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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2006-05-22 15:12:17 UTC
Update Date2020-02-26 21:24:18 UTC
HMDB IDHMDB0002894
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 .
Structure
Data?1582752258
Synonyms
ValueSource
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
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
SMILES
CC1=C(N)NC(=O)N=C1
InChI Identifier
InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)
InChI KeyLRSASMSXMSNRBT-UHFFFAOYSA-N
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
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point270 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility34.5 mg/mLNot Available
LogPNot AvailableNot Available
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
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (1 TMS)splash10-001i-4900000000-73c143c463607343e59dSpectrum
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0udi-3950000000-332af504e32034e6ea67Spectrum
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0059-3934000000-6eb3288b70641721809aSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-2970000000-9bae58e66a60384a4b47Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1890000000-547f8dd8c93c7e653e8cSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1960000000-eb731b2f4381755effcfSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0fk9-8970000000-8e71ebdb5a55e2426344Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-4900000000-73c143c463607343e59dSpectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0udi-3950000000-332af504e32034e6ea67Spectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0059-3934000000-6eb3288b70641721809aSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-6900000000-cb2ceeb7f5bd935faa19Spectrum
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-0089-9600000000-aa86d3c38a48514c2a4dSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-045ecf28f36874a7b146Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-17d0aa6deb42e4974069Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-6900000000-2ba4efb5ece00114fe13Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-9300000000-1a71fa46d7b0fd6269f3Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0zgi-9000000000-61088abf446eafee8dd2Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-0900000000-a1c6199ce762a7fb6855Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-1900000000-e85c44ed5cd560d17d60Spectrum
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-004i-0900000000-7ce4adb73357e05cc8b5Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-63ea0e71e72b5a60804bSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-8b8c84afdb6f620a4706Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0pb9-9300000000-a069a5c69d4eb3143d95Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-1900000000-04225473bccf83af00d8Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00e9-9500000000-e5c525a63af7fcf81390Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-8eb88ca79a619c9357aeSpectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen LocationsNot Available
Tissue Locations
  • Fibroblasts
Pathways
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
FooDB IDFDB004432
KNApSAcK IDNot Available
Chemspider ID58551
KEGG Compound IDC02376
BioCyc IDCPD0-2018
BiGG IDNot Available
Wikipedia Link5-Methylcytosine
METLIN ID3247
PubChem Compound65040
PDB IDNot Available
ChEBI ID27551
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
References
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 ]

Enzymes

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:
DNMT3A
Uniprot ID:
Q9Y6K1
Molecular weight:
101857.595
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:
DNMT3B
Uniprot ID:
Q9UBC3
Molecular weight:
81309.795
General function:
Involved in DNA binding
Specific function:
Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp).
Gene Name:
TRDMT1
Uniprot ID:
O14717
Molecular weight:
44596.17
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:
NSUN2
Uniprot ID:
Q08J23
Molecular weight:
82392.405
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:
Q59FP7
Molecular weight:
182018.2