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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-07 01:16:00 UTC
HMDB IDHMDB0000299
Secondary Accession Numbers
  • HMDB00299
Metabolite Identification
Common NameXanthosine
DescriptionBiological Source: Xanthosine is produced by guanine-free mutants of bacteria e.g. Bacillus subtilis, Aerobacter aerogenes. Also reported from seeds of Trifolium alexandrinum Physical Description: Prismatic cryst. (H2O) (Chemnetbase) The deamination product of guanosine. Xanthosine monophosphate is an intermediate in purine metabolism, formed from IMP, and forming GMP.(Wikipedia). Xanthylic acid can be used in quantitative measurements of the Inosine monophosphate dehydrogenase enzyme activities in purine metabolism, as recommended to ensure optimal thiopurine therapy for children with acute lymphoblastic leukaemia (ALL). (PMID: 16725387 ).
Structure
Thumb
Synonyms
ValueSource
9-beta-D-Ribofuranosyl-3,9-dihydro-1H-purine-2,6-dioneChEBI
9-beta-D-RibofuranosylxanthineChEBI
Xanthine 9-beta-D-ribofuranosideChEBI
Xanthine ribosideChEBI
9-b-D-Ribofuranosyl-3,9-dihydro-1H-purine-2,6-dioneGenerator
9-β-D-ribofuranosyl-3,9-dihydro-1H-purine-2,6-dioneGenerator
9-b-D-RibofuranosylxanthineGenerator
9-β-D-ribofuranosylxanthineGenerator
Xanthine 9-b-D-ribofuranosideGenerator
Xanthine 9-β-D-ribofuranosideGenerator
3,9-dihydro-9-b-D-Ribofuranosyl-1H-purine-2,6-dioneHMDB
3,9-dihydro-9-beta-delta-Ribofuranosyl-1H-purine-2,6-dioneHMDB
3,9-dihydro-9-D-Ribofuranosyl-1H-purine-2,6-dioneHMDB
3,9-dihydro-9-delta-Ribofuranosyl-1H-purine-2,6-dioneHMDB
9-beta-delta-RibofuranosylxanthineHMDB
9-D-RibofuranosylxanthineHMDB
9-delta-RibofuranosylxanthineHMDB
9 beta-D-RibofuranosylxanthineMeSH
Chemical FormulaC10H12N4O6
Average Molecular Weight284.2255
Monoisotopic Molecular Weight284.075684136
IUPAC Name9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purine-2,6-diol
Traditional Name9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purine-2,6-diol
CAS Registry Number146-80-5
SMILES
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=C(O)N=C2O
InChI Identifier
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
InChI KeyUBORTCNDUKBEOP-UUOKFMHZSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as purine nucleosides. These are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPurine nucleosides
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
  • Azole
  • Heteroaromatic compound
  • Oxolane
  • 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
Ontology
Disposition

Biological Location:

  Subcellular:

  Biofluid and excreta:

Source:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
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
Polarizability25.54 ųChemAxon
Number of Rings3ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
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
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
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
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Feces
  • Urine
Tissue LocationNot Available
Pathways
NameSMPDB/PathwhizKEGG
AICA-RibosiduriaPw000082Pw000082 greyscalePw000082 simpleNot Available
Adenine phosphoribosyltransferase deficiency (APRT)Pw000511Pw000511 greyscalePw000511 simpleNot Available
Adenosine Deaminase DeficiencyPw000075Pw000075 greyscalePw000075 simpleNot Available
Adenylosuccinate Lyase DeficiencyPw000076Pw000076 greyscalePw000076 simpleNot Available
Azathioprine PathwayPw000266Pw000266 greyscalePw000266 simpleNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified5.08 +/- 0.30 uMAdult (>18 years old)BothNormal details
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedNormal details
UrineDetected and Quantified0.59 +/- 0.36 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedCrohns disease details
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedUlcerative colitis details
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedUnclassified IBD details
UrineDetected and Quantified0.99 umol/mmol creatinineAdult (>18 years old)BothBreast tumour details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB001604
KNApSAcK IDC00007222
Chemspider ID58484
KEGG Compound IDC01762
BioCyc IDNot Available
BiGG ID38352
Wikipedia LinkNot Available
METLIN ID3408
PubChem Compound64959
PDB IDNot Available
ChEBI ID18107
References
Synthesis ReferenceEnei, Hitoshi; Sato, Katsuaki; Hirose, Yoshio. Xanthosine production by fermentation. Jpn. Kokai Tokkyo Koho (1975), 3 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]

Enzymes

General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:
NT5E
Uniprot ID:
P21589
Molecular weight:
57948.125
Reactions
Xanthylic acid + Water → Xanthosine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Molecular weight:
68803.055
Reactions
Xanthylic acid + Water → Xanthosine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Molecular weight:
41020.145
Reactions
Xanthylic acid + Water → Xanthosine + Phosphoric aciddetails
General function:
Involved in metal ion binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Molecular weight:
Not Available
Reactions
Xanthylic acid + Water → Xanthosine + Phosphoric aciddetails
General function:
Involved in phosphatase activity
Specific function:
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Molecular weight:
Not Available
Reactions
Xanthylic acid + Water → Xanthosine + Phosphoric aciddetails
General function:
Involved in hydrolase activity
Specific function:
Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) and xanthosine 5'-triphosphate (XTP) to their respective monophosphate derivatives. The enzyme does not distinguish between the deoxy- and ribose forms. Probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.
Gene Name:
ITPA
Uniprot ID:
Q9BY32
Molecular weight:
16833.23
General function:
Involved in magnesium ion binding
Specific function:
Can act both as nucleotidase and as phosphotransferase.
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Molecular weight:
33914.91
Reactions
Xanthylic acid + Water → Xanthosine + Phosphoric aciddetails
General function:
Involved in 5'-nucleotidase activity
Specific function:
May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:
NT5C2
Uniprot ID:
P49902
Molecular weight:
64969.2
Reactions
Xanthylic acid + Water → Xanthosine + Phosphoric aciddetails
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:
PNP
Uniprot ID:
P00491
Molecular weight:
32117.69
Reactions
Xanthosine + Phosphoric acid → Xanthine + Ribose 1-phosphatedetails