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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2009-01-29 12:23:57 UTC
Update Date2017-12-07 02:31:50 UTC
HMDB IDHMDB0011601
Secondary Accession Numbers
  • HMDB11601
Metabolite Identification
Common Name3-Methylcytosine
Description3-methylcytosine is cytotoxic and mutagenic methylated base in DNA which can be generated by endogenous and environmental alkylation agents. The toxic lesions 3-methylcytosine is corrected by oxidative DNA demethylation catalyzed by DNA dioxygenases. These enzymes release the methyl moiety as formaldehyde, directly reversing the base damage. (PMID: 17112791 ).
Structure
Thumb
Synonyms
ValueSource
N3-MethylcytosineChEBI
Chemical FormulaC5H7N3O
Average Molecular Weight125.1286
Monoisotopic Molecular Weight125.058911861
IUPAC Name6-amino-1-methyl-1,2-dihydropyrimidin-2-one
Traditional Name6-amino-1-methylpyrimidin-2-one
CAS Registry Number4776-08-3
SMILES
CN1C(N)=CC=NC1=O
InChI Identifier
InChI=1S/C5H7N3O/c1-8-4(6)2-3-7-5(8)9/h2-3H,6H2,1H3
InChI KeyKOLPWZCZXAMXKS-UHFFFAOYSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyrimidones. These are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Aminopyrimidine
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Source:

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 Solubility25.5 g/LALOGPS
logP-0.77ALOGPS
logP-0.92ChemAxon
logS-0.69ALOGPS
pKa (Strongest Basic)3.75ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area58.69 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity42.91 m³·mol⁻¹ChemAxon
Polarizability11.83 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00b9-9600000000-1844a081213b3ead252dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-068a24b689fa566d73ffView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-056r-5900000000-65cc3c0f336953b85086View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0fr6-9000000000-e5737f8d7b89ece805cfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-1900000000-7e25edf95b9a8b79baa0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01bd-9200000000-985e6cb391c32bf22431View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-6b4b0a748e1d9e56a4feView in MoNA
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB028312
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound140523
PDB IDNot Available
ChEBI ID39992
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Sedgwick B, Bates PA, Paik J, Jacobs SC, Lindahl T: Repair of alkylated DNA: recent advances. DNA Repair (Amst). 2007 Apr 1;6(4):429-42. Epub 2006 Nov 16. [PubMed:17112791 ]