Record Information
Version1.0
Creation date2010-04-08 22:06:14 UTC
Update date2019-11-26 03:00:01 UTC
Primary IDFDB004432
Secondary Accession NumbersNot Available
Chemical Information
FooDB Name5-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 a methylated form of cytosine in which a methyl group is attached to carbon 5, altering its structure without altering its base-pairing properties. -- Wikipedia; 5-Methylcytosine is an epigenetic modification formed by the action of DNA methyltransferases. 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. In plants, 5-methylcytosine occurs at both CpG and CpNpG sequences. In fungi and animals, 5-methylcytosine predominately occurs at CpG dinucleotides. Although most eukaryotes methylate only a small percentage of these sites, in vertebrates 70-80% of CpG cytosines are methylated. -- Wikipedia; 5-Methylcytosine is an epigenetic modification formed by the action of DNA methyltransferases. Its function varies significantly among species:; A methylated nucleotide base found in eukaryotic DNA. In animals, the DNA methylation of cytosine to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In plants, the methylated sequence is CpNpGp, where N can be any base. -- Pubchem.
CAS Number554-01-8
Structure
Thumb
Synonyms
SynonymSource
4-Amino-5-methyl-2(1H)-pyrimidinoneChEBI
4-Amino-5-methyl-2-pyrimidinolChEBI
4-Amino-5-methyl-2-(1H)-pyrimidinoneHMDB
5-Methyl-cytosineHMDB
5-Methylcytosine>96HMDB
Monohydrochloride, 5-methylcytosineHMDB
5 MethylcytosineHMDB
5 Methylcytosine monohydrochlorideHMDB
5-Methylcytosine monohydrochlorideHMDB
2(1H)-Pyrimidinone, 4-amino-5-methyl-biospider
2(1H)-Pyrimidinone, 4-amino-5-methyl- (9CI)biospider
4-amino-5-methyl-2-(1H)-Pyrimidinonebiospider
4-amino-5-Methyl-2(1H)-pyrimidinoneChEBI
5-methyl-Cytosinebiospider
5-Methylcytosine (VAN)biospider
Cytosine, 5-methyl-biospider
Cytosine, 5-methyl- (VAN)biospider
Cytosine, 5-methyl- (VAN) (8CI)biospider
Predicted Properties
PropertyValueSource
Water Solubility8.91 g/LALOGPS
logP-0.63ALOGPS
logP-0.75ChemAxon
logS-1.2ALOGPS
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC5H7N3O
IUPAC name6-amino-5-methyl-1,2-dihydropyrimidin-2-one
InChI IdentifierInChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)
InChI KeyLRSASMSXMSNRBT-UHFFFAOYSA-N
Isomeric SMILESCC1=C(N)NC(=O)N=C1
Average Molecular Weight125.1286
Monoisotopic Molecular Weight125.058911861
Classification
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
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting Point270 oC
Boiling PointNot Available
Experimental Water Solubility34.5 mg/mLMERCK INDEX (1996)
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
GC-MS5-Methylcytosine, 1 TMS, GC-MS Spectrumsplash10-001i-4900000000-73c143c463607343e59dSpectrum
GC-MS5-Methylcytosine, 2 TMS, GC-MS Spectrumsplash10-0udi-3950000000-332af504e32034e6ea67Spectrum
GC-MS5-Methylcytosine, 3 TMS, GC-MS Spectrumsplash10-0059-3934000000-6eb3288b70641721809aSpectrum
GC-MS5-Methylcytosine, non-derivatized, GC-MS Spectrumsplash10-0udi-2970000000-9bae58e66a60384a4b47Spectrum
GC-MS5-Methylcytosine, non-derivatized, GC-MS Spectrumsplash10-0udi-1890000000-547f8dd8c93c7e653e8cSpectrum
GC-MS5-Methylcytosine, non-derivatized, GC-MS Spectrumsplash10-0udi-1960000000-eb731b2f4381755effcfSpectrum
GC-MS5-Methylcytosine, non-derivatized, GC-MS Spectrumsplash10-0fk9-8970000000-8e71ebdb5a55e2426344Spectrum
GC-MS5-Methylcytosine, non-derivatized, GC-MS Spectrumsplash10-001i-4900000000-73c143c463607343e59dSpectrum
GC-MS5-Methylcytosine, non-derivatized, GC-MS Spectrumsplash10-0udi-3950000000-332af504e32034e6ea67Spectrum
GC-MS5-Methylcytosine, non-derivatized, GC-MS Spectrumsplash10-0059-3934000000-6eb3288b70641721809aSpectrum
Predicted GC-MS5-Methylcytosine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-004i-6900000000-cb2ceeb7f5bd935faa19Spectrum
Predicted GC-MS5-Methylcytosine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MS5-Methylcytosine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - , negativesplash10-0089-9600000000-aa86d3c38a48514c2a4d2017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-045ecf28f36874a7b1462017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-17d0aa6deb42e49740692017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-6900000000-2ba4efb5ece00114fe132017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-9300000000-1a71fa46d7b0fd6269f32017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0zgi-9000000000-61088abf446eafee8dd22017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-0900000000-a1c6199ce762a7fb68552017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-1900000000-e85c44ed5cd560d17d602017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - , positivesplash10-004i-0900000000-7ce4adb73357e05cc8b52017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-004i-3900000000-b2832b699d97e3d2bfaa2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-008c-9300000000-7427dfe87925963304112021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-bb76593a12a5655ad7562021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0006-9000000000-011e24f4e333703cb5cb2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-a84f7e26153cb2255dc52021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-7e7dde0bdedd7250d6172021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-bb789d0a4d3bce440b9a2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-004i-1900000000-e85c44ed5cd560d17d602021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-efc3476af90e31d453f82021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0a7i-5900000000-e991fa239913a7dfb67d2021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-63ea0e71e72b5a60804b2015-09-14View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-8b8c84afdb6f620a47062015-09-14View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0pb9-9300000000-a069a5c69d4eb3143d952015-09-14View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-1900000000-04225473bccf83af00d82015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00e9-9500000000-e5c525a63af7fcf813902015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-8eb88ca79a619c9357ae2015-09-15View Spectrum
NMRNot Available
ChemSpider ID58551
ChEMBL IDNot Available
KEGG Compound IDC02376
Pubchem Compound ID65040
Pubchem Substance IDNot Available
ChEBI IDNot Available
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB02894
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke ID5-METHYLCYTOSINE
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia ID5-Methylcytosine
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference— Duke, James. 'Dr. Duke's Phytochemical and Ethnobotanical Databases. United States Department of Agriculture.' Agricultural Research Service, Accessed April 27 (2004).