Showing metabocard for 5-Methylcytosine (BMDB0002894)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 23:02:04 UTC
Update Date2020-05-11 20:02:50 UTC
BMDB IDBMDB0002894
Secondary Accession Numbers
  • BMDB02894
Metabolite Identification
Common Name5-Methylcytosine
Description5-Methylcytosine 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. 5-Methylcytosine exists as a solid, possibly soluble (in water), and a strong basic compound (based on its pKa) molecule. 5-Methylcytosine exists in all living organisms, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
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
StatusDetected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
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
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 FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Fibroblasts
  • Milk
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FibroblastsExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0002894
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
References
Synthesis ReferenceUmetani, Hideki. Method for preparing 5-methylcytosine. Jpn. Kokai Tokkyo Koho (2006), 8 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]

Enzymes

Enzyme Details
1. tRNA (cytosine-5-)-methyltransferase
General function:
Replication, recombination and repair
Specific function:
Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp).
Gene Name:
TRDMT1
Uniprot ID:
Q7YS61
Molecular weight:
44570.0
Enzyme Details
2. DNA (cytosine-5)-methyltransferase 1
General function:
Replication, recombination and repair
Specific function:
Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B 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. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells. Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing. Promotes tumor growth.
Gene Name:
DNMT1
Uniprot ID:
Q24K09
Molecular weight:
182842.0
Enzyme Details
3. DNA methyltransferase b
General function:
Replication, recombination and repair
Specific function:
Not Available
Gene Name:
Dnmt1
Uniprot ID:
B1P383
Molecular weight:
153086.0