Human Metabolome Database Version 3.5

Showing metabocard for 5-Methylcytosine (HMDB02894)

Record Information
Version 3.5
Creation Date 2006-05-22 09:12:17 -0600
Update Date 2013-02-08 17:12:10 -0700
Secondary Accession Numbers None
Metabolite Identification
Common Name 5-Methylcytosine
Description 5-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 Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
  1. 4-Amino-5-methyl-2-(1H)-Pyrimidinone
  2. 4-Amino-5-methyl-2-pyrimidinol
  3. 5-Methyl-Cytosine
  4. 5-Methylcytosine
  5. 5-Methylcytosine>96
Chemical Formula C5H7N3O
Average Molecular Weight 125.1286
Monoisotopic Molecular Weight 125.058911861
IUPAC Name 6-amino-5-methyl-1,2-dihydropyrimidin-2-one
Traditional IUPAC Name 5-methylcytosine
CAS Registry Number 554-01-8
InChI Identifier InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Aromatic Heteromonocyclic Compounds
Class Diazines
Sub Class Pyrimidines and Pyrimidine Derivatives
Other Descriptors
  • Aminopyrimidines and Derivatives
  • Pyrimidines and Pyrimidine Derivatives
  • a small molecule(Cyc)
  • pyrimidines(ChEBI)
  • Hydropyrimidine
Direct Parent Pyrimidones
Status Detected and Quantified
  • Endogenous
  • Component of Methionine metabolism
Application Not Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 270 °C Not Available
Boiling Point Not Available Not Available
Water Solubility 34.5 mg/mL Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 8.91 g/L ALOGPS
LogP -0.63 ALOGPS
LogP -0.75 ChemAxon
LogS -1.15 ALOGPS
pKa (strongest acidic) 10.08 ChemAxon
pKa (strongest basic) 3.75 ChemAxon
Hydrogen Acceptor Count 3 ChemAxon
Hydrogen Donor Count 2 ChemAxon
Polar Surface Area 67.48 A2 ChemAxon
Rotatable Bond Count 0 ChemAxon
Refractivity 42.37 ChemAxon
Polarizability 11.89 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
MS/MS Spectrum GC-MS
MS/MS Spectrum GC-MS
MS/MS Spectrum GC-MS
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Prostate Tissue
Tissue Location
  • Fibroblasts
Pathways Not Available
Normal Concentrations
Not Available
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Prostate Tissue Detected and Quantified 0.5 (0.0-1.0) umol/g tissue Adult (>18 years old) Both Prostate concentration
Associated Disorders and Diseases
Disease References
Prostate cancer
  • Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411 Link_out
      Associated OMIM IDs
      DrugBank ID Not Available
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB004432
      KNApSAcK ID Not Available
      Chemspider ID 58551 Link_out
      KEGG Compound ID C02376 Link_out
      BioCyc ID Not Available
      BiGG ID Not Available
      Wikipedia Link 5-Methylcytosine Link_out
      NuGOwiki Link HMDB02894 Link_out
      Metagene Link HMDB02894 Link_out
      METLIN ID 3247 Link_out
      PubChem Compound 65040 Link_out
      PDB ID Not Available
      ChEBI ID 27551 Link_out
      Synthesis Reference Umetani, 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 Link_out

      Name: DNA (cytosine-5)-methyltransferase 3A
      Reactions: Not Available
      Gene Name: DNMT3A
      Uniprot ID: Q9Y6K1 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: DNA (cytosine-5)-methyltransferase 3B
      Reactions: Not Available
      Gene Name: DNMT3B
      Uniprot ID: Q9UBC3 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: tRNA (cytosine(38)-C(5))-methyltransferase
      Reactions: Not Available
      Gene Name: TRDMT1
      Uniprot ID: O14717 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: tRNA (cytosine(34)-C(5))-methyltransferase
      Reactions: Not Available
      Gene Name: NSUN2
      Uniprot ID: Q08J23 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytosine-specific methyltransferase
      Reactions: Not Available
      Gene Name: Not Available
      Uniprot ID: Q59FP7 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA