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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 18:47:13 UTC
Update Date2021-09-26 23:14:16 UTC
HMDB IDHMDB0257731
Secondary Accession NumbersNone
Metabolite Identification
Common Name4-Amino-1-[(2R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one
Description2-(2-hydroxy-4-imino-5-methyl-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. Based on a literature review very few articles have been published on 2-(2-hydroxy-4-imino-5-methyl-1,4-dihydropyrimidin-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 4-amino-1-[(2r,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 4-Amino-1-[(2R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
Synonyms
ValueSource
5-MethylarabinosylcytosineMeSH
1 beta-D-Arabinofuranosyl-5-methylcytosineMeSH
5-Methyl ara-CMeSH
Chemical FormulaC10H15N3O5
Average Molecular Weight257.246
Monoisotopic Molecular Weight257.101170595
IUPAC Name4-amino-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one
Traditional Name5-methylcytidine
CAS Registry NumberNot Available
SMILES
CC1=CN(C2OC(CO)C(O)C2O)C(=O)N=C1N
InChI Identifier
InChI=1S/C10H15N3O5/c1-4-2-13(10(17)12-8(4)11)9-7(16)6(15)5(3-14)18-9/h2,5-7,9,14-16H,3H2,1H3,(H2,11,12,17)
InChI KeyZAYHVCMSTBRABG-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Aminopyrimidine
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Imidolactam
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Primary alcohol
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID230562
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound262543
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]