Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-01-29 12:23:57 UTC
Update Date2023-02-21 17:17:29 UTC
HMDB IDHMDB0011601
Secondary Accession Numbers
  • HMDB11601
Metabolite Identification
Common Name3-Methylcytosine
Description3-Methylcytosine belongs to the class of organic compounds known as pyrimidones. Pyrimidones 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. 3-Methylcytosine has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 3-methylcytosine a potential biomarker for the consumption of these foods. 3-Methylcytosine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on 3-Methylcytosine.
Structure
Data?1676999849
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
Description Belongs to the class of organic compounds known as pyrimidones. Pyrimidones 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
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+124.80731661259
DarkChem[M-H]-121.91531661259
DeepCCS[M+H]+119.76530932474
DeepCCS[M-H]-116.66730932474
DeepCCS[M-2H]-153.17730932474
DeepCCS[M+Na]+128.32630932474
AllCCS[M+H]+126.832859911
AllCCS[M+H-H2O]+122.032859911
AllCCS[M+NH4]+131.232859911
AllCCS[M+Na]+132.532859911
AllCCS[M-H]-121.932859911
AllCCS[M+Na-2H]-124.132859911
AllCCS[M+HCOO]-126.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-MethylcytosineCN1C(N)=CC=NC1=O2401.7Standard polar33892256
3-MethylcytosineCN1C(N)=CC=NC1=O1482.8Standard non polar33892256
3-MethylcytosineCN1C(N)=CC=NC1=O1647.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Methylcytosine,1TMS,isomer #1CN1C(N[Si](C)(C)C)=CC=NC1=O1618.3Semi standard non polar33892256
3-Methylcytosine,1TMS,isomer #1CN1C(N[Si](C)(C)C)=CC=NC1=O1628.2Standard non polar33892256
3-Methylcytosine,1TMS,isomer #1CN1C(N[Si](C)(C)C)=CC=NC1=O2064.7Standard polar33892256
3-Methylcytosine,2TMS,isomer #1CN1C(N([Si](C)(C)C)[Si](C)(C)C)=CC=NC1=O1585.7Semi standard non polar33892256
3-Methylcytosine,2TMS,isomer #1CN1C(N([Si](C)(C)C)[Si](C)(C)C)=CC=NC1=O1677.5Standard non polar33892256
3-Methylcytosine,2TMS,isomer #1CN1C(N([Si](C)(C)C)[Si](C)(C)C)=CC=NC1=O1927.9Standard polar33892256
3-Methylcytosine,1TBDMS,isomer #1CN1C(N[Si](C)(C)C(C)(C)C)=CC=NC1=O1908.8Semi standard non polar33892256
3-Methylcytosine,1TBDMS,isomer #1CN1C(N[Si](C)(C)C(C)(C)C)=CC=NC1=O1814.5Standard non polar33892256
3-Methylcytosine,1TBDMS,isomer #1CN1C(N[Si](C)(C)C(C)(C)C)=CC=NC1=O2196.4Standard polar33892256
3-Methylcytosine,2TBDMS,isomer #1CN1C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=CC=NC1=O2036.8Semi standard non polar33892256
3-Methylcytosine,2TBDMS,isomer #1CN1C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=CC=NC1=O2110.5Standard non polar33892256
3-Methylcytosine,2TBDMS,isomer #1CN1C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=CC=NC1=O2099.3Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylcytosine GC-MS (Non-derivatized) - 70eV, Positivesplash10-00b9-9600000000-1844a081213b3ead252d2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylcytosine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 10V, Positive-QTOFsplash10-004i-0900000000-068a24b689fa566d73ff2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 20V, Positive-QTOFsplash10-056r-5900000000-65cc3c0f336953b850862017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 40V, Positive-QTOFsplash10-0fr6-9000000000-e5737f8d7b89ece805cf2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 10V, Negative-QTOFsplash10-00di-1900000000-7e25edf95b9a8b79baa02017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 20V, Negative-QTOFsplash10-01bd-9200000000-985e6cb391c32bf224312017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 40V, Negative-QTOFsplash10-0006-9000000000-6b4b0a748e1d9e56a4fe2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 10V, Negative-QTOFsplash10-00di-2900000000-51269272bcc03c3bc7352021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 20V, Negative-QTOFsplash10-014l-9100000000-a4b14dbc3fe3506375332021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 40V, Negative-QTOFsplash10-014l-9000000000-5bff62817b63d65f94d52021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 10V, Positive-QTOFsplash10-004i-1900000000-512940c3012d0f1a25152021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 20V, Positive-QTOFsplash10-004l-9500000000-8c17f35bf9905c92dbcc2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcytosine 40V, Positive-QTOFsplash10-0uxr-9000000000-9701d242da20bc1926e92021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028312
KNApSAcK IDNot Available
Chemspider ID123940
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethylcytosine
METLIN IDNot Available
PubChem Compound140523
PDB IDNot Available
ChEBI ID39992
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. 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 ]