Xanthosine (PAMDB000125)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000125
Identification
Name: Xanthosine
Description:Xanthosine is a nucleoside derived from xanthine and ribose. It is a deamination product of guanosine. Xanthosine monophosphate is an intermediate in purine metabolism, formed from IMP, and forming GMP.(Wikipedia)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 3,9-Dihydro-9-b-D-ribofuranosyl-1H-purine-2,6-dione
  • 3,9-dihydro-9-b-delta-Ribofuranosyl-1H-purine-2,6-dione
  • 3,9-dihydro-9-b-δ-Ribofuranosyl-1H-purine-2,6-dione
  • 3,9-Dihydro-9-beta-delta-ribofuranosyl-1H-purine-2,6-dione
  • 3,9-Dihydro-9-D-ribofuranosyl-1H-purine-2,6-dione
  • 3,9-Dihydro-9-delta-ribofuranosyl-1H-purine-2,6-dione
  • 3,9-dihydro-9-β-δ-Ribofuranosyl-1H-purine-2,6-dione
  • 3,9-dihydro-9-δ-Ribofuranosyl-1H-purine-2,6-dione
  • 9 β-D-ribofuranosylxanthine
  • 9 b-D-Ribofuranosylxanthine
  • 9 beta-D-Ribofuranosylxanthine
  • 9 β-D-Ribofuranosylxanthine
  • 9-b-D-Ribofuranosylxanthine
  • 9-b-delta-Ribofuranosylxanthine
  • 9-b-δ-Ribofuranosylxanthine
  • 9-beta-delta-Ribofuranosylxanthine
  • 9-D-Ribofuranosylxanthine
  • 9-delta-Ribofuranosylxanthine
  • 9-β-δ-Ribofuranosylxanthine
  • 9-δ-Ribofuranosylxanthine
  • Xanthosine
Chemical Formula: C10H12N4O6
Average Molecular Weight: 284.2255
Monoisotopic Molecular Weight: 284.075684136
InChI Key: UBORTCNDUKBEOP-UUOKFMHZSA-N
InChI:InChI=1S/C10H12N4O6/c15-1-3-5(16)6(17)9(20-3)14-2-11-4-7(14)12-10(19)13-8(4)18/h2-3,5-6,9,15-17H,1H2,(H2,12,13,18,19)/t3-,5-,6-,9-/m1/s1
CAS number: 146-80-5
IUPAC Name:9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purine-2,6-diol
Traditional IUPAC Name: 9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purine-2,6-diol
SMILES:OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=C(O)N=C2O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as purine nucleosides. These are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Purine nucleosides
Sub ClassNot Available
Direct Parent Purine nucleosides
Alternative Parents
Substituents
  • Purine ribonucleoside
  • Alkaloid or derivatives
  • Xanthine
  • N-glycosyl compound
  • Glycosyl compound
  • Purine
  • Imidazopyrimidine
  • Hydroxypyrimidine
  • Pyrimidine
  • N-substituted imidazole
  • Monosaccharide
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility27.8 mg/mLALOGPS
logP-1.6ALOGPS
logP-1.2ChemAxon
logS-1ALOGPS
pKa (Strongest Acidic)11.33ChemAxon
pKa (Strongest Basic)0.078ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area153.98 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity62.4 m3·mol-1ChemAxon
Polarizability25.54 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Water + Xanthylic acid > Phosphate + Xanthosine
Water + Xanthosine > Ribose + Xanthine
Phosphate + Xanthosine <> Ribose-1-phosphate + Xanthine
Xanthosine + Phosphate <> Xanthine + alpha-D-Ribose 1-phosphate
Xanthosine + Water > D-ribose + Xanthine
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0032-0963000000-08e48347b76242e521e6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0udi-0900000000-e3e76f5bf26f34680c35View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0udi-7900000000-6e1f70509da5adf99678View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0a4r-9500000000-3cce63949eec45fa9204View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0udi-0910000000-b2c7e01e9105bba310aaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0udi-0910000000-e6e1d21c0d22b3ad2821View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Dudley E, Lemiere F, Van Dongen W, Tuytten R, El-Sharkawi S, Brenton AG, Esmans EL, Newton RP: Analysis of urinary nucleosides. IV. Identification of urinary purine nucleosides by liquid chromatography/electrospray mass spectrometry. Rapid Commun Mass Spectrom. 2004;18(22):2730-8. Pubmed: 15499664
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Khalil PN, Erb N, Khalil MN, Escherich G, Janka-Schaub GE: Validation and application of a high-performance liquid chromatographic-based assay for determination of the inosine 5'-monophosphate dehydrogenase activity in erythrocytes. J Chromatogr B Analyt Technol Biomed Life Sci. 2006 Sep 14;842(1):1-7. Epub 2006 May 24. Pubmed: 16725387
  • Liebich HM, Di Stefano C, Wixforth A, Schmid HR: Quantitation of urinary nucleosides by high-performance liquid chromatography. J Chromatogr A. 1997 Feb 28;763(1-2):193-7. Pubmed: 9129323
  • Marti R, Nishigaki Y, Hirano M: Elevated plasma deoxyuridine in patients with thymidine phosphorylase deficiency. Biochem Biophys Res Commun. 2003 Mar 28;303(1):14-8. Pubmed: 12646159
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Enei, Hitoshi; Sato, Katsuaki; Hirose, Yoshio. Xanthosine production by fermentation. Jpn. Kokai Tokkyo Koho (1975), 3 pp.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID18107
HMDB IDHMDB00299
Pubchem Compound ID64959
Kegg IDC01762
ChemSpider ID58484
Wikipedia IDXanthosine
BioCyc IDXANTHOSINE
EcoCyc IDXANTHOSINE

Enzymes

Protein Details
• Multifunctional protein surE
General function:
Involved in hydrolase activity
Specific function:
Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'- monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain- length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. Also plays a significant physiological role in stress-response and is required for the survival of Pseudomonas aeruginosa in stationary growth phase
Gene Name:
surE
Locus Tag:
PA3625
Molecular weight:
26.4 kDa
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.
Protein Details
• Class B acid phosphatase
General function:
Involved in acid phosphatase activity
Specific function:
Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:
aphA
Locus Tag:
PA1409
Molecular weight:
38 kDa
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.

Transporters