Showing metabocard for Xanthosine (BMDB0000299)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:28:01 UTC
Update Date2020-05-21 16:28:53 UTC
BMDB IDBMDB0000299
Secondary Accession Numbers
  • BMDB00299
Metabolite Identification
Common NameXanthosine
DescriptionXanthosine, also known as xanthine riboside, 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. Xanthosine is an extremely weak basic (essentially neutral) compound (based on its pKa). Xanthosine exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
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-RibofuranosylxanthineHMDB
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
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
Ontology
StatusDetected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Liver
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
LiverDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
LiverDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
LiverDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
PlacentaExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0000299
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB001604
KNApSAcK IDC00007222
Chemspider ID58484
KEGG Compound IDC01762
BioCyc IDXANTHOSINE
BiGG ID38352
Wikipedia LinkXanthosine
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)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Cytosolic purine 5'-nucleotidase
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:
O46411
Molecular weight:
64841.0
Reactions
Xanthylic acid + Water → Xanthosine + Hydrogen phosphatedetails
Enzyme Details
2. 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