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
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MS (1 TMS)splash10-001i-4900000000-73c143c463607343e59dView in MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0udi-3950000000-332af504e32034e6ea67View in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0059-3934000000-6eb3288b70641721809aView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-2970000000-9bae58e66a60384a4b47View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1890000000-547f8dd8c93c7e653e8cView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1960000000-eb731b2f4381755effcfView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0fk9-8970000000-8e71ebdb5a55e2426344View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-001i-4900000000-73c143c463607343e59dView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0udi-3950000000-332af504e32034e6ea67View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0059-3934000000-6eb3288b70641721809aView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-6900000000-cb2ceeb7f5bd935faa19View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-0089-9600000000-aa86d3c38a48514c2a4dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-045ecf28f36874a7b146View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-0900000000-17d0aa6deb42e4974069View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-6900000000-2ba4efb5ece00114fe13View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a59-9300000000-1a71fa46d7b0fd6269f3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0zgi-9000000000-61088abf446eafee8dd2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-0900000000-a1c6199ce762a7fb6855View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-004i-1900000000-e85c44ed5cd560d17d60View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-004i-0900000000-7ce4adb73357e05cc8b5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-004i-3900000000-b2832b699d97e3d2bfaaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-008c-9300000000-7427dfe8792596330411View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-bb76593a12a5655ad756View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0006-9000000000-011e24f4e333703cb5cbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-a84f7e26153cb2255dc5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-004i-0900000000-7e7dde0bdedd7250d617View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-bb789d0a4d3bce440b9aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-004i-1900000000-e85c44ed5cd560d17d60View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-efc3476af90e31d453f8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-0a7i-5900000000-e991fa239913a7dfb67dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-63ea0e71e72b5a60804bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-8b8c84afdb6f620a4706View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0pb9-9300000000-a069a5c69d4eb3143d95View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-1900000000-04225473bccf83af00d8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00e9-9500000000-e5c525a63af7fcf81390View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-8eb88ca79a619c9357aeView in MoNA
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
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