Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000469
Identification
Name: 5-Methylcytosine
Description:5-Methylcytosine is a methylated form of cytosine in which a methyl group is attached to carbon 5, altering its structure without altering its base-pairing properties. 5-Methylcytosine is an epigenetic modification formed by the action of DNA methyltransferases. Its function varies significantly among species. In bacteria, 5-methylcytosine can be found at a variety of sites, and is often used as a marker to protect DNA from being cut by native methylation-sensitive restriction enzymes. (Wikipedia)
Structure
Thumb
Synonyms:
  • 2(1H)-Pyrimidinone, 4-amino-5-methyl-
  • 4-Amino-5-methyl-2(1H)-Pyrimidinone
  • 4-Amino-5-methyl-2-(1H)-Pyrimidinone
  • 4-Amino-5-methyl-2-pyrimidinol
  • 5-Methyl-Cytosine
  • 5-Methylcytosine
  • 5-Methylcytosine>96
  • Cytosine, 5-methyl-
  • Cytosine, 5-methyl- (VAN)
Chemical Formula: C5H7N3O
Average Molecular Weight: 125.1286
Monoisotopic Molecular Weight: 125.058911861
InChI Key: LRSASMSXMSNRBT-UHFFFAOYSA-N
InChI:InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)
CAS number: 554-01-8
IUPAC Name:6-amino-5-methyl-1,2-dihydropyrimidin-2-one
Traditional IUPAC Name: 5-methylcytosine
SMILES:CC1=C(N)NC(=O)N=C1
Chemical Taxonomy
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.
Kingdom Organic compounds
Super ClassOrganoheterocyclic compounds
Class Diazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct Parent Pyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Aminopyrimidine
  • Primary aromatic amine
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: 270 °C
Experimental Properties:
PropertyValueSource
Water Solubility:34.5 mg/mL [MERCK INDEX (1996)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility8.91 mg/mLALOGPS
logP-0.63ALOGPS
logP-0.75ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)10.08ChemAxon
pKa (Strongest Basic)3.75ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area67.48 Å2ChemAxon
Rotatable Bond Count0ChemAxon
Refractivity42.37 m3·mol-1ChemAxon
Polarizability11.89 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MS (1 TMS)splash10-001i-4900000000-73c143c463607343e59dView in MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0udi-3950000000-332af504e32034e6ea67View in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0059-3934000000-6eb3288b70641721809aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-63ea0e71e72b5a60804bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-8b8c84afdb6f620a4706View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0pb9-9300000000-a069a5c69d4eb3143d95View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-1900000000-04225473bccf83af00d8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00e9-9500000000-e5c525a63af7fcf81390View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-8eb88ca79a619c9357aeView in MoNA
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Pfeifer GP, You YH, Besaratinia A: Mutations induced by ultraviolet light. Mutat Res. 2005 Apr 1;571(1-2):19-31. Epub 2005 Jan 20. Pubmed: 15748635
Synthesis Reference: Umetani, Hideki. Method for preparing 5-methylcytosine. Jpn. Kokai Tokkyo Koho (2006), 8 pp.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID27551
HMDB IDHMDB02894
Pubchem Compound ID65040
Kegg IDC02376
ChemSpider ID58551
Wikipedia5-Methylcytosine
BioCyc IDCPD0-2018
EcoCyc IDCPD0-2018