Record Information
Version2.0
Creation Date2012-05-31 10:25:59 -0600
Update Date2015-09-13 12:56:07 -0600
Secondary Accession Numbers
  • ECMDB00299
Identification
Name:Xanthosine
DescriptionXanthosine 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
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
Weight:Average: 284.2255
Monoisotopic: 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
Description belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleosides
Sub ClassNot Available
Direct ParentPurine nucleosides
Alternative Parents
Substituents
  • Purine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Xanthine
  • 6-oxopurine
  • Purinone
  • Pentose monosaccharide
  • Purine
  • Imidazopyrimidine
  • Alkaloid or derivatives
  • Pyrimidone
  • Pyrimidine
  • Monosaccharide
  • N-substituted imidazole
  • Imidazole
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Azole
  • Vinylogous amide
  • Lactam
  • Urea
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Primary alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility27.8 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity62.4 m³·mol⁻¹ChemAxon
Polarizability25.55 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
purine ribonucleosides degradationPW002076 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0032-0963000000-08e48347b76242e521e6View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0032-0963000000-08e48347b76242e521e6View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05fu-9250000000-9694fd3e1c7370e27866View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positivesplash10-0059-2110049000-cbeec0d3159947f31d5fView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0udi-0910000000-b2c7e01e9105bba310aaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0udi-0910000000-e6e1d21c0d22b3ad2821View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-0uk9-8900000000-b0f93d77cf447ada9ed9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0udi-1900000000-19c92745c311f6435fd3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-0udi-2910000000-6f97748a645ffb972e67View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-03di-0900000000-a999e0e022115ec9ec7aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0910000000-63959f162289e268a620View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0zg0-8900000000-f8aa72afbf821cfb2cf2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0udi-4900000000-943b0d3fbe3cd8345d54View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-06rl-9400000000-3072bed88bbdca66de69View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0udi-0900000000-f3b10c4bf03522fbd1ffView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0940000000-f59c82b81d81cd9c6b68View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-0udi-0900000000-e0cf07456bb1d35aec56View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0udi-0900000000-6189db27589e05c3f039View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0940000000-2394018b58d040767e06View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-fec1dd4fe1f5f7e56482View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0f79-1900000000-850759ea222062877fa9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f8c-1590000000-4fdccf755ee2b8b75ac6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0f6x-6910000000-308e886a8ecec5d8cd09View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9500000000-af861bef2f6b2f10296cView in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
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

General function:
Involved in hydrolase activity
Specific function:
Degradation of external UDP-glucose to uridine monophosphate and glucose-1-phosphate, which can then be used by the cell
Gene Name:
ushA
Uniprot ID:
P07024
Molecular weight:
60824
Reactions
UDP-sugar + H(2)O = UMP + alpha-D-aldose 1-phosphate.
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
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 E.coli in stationary growth phase
Gene Name:
surE
Uniprot ID:
P0A840
Molecular weight:
26900
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.
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows high phosphatase activity toward three nucleoside 5'-monophosphates, UMP, dUMP, and dTMP, and very low activity against TDP, IMP, UDP, GMP, dGMP, AMP, dAMP, and 6- phosphogluconate. Is strictly specific to substrates with 5'- phosphates and shows no activity against nucleoside 2'- or 3'- monophosphates. Might be involved in the pyrimidine nucleotide substrate cycles
Gene Name:
yjjG
Uniprot ID:
P0A8Y1
Molecular weight:
25300
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules
Gene Name:
deoD
Uniprot ID:
P0ABP8
Molecular weight:
25950
Reactions
Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
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
Uniprot ID:
P0AE22
Molecular weight:
26103
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.
General function:
Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
Specific function:
Hydrolyzes both purine and pyrimidine ribonucleosides with a broad-substrate specificity with decreasing activity in the order uridine, xanthosine, inosine, adenosine, cytidine, guanosine
Gene Name:
rihC
Uniprot ID:
P22564
Molecular weight:
32560
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows strict specificity toward deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. Might be involved in the regulation of all dNTP pools in E.coli
Gene Name:
yfbR
Uniprot ID:
P76491
Molecular weight:
22708
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
The nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the nucleoside molecule, with the formation of the corresponding free bases and pentose-1-phosphate. This protein can degrade all purine nucleosides except adenosine and deoxyadenosine
Gene Name:
xapA
Uniprot ID:
P45563
Molecular weight:
29834

Transporters

General function:
Involved in nucleoside transmembrane transporter activity
Specific function:
Nucleoside transport
Gene Name:
xapB
Uniprot ID:
P45562
Molecular weight:
46139
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368