Xanthine (PAMDB000121)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000121
Identification
Name: Xanthine
Description:Xanthine is an intermediate in the degradation of adenosine monophosphate to uric acid, being formed by oxidation of hypoxanthine. The methylated xanthine compounds caffeine, theobromine, and theophylline and their derivatives are used in medicine for their bronchodilator effects. (Dorland, 28th ed.)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 1H-Purine-2,6-diol
  • 2,6(1,3)-Purinedion
  • 2,6-Dihydroxypurine
  • 2,6-Dioxopurine
  • 3,7-Dihydro-1H-purine-2,6-dione
  • 3,7-Dihydropurine-2,6-dione
  • 9H-Purine-2,6(1H,3H)-dione
  • 9H-Purine-2,6-diol
  • Dioxopurine
  • Isoxanthine
  • Pseudoxanthine
  • Purine-2,6(1H,3H)-dione
  • Purine-2,6-diol
  • Xanthic oxide
  • Xanthin
  • Xanthine
Chemical Formula: C5H4N4O2
Average Molecular Weight: 152.1109
Monoisotopic Molecular Weight: 152.033425392
InChI Key: LRFVTYWOQMYALW-UHFFFAOYSA-N
InChI:InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)
CAS number: 69-89-6
IUPAC Name:2,3,6,7-tetrahydro-1H-purine-2,6-dione
Traditional IUPAC Name: xanthine
SMILES:O=C1NC2=C(NC=N2)C(=O)N1
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus.
Kingdom Organic compounds
Super ClassAlkaloids and derivatives
Class Not Available
Sub ClassNot Available
Direct Parent Alkaloids and derivatives
Alternative Parents
Substituents
  • Alkaloid or derivatives
  • Xanthine
  • Purinone
  • Purine
  • Imidazopyrimidine
  • Hydroxypyrimidine
  • Pyrimidone
  • Pyrimidine
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: >300 °C
Experimental Properties:
PropertyValueSource
Water Solubility:0.069 mg/mL at 16 oC [MERCK INDEX [1996)]; 9.5 mg/mL (sodium salt, HMP experimental]PhysProp
LogP:-0.73 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility4.91 mg/mLALOGPS
logP-0.65ALOGPS
logP-0.21ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)7.95ChemAxon
pKa (Strongest Basic)-0.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.88 Å2ChemAxon
Rotatable Bond Count0ChemAxon
Refractivity36.92 m3·mol-1ChemAxon
Polarizability12.7 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Water + Hypoxanthine + NAD > Hydrogen ion + NADH + Xanthine
Water + NAD + Xanthine <> Hydrogen ion + NADH + Uric acid
Water + Xanthosine > Ribose + Xanthine
Phosphoribosyl pyrophosphate + Xanthine <> Pyrophosphate + Xanthylic acid
Phosphate + Xanthosine <> Ribose-1-phosphate + Xanthine
Guanine + Hydrogen ion + Water > Ammonium + Xanthine
Guanine + Water <> Xanthine + Ammonia
Xanthosine + Phosphate <> Xanthine + alpha-D-Ribose 1-phosphate
isoguanine + Water > Xanthine + Ammonia
Xanthosine + Water > D-ribose + Xanthine
Xanthine + NAD + Water > Uric acid + NADH
Hypoxanthine + NAD + Water > Xanthine + NADH
More...

Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0f6t-0924000000-9b80e0a2a60c73ca0180View in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0udi-0900000000-a70539989d121bfacee0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0a4i-6900000000-b047b06406308dbaeda8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0a4i-9300000000-ed480ed920c3e9b576ecView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-0zfr-0900000000-efb049914c9bce596267View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900000000-2e9e069e2df414aed037View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0w29-0900000000-fa52193346bc456d89e8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a5i-9400000000-bbf70998e8b7515cb440View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0900000000-566d663553ce4f0ec207View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0zfr-1900000000-d0a5d2c0f89f8d42d903View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-351d9f8ee3470f911829View in MoNA
MSMass Spectrum (Electron Ionization)splash10-0udi-7900000000-2d5ab5d5db8ff4981467View in MoNA
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Becker MA, Kisicki J, Khosravan R, Wu J, Mulford D, Hunt B, MacDonald P, Joseph-Ridge N: Febuxostat (TMX-67), a novel, non-purine, selective inhibitor of xanthine oxidase, is safe and decreases serum urate in healthy volunteers. Nucleosides Nucleotides Nucleic Acids. 2004 Oct;23(8-9):1111-6. Pubmed: 15571211
  • Castro-Gago M, Rodriguez IN, Rodriguez-Nunez A, Guitian JP, Rocamonde SL, Rodriguez-Segade S: Therapeutic criteria in hydrocephalic children. Childs Nerv Syst. 1989 Dec;5(6):361-3. Pubmed: 2611770
  • Cooper N, Khosravan R, Erdmann C, Fiene J, Lee JW: Quantification of uric acid, xanthine and hypoxanthine in human serum by HPLC for pharmacodynamic studies. J Chromatogr B Analyt Technol Biomed Life Sci. 2006 Jun 6;837(1-2):1-10. Epub 2006 May 2. Pubmed: 16631418
  • Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. Pubmed: 6656991
  • Ginsburg I: Could synergistic interactions among reactive oxygen species, proteinases, membrane-perforating enzymes, hydrolases, microbial hemolysins and cytokines be the main cause of tissue damage in infectious and inflammatory conditions? Med Hypotheses. 1998 Oct;51(4):337-46. Pubmed: 9824842
  • Gudbjornsson B, Zak A, Niklasson F, Hallgren R: Hypoxanthine, xanthine, and urate in synovial fluid from patients with inflammatory arthritides. Ann Rheum Dis. 1991 Oct;50(10):669-72. Pubmed: 1958086
  • Ihara H, Shino Y, Morita Y, Kawaguchi E, Hashizume N, Yoshida M: Is skeletal muscle damaged by the oxidative stress following anaerobic exercise? J Clin Lab Anal. 2001;15(5):239-43. Pubmed: 11574951
  • 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
  • Kawasaki N, Tanimoto T, Tanaka A, Hayakawa T, Miyasaka N: Determination of non-protein-bound iron in human synovial fluid by high-performance liquid chromatography with electrochemical detection. J Chromatogr B Biomed Appl. 1994 Jun 17;656(2):436-40. Pubmed: 7987499
  • Kaya M, Moriwaki Y, Ka T, Inokuchi T, Yamamoto A, Takahashi S, Tsutsumi Z, Tsuzita J, Oku Y, Yamamoto T: Plasma concentrations and urinary excretion of purine bases (uric acid, hypoxanthine, and xanthine) and oxypurinol after rigorous exercise. Metabolism. 2006 Jan;55(1):103-7. Pubmed: 16324927
  • 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
  • Kiss A, Barenyi M, Csontai A: Xanthine stone in the urinary bladder of a male child. Urol Int. 1999;63(4):242-4. Pubmed: 10743702
  • Kjaergaard N, Moller-Petersen JF, Kristiansen FV, Petersen PL, Ekelund S, Skovbo P: Xanthine and hypoxanthine in amniotic fluid during pregnancy. Dan Med Bull. 1990 Dec;37(6):559-60. Pubmed: 2127397
  • Liu Z, Li T, Wang E: Simultaneous determination of guanine, uric acid, hypoxanthine and xanthine in human plasma by reversed-phase high-performance liquid chromatography with amperometric detection. Analyst. 1995 Aug;120(8):2181-4. Pubmed: 7677251
  • Niklasson F: Simultaneous liquid-chromatographic determination of hypoxanthine, xanthine, urate, and creatinine in cerebrospinal fluid, with direct injection. Clin Chem. 1983 Aug;29(8):1543-6. Pubmed: 6872216
  • 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
  • Teeuwen HW, Elbers EL, van Rossum JM: Rapid and sensitive gas-chromatographic determination of caffeine in blood plasma, saliva, and xanthine beverages. Mol Biol Rep. 1991 Feb;15(1):1-7. Pubmed: 1875916
  • 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
  • Wiley DM, Szabo I, Maguire MH, Finley BE, Bennett TL: Measurement of hypoxanthine and xanthine in late-gestation human amniotic fluid by reversed-phase high-performance liquid chromatography with photodiode-array detection. J Chromatogr. 1990 Nov 30;533:73-86. Pubmed: 2081781
  • 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: Procedure for the production of xanthine and xanthine-like materials. Fr. (1967), 4 pp.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID17712
HMDB IDHMDB00292
Pubchem Compound ID1188
Kegg IDC00385
ChemSpider ID1151
WikipediaXanthine
BioCyc IDXANTHINE
EcoCyc IDXANTHINE
Ligand ExpoXAN

Enzymes

Protein Details
• Guanine deaminase
General function:
Involved in hydrolase activity
Specific function:
Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia
Gene Name:
guaD
Locus Tag:
PA1521
Molecular weight:
48.3 kDa
Reactions
Guanine + H(2)O = xanthine + NH(3).
Protein Details
• Putative xanthine dehydrogenase yagS FAD-binding subunit
General function:
Involved in flavin adenine dinucleotide binding
Specific function:
Xanthine + NAD(+) + H(2)O = urate + NADH
Gene Name:
yagS
Locus Tag:
PA1932
Molecular weight:
35.6 kDa
Reactions
Xanthine + NAD(+) + H(2)O = urate + NADH.
Hypoxanthine + NAD(+) + H(2)O = xanthine + NADH.
Protein Details
• Xanthine dehydrogenase molybdenum-binding subunit
General function:
Involved in oxidoreductase activity
Specific function:
Presumed to be a dehydrogenase, but possibly an oxidase. Participates in limited purine salvage (requires aspartate) but does not support aerobic growth on purines as the sole carbon source (purine catabolism). Deletion results in increased adenine sensitivity, suggesting that this protein contributes to the conversion of adenine to guanine nucleotides during purine salvage
Gene Name:
xdhA
Locus Tag:
PA1524
Molecular weight:
52.9 kDa
Reactions
Xanthine + NAD(+) + H(2)O = urate + NADH.
Hypoxanthine + NAD(+) + H(2)O = xanthine + NADH.
Protein Details
• Xanthine dehydrogenase FAD-binding subunit
General function:
Involved in flavin adenine dinucleotide binding
Specific function:
Presumed to be a dehydrogenase, but possibly an oxidase. Participates in limited purine salvage (requires aspartate) but does not support aerobic growth on purines as the sole carbon source (purine catabolism)
Gene Name:
xdhB
Locus Tag:
PA1523
Molecular weight:
87.7 kDa
Reactions
Xanthine + NAD(+) + H(2)O = urate + NADH.
Hypoxanthine + NAD(+) + H(2)O = xanthine + NADH.
Protein Details
• PaoABC aldehyde oxidoreductase, 2Fe-2S subunit
General function:
Not Available
Specific function:
Not Available
Gene Name:
paoA
Locus Tag:
PA1931
Molecular weight:
18.3 kDa

Transporters

Protein Details
• Xanthine permease XanP
General function:
Involved in transporter activity
Specific function:
Specific, proton motive force-dependent high-affinity transporter for xanthine
Gene Name:
xanP
Locus Tag:
PA0352
Molecular weight:
47.9 kDa