel VR, Pacher P, Stevens MJ, Obrosova IG: Aldose reductase inhibition counteracts nitrosative stress and poly(ADP-ribose) polymerase activation in diabetic rat kidney and high-glucose-exposed human mesangial cells. Free Radic Biol Med. 2006 Apr 15;40(8):1454-65. Epub 2006 Jan 31. Pubmed: 16631535 Link_out
      2. Dancis J, Lee J, Mendoza S, Liebes L: Nucleoside transport by perfused human placenta. Placenta. 1993 Sep-Oct;14(5):547-54. Pubmed: 8290494 Link_out
      3. Quadrilatero J, Rush JW: Increased DNA fragmentation and altered apoptotic protein levels in skeletal muscle of spontaneously hypertensive rats. J Appl Physiol. 2006 Oct;101(4):1149-61. Epub 2006 Jun 15. Pubmed: 16778006 Link_out
      4. Carloto A, Costas MJ, Cameselle JC, McLennan AG, Ribeiro JM: The specific, submicromolar-Km ADP-ribose pyrophosphatase purified from human placenta is enzymically indistinguishable from recombinant NUDT9 protein, including a selectivity for Mn2+ as activating cation and increase in Km for ADP-ribose, both elicited by H2O2. Biochim Biophys Acta. 2006 Oct;1760(10):1545-51. Epub 2006 Jun 9. Pubmed: 16860484 Link_out
      5. Genovese T, Mazzon E, Di Paola R, Muia C, Crisafulli C, Caputi AP, Cuzzocrea S: ROLE OF ENDOGENOUS AND EXOGENOUS LIGANDS FOR THE PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR alpha IN THE DEVELOPMENT OF BLEOMYCIN-INDUCED LUNG INJURY. Shock. 2005 Dec;24(6):547-55. Pubmed: 16317386 Link_out
      6. Abe H, Tanuma S: Properties of poly(ADP-ribose) glycohydrolase purified from pig testis nuclei. Arch Biochem Biophys. 1996 Dec 1;336(1):139-46. Pubmed: 8951044 Link_out
      7. Augustin A, Muller-Steffner H, Schuber F: Molecular cloning and functional expression of bovine spleen ecto-NAD+ glycohydrolase: structural identity with human CD38. Biochem J. 2000 Jan 1;345 Pt 1:43-52. Pubmed: 10600637 Link_out
      8. Dodd SL, Johnson CA, Fernholz K, St Cyr JA: The role of ribose in human skeletal muscle metabolism. Med Hypotheses. 2004;62(5):819-24. Pubmed: 15082114 Link_out
      9. Cheng C, Zochodne DW: Sensory neurons with activated caspase-3 survive long-term experimental diabetes. Diabetes. 2003 Sep;52(9):2363-71. Pubmed: 12941777 Link_out
      10. Szabo E, Virag L, Bakondi E, Gyure L, Hasko G, Bai P, Hunyadi J, Gergely P, Szabo C: Peroxynitrite production, DNA breakage, and poly(ADP-ribose) polymerase activation in a mouse model of oxazolone-induced contact hypersensitivity. J Invest Dermatol. 2001 Jul;117(1):74-80. Pubmed: 11442752 Link_out
      11. Jacobson EL, Giacomoni PU, Roberts MJ, Wondrak GT, Jacobson MK: Optimizing the energy status of skin cells during solar radiation. J Photochem Photobiol B. 2001 Oct;63(1-3):141-7. Pubmed: 11684461 Link_out
      12. Wurzer G, Herceg Z, Wesierska-Gadek J: Increased resistance to anticancer therapy of mouse cells lacking the poly(ADP-ribose) polymerase attributable to up-regulation of the multidrug resistance gene product P-glycoprotein. Cancer Res. 2000 Aug 1;60(15):4238-44. Pubmed: 10945636 Link_out
      13. Okamoto H: The Reg gene family and Reg proteins: with special attention to the regeneration of pancreatic beta-cells. J Hepatobiliary Pancreat Surg. 1999;6(3):254-62. Pubmed: 10526060 Link_out
      14. McNealy T, Frey M, Trojan L, Knoll T, Alken P, Michel MS: Intrinsic presence of poly (ADP-ribose) is significantly increased in malignant prostate compared to benign prostate cell lines. Anticancer Res. 2003 Mar-Apr;23(2B):1473-8. Pubmed: 12820412 Link_out
      15. Alexy T, Toth A, Marton Z, Horvath B, Koltai K, Feher G, Kesmarky G, Kalai T, Hideg K, Sumegi B, Toth K: Inhibition of ADP-evoked platelet aggregation by selected poly(ADP-ribose) polymerase inhibitors. J Cardiovasc Pharmacol. 2004 Mar;43(3):423-31. Pubmed: 15076227 Link_out
      16. Jiang Q, Wong J, Fyrst H, Saba JD, Ames BN: gamma-Tocopherol or combinations of vitamin E forms induce cell death in human prostate cancer cells by interrupting sphingolipid synthesis. Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17825-30. Epub 2004 Dec 13. Pubmed: 15596715 Link_out
      17. Toth O, Szabo C, Kecskes M, Poto L, Nagy A, Losonczy H: In vitro effect of the potent poly(ADP-ribose) polymerase (PARP) inhibitor INO-1001 alone and in combination with aspirin, eptifibatide, tirofiban, enoxaparin or alteplase on haemostatic parameters. Life Sci. 2006 Jun 20;79(4):317-23. Epub 2006 Feb 9. Pubmed: 16480745 Link_out
      18. Wall KA, Klis M, Kornet J, Coyle D, Ame JC, Jacobson MK, Slama JT: Inhibition of the intrinsic NAD+ glycohydrolase activity of CD38 by carbocyclic NAD analogues. Biochem J. 1998 Nov 1;335 ( Pt 3):631-6. Pubmed: 9794804 Link_out
      19. Tamagno E, Parola M, Bardini P, Piccini A, Borghi R, Guglielmotto M, Santoro G, Davit A, Danni O, Smith MA, Perry G, Tabaton M: Beta-site APP cleaving enzyme up-regulation induced by 4-hydroxynonenal is mediated by stress-activated protein kinases pathways. J Neurochem. 2005 Feb;92(3):628-36. Pubmed: 15659232 Link_out
      20. Boros LG, Steinkamp MP, Fleming JC, Lee WN, Cascante M, Neufeld EJ: Defective RNA ribose synthesis in fibroblasts from patients with thiamine-responsive megaloblastic anemia (TRMA). Blood. 2003 Nov 15;102(10):3556-61. Epub 2003 Jul 31. Pubmed: 12893755 Link_out
      21. Takeda Y, Usukura M, Yoneda T, Oda N, Ito Y, Mabuchi H: The expression of messenger RNA for ADP-ribosyl cyclase in aldosterone-producing adenomas. Clin Endocrinol (Oxf). 2005 Apr;62(4):504-8. Pubmed: 15807884 Link_out
      22. Thomas D, Yang H, Boffa DJ, Ding R, Sharma VK, Lagman M, Li B, Hering B, Mohanakumar T, Lakey J, Kapur S, Hancock WW, Suthanthiran M: Proapoptotic Bax is hyperexpressed in isolated human islets compared with antiapoptotic Bcl-2. Transplantation. 2002 Dec 15;74(11):1489-96. Pubmed: 12490780 Link_out
      23. 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
      24. Dhanoa TS, Housner JA: Ribose: more than a simple sugar? Curr Sports Med Rep. 2007 Jul;6(4):254-7. Pubmed: 17618002 Link_out

      Enzymes
      Name: Ribokinase
      Reactions:
      Adenosine triphosphate + D-Ribose unknown ADP + D-Ribose 5-phosphate details
      Gene Name: RBKS
      Uniprot ID: Q9H477 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA