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5-Methylcytosine (M2MDB000469)

Record Information
Version2.0
Creation Date2012-05-31 13:57:18 -0600
Update Date2015-09-13 12:56:12 -0600
Secondary Accession Numbers
  • ECMDB02894
Identification
Name:5-Methylcytosine
Description5-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
MOLSDFPDBSMILESInChI
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
Weight:Average: 125.1286
Monoisotopic: 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
Description belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. 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 ParentHydroxypyrimidines
Alternative Parents
Substituents
  • Hydroxypyrimidine
  • Imidolactam
  • Hydropyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic 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 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity42.37 m³·mol⁻¹ChemAxon
Polarizability11.89 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
5-Methylcytosine + Water <> Thymine + Ammonia
5 5-Methylcytosine + Water <> Thymine + Ammonia
SMPDB Pathways:
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
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
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-2970000000-9bae58e66a60384a4b47View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1890000000-547f8dd8c93c7e653e8cView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1960000000-eb731b2f4381755effcfView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0fk9-8970000000-8e71ebdb5a55e2426344View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-4900000000-73c143c463607343e59dView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0udi-3950000000-332af504e32034e6ea67View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0059-3934000000-6eb3288b70641721809aView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-6900000000-cb2ceeb7f5bd935faa19View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-0089-9600000000-aa86d3c38a48514c2a4dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-045ecf28f36874a7b146View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-17d0aa6deb42e4974069View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-6900000000-2ba4efb5ece00114fe13View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-9300000000-1a71fa46d7b0fd6269f3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0zgi-9000000000-61088abf446eafee8dd2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-0900000000-a1c6199ce762a7fb6855View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-1900000000-e85c44ed5cd560d17d60View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-004i-0900000000-7ce4adb73357e05cc8b5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-004i-3900000000-b2832b699d97e3d2bfaaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-008c-9300000000-7427dfe8792596330411View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-bb76593a12a5655ad756View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0006-9000000000-011e24f4e333703cb5cbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-a84f7e26153cb2255dc5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-7e7dde0bdedd7250d617View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-bb789d0a4d3bce440b9aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-004i-1900000000-e85c44ed5cd560d17d60View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-efc3476af90e31d453f8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0a7i-5900000000-e991fa239913a7dfb67dView 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
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
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

Enzymes

Protein Details
1. Cytosine deaminase
General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Specific function:
Cytosine + H(2)O = uracil + NH(3)
Gene Name:
codA
Uniprot ID:
P25524
Molecular weight:
47591
Reactions
Cytosine + H(2)O = uracil + NH(3).