Showing metabocard for Xanthine (BMDB0000292)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (4) Show 4 proteinsXML
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Record Information
Version1.0
Creation Date2016-09-30 22:27:56 UTC
Update Date2020-06-04 20:46:39 UTC
BMDB IDBMDB0000292
Secondary Accession Numbers
  • BMDB00292
Metabolite Identification
Common NameXanthine
DescriptionXanthine, also known as Xan or 2,6-dioxopurine, belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety. Xanthine exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. Xanthine exists in all living species, ranging from bacteria to humans. Xanthine is a potentially toxic compound. Xanthine has been found to be associated with several diseases known as crohn's disease, colorectal cancer, degenerative disc disease, and cystic fibrosis; also xanthine has been linked to the inborn metabolic disorders including lesch-nyhan syndrome.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Chemical FormulaC5H4N4O2
Average Molecular Weight152.1109
Monoisotopic Molecular Weight152.033425392
IUPAC Name2,3,6,7-tetrahydro-1H-purine-2,6-dione
Traditional Namexanthine
CAS Registry Number69-89-6
SMILES
O=C1NC2=C(NC=N2)C(=O)N1
InChI Identifier
InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)
InChI KeyLRFVTYWOQMYALW-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassImidazopyrimidines
Sub ClassPurines and purine derivatives
Direct ParentXanthines
Alternative Parents
Substituents
  • Xanthine
  • 6-oxopurine
  • Purinone
  • Alkaloid or derivatives
  • Pyrimidone
  • Pyrimidine
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Vinylogous amide
  • Lactam
  • Urea
  • Azacycle
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Peroxisome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.069 mg/mL at 16 °C; 9.5 mg/mL (sodium salt)MERCK INDEX (1996); Human Metabolome Project (salt)
LogP-0.73HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
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 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity36.92 m³·mol⁻¹ChemAxon
Polarizability12.7 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
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)splash10-0f6t-0924000000-9b80e0a2a60c73ca0180View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0f6t-0924000000-9b80e0a2a60c73ca0180View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0f6t-0924000000-30dc5892eecde860846aView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0kai-7900000000-2dc30b0fc4cff2239dbeView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0zfr-0900000000-efb049914c9bce596267View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-0udi-0900000000-5fee91293851bb02193eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-000i-0900000000-4568a814903ff411923aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9000000000-e078a358156f5a04d4c1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-3900000000-250f7dc30d6fd96a4ef6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0ik9-0900000000-3a6dad2473c1654789f6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0900000000-a4e9443b51c3ac2fc58bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9000000000-d23801a49488b1a5f0a2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-4900000000-b177a2a36043e5e87efcView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0udi-0900000000-cb3b35c3117b7f36bf5cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0zfr-0900000000-8d2a19e7c37d2cb7658fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-05mo-9300000000-33d00ab2288aaa055517View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0ik9-1900000000-3a6dad2473c1654789f6View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-37e76df2401a85967caaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0udi-0900000000-4132da06dda895afc3abView 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 Spectrum (1D, 500 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100.7 MHz, DMSO-d6, experimental)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, D2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, D2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
2D NMR[1H, 1H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, 100%_DMSO, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Peroxisome
Biospecimen Locations
  • Bladder
  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Mammary Gland
  • Milk
  • Muscle
  • Placenta
  • Prostate Tissue
  • Skeletal Muscle
  • Testis
Pathways
Normal Concentrations
Abnormal Concentrations
Not Available
HMDB IDHMDB0000292
DrugBank IDDB02134
Phenol Explorer Compound IDNot Available
FooDB IDFDB001977
KNApSAcK IDC00019660
Chemspider ID1151
KEGG Compound IDC00385
BioCyc IDXANTHINE
BiGG ID34825
Wikipedia LinkXanthine
METLIN ID82
PubChem Compound1188
PDB IDNot Available
ChEBI ID17712
References
Synthesis ReferenceProcedure for the production of xanthine and xanthine-like materials. Fr. (1967), 4 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Tiemeyer W, Stohrer M, Giesecke D: Metabolites of nucleic acids in bovine milk. J Dairy Sci. 1984 Apr;67(4):723-8. doi: 10.3168/jds.S0022-0302(84)81361-2. [PubMed:6539345 ]

Enzymes

Enzyme Details
1. Hypoxanthine-guanine phosphoribosyltransferase
General function:
Nucleotide transport and metabolism
Specific function:
Converts guanine to guanosine monophosphate, and hypoxanthine to inosine monophosphate. Transfers the 5-phosphoribosyl group from 5-phosphoribosylpyrophosphate onto the purine. Plays a central role in the generation of purine nucleotides through the purine salvage pathway (By similarity).
Gene Name:
HPRT1
Uniprot ID:
Q3SZ18
Molecular weight:
24498.0
Reactions
Xanthylic acid + Pyrophosphate → Xanthine + Phosphoribosyl pyrophosphatedetails
Enzyme Details
2. Xanthine dehydrogenase/oxidase
General function:
Nucleotide transport and metabolism
Specific function:
Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species.
Gene Name:
XDH
Uniprot ID:
P80457
Molecular weight:
146790.0
Enzyme Details
3. Purine nucleoside phosphorylase
General function:
Nucleotide transport and metabolism
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:
P55859
Molecular weight:
32037.0
Reactions
Xanthosine + Hydrogen phosphate → Xanthine + Ribose 1-phosphatedetails
Enzyme Details
4. Guanine deaminase
General function:
Not Available
Specific function:
Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia.
Gene Name:
GDA
Uniprot ID:
F1MLX9
Molecular weight:
51059.0
Reactions
Guanine + Water → Xanthine + Ammoniadetails