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Record Information
StatusExpected but not Quantified
Creation Date2006-05-22 15:12:17 UTC
Update Date2019-01-11 19:17:16 UTC
Secondary Accession Numbers
  • HMDB02894
Metabolite Identification
Common Name5-Methylcytosine
Description5-Methylcytosine is 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; 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.
Monohydrochloride, 5-methylcytosineHMDB
5 MethylcytosineHMDB
5 Methylcytosine monohydrochlorideHMDB
5-Methylcytosine monohydrochlorideHMDB
Chemical FormulaC5H7N3O
Average Molecular Weight125.1286
Monoisotopic Molecular Weight125.058911861
IUPAC Name6-amino-5-methyl-1,2-dihydropyrimidin-2-one
Traditional Name5-methylcytosine
CAS Registry Number554-01-8
InChI Identifier
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
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentHydroxypyrimidines
Alternative Parents
  • 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

Route of exposure:


Biological location:


Naturally occurring process:

Physical Properties
Experimental Properties
Melting Point270 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility34.5 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
Water Solubility8.91 g/LALOGPS
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
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (1 TMS)splash10-001i-4900000000-73c143c463607343e59dJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0udi-3950000000-332af504e32034e6ea67JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0059-3934000000-6eb3288b70641721809aJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-2970000000-9bae58e66a60384a4b47JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1890000000-547f8dd8c93c7e653e8cJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1960000000-eb731b2f4381755effcfJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0fk9-8970000000-8e71ebdb5a55e2426344JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-4900000000-73c143c463607343e59dJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0udi-3950000000-332af504e32034e6ea67JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0059-3934000000-6eb3288b70641721809aJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-6900000000-cb2ceeb7f5bd935faa19JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-0089-9600000000-aa86d3c38a48514c2a4dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-045ecf28f36874a7b146JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-17d0aa6deb42e4974069JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-6900000000-2ba4efb5ece00114fe13JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-9300000000-1a71fa46d7b0fd6269f3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0zgi-9000000000-61088abf446eafee8dd2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-0900000000-a1c6199ce762a7fb6855JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-1900000000-e85c44ed5cd560d17d60JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-004i-0900000000-7ce4adb73357e05cc8b5JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-63ea0e71e72b5a60804bJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-8b8c84afdb6f620a4706JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0pb9-9300000000-a069a5c69d4eb3143d95JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-1900000000-04225473bccf83af00d8JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00e9-9500000000-e5c525a63af7fcf81390JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-8eb88ca79a619c9357aeJSpectraViewer | MoNA
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen LocationsNot Available
Tissue Locations
  • Fibroblasts
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 IDFDB004432
KNApSAcK IDNot Available
Chemspider ID58551
KEGG Compound IDC02376
BioCyc IDCPD0-2018
BiGG IDNot Available
Wikipedia Link5-Methylcytosine
PubChem Compound65040
PDB IDNot Available
ChEBI ID27551
Synthesis ReferenceUmetani, Hideki. Method for preparing 5-methylcytosine. Jpn. Kokai Tokkyo Koho (2006), 8 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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 ]


General function:
Involved in DNA binding
Specific function:
Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZNF238. Can actively repress transcription through the recruitment of HDAC activity (By similarity).
Gene Name:
Uniprot ID:
Molecular weight:
General function:
Involved in DNA binding
Specific function:
Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1.
Gene Name:
Uniprot ID:
Molecular weight:
General function:
Involved in DNA binding
Specific function:
Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp).
Gene Name:
Uniprot ID:
Molecular weight:
General function:
Involved in tRNA (cytosine-5-)-methyltransferase activity
Specific function:
RNA methyltransferase that methylates tRNAs, and possibly RNA polymerase III transcripts. Methylates cytosine to 5-methylcytosine (m5C) at position 34 of intron-containing tRNA(Leu)(CAA) precursors. Not able to modify tRNAs at positions 48 or 49. May act downstream of Myc to regulate epidermal cell growth and proliferation. Required for proper spindle assembly and chromosome segregation, independently of its methyltransferase activity.
Gene Name:
Uniprot ID:
Molecular weight:
General function:
Involved in DNA binding
Specific function:
S-adenosyl-L-methionine + DNA = S-adenosyl-L- homocysteine + DNA containing 5-methylcytosine
Gene Name:
Not Available
Uniprot ID:
Molecular weight: