2.0 2012-05-31 14:52:18 -0600 2015-06-03 17:20:21 -0600 ECMDB20591 M2MDB001392 N3-Methylcytosine N3-methylcytosine is a member of the chemical class known as Pyrimidones. These are compounds whose pyrimidine ring bears a ketone. 5-Methylcytosine is a methylated form of the DNA base cytosine that may be involved in the regulation of gene transcription. When cytosine is methylated, the DNA maintains the same sequence, but the expression of methylated genes can be altered (the study of this is part of the field of epigenetics). 5-Methylcytosine is incorporated in the nucleoside 5-methylcytidine. In 5-methylcytosine, a methyl group, is attached to the 5th carbon atom (counting counterclockwise from the NH nitrogen at the six o'clock position, not the 2 o'clock). This methyl group distinguishes 5-methylcytosine from cytosine. (WikiPedia) 3-methyl-(7CI,8CI)-Cytosine, 3-Methylcytosine 3-METHYLCYTOSINE 6-amino-1-methyl-2(1H)-Pyrimidinone 6-Amino-1-methyl-3H-pyrimidin-1-ium-2-one C5H8N3O 126.1365 126.066736893 6-amino-1-methyl-2-oxo-2,3-dihydropyrimidin-1-ium 3-methylcytosine C[N+]1=C(N)C=CNC1=O InChI=1S/C5H7N3O/c1-8-4(6)2-3-7-5(8)9/h2-3H,1H3,(H2,6,7,9)/p+1 UPHQQDZIRIHPHU-UHFFFAOYSA-O Cytoplasm Periplasm logp -1.69 ALOGPS logs -1.15 ALOGPS solubility 1.15e+01 g/l ALOGPS logp -4.3 ChemAxon pka_strongest_acidic 8.52 ChemAxon pka_strongest_basic -4.8 ChemAxon iupac 6-amino-1-methyl-2-oxo-2,3-dihydropyrimidin-1-ium ChemAxon average_mass 126.1365 ChemAxon mono_mass 126.066736893 ChemAxon smiles C[N+]1=C(N)C=CNC1=O ChemAxon formula C5H8N3O ChemAxon inchi InChI=1S/C5H7N3O/c1-8-4(6)2-3-7-5(8)9/h2-3H,1H3,(H2,6,7,9)/p+1 ChemAxon inchikey UPHQQDZIRIHPHU-UHFFFAOYSA-O ChemAxon polar_surface_area 58.13 ChemAxon refractivity 33.65 ChemAxon polarizability 12.27 ChemAxon rotatable_bond_count 0 ChemAxon acceptor_count 2 ChemAxon donor_count 2 ChemAxon physiological_charge 1 ChemAxon formal_charge 1 ChemAxon Specdb::NmrOneD 282789 Specdb::NmrOneD 282790 Specdb::NmrOneD 282791 Specdb::NmrOneD 282792 Specdb::NmrOneD 282793 Specdb::NmrOneD 282794 Specdb::NmrOneD 282795 Specdb::NmrOneD 282796 Specdb::NmrOneD 282797 Specdb::NmrOneD 282798 Specdb::NmrOneD 282799 Specdb::NmrOneD 282800 Specdb::NmrOneD 282801 Specdb::NmrOneD 282802 Specdb::NmrOneD 282803 Specdb::NmrOneD 282804 Specdb::NmrOneD 282805 Specdb::NmrOneD 282806 Specdb::NmrOneD 282807 Specdb::NmrOneD 282808 Specdb::MsMs 25055 Specdb::MsMs 25056 Specdb::MsMs 25057 Specdb::MsMs 31613 Specdb::MsMs 31614 Specdb::MsMs 31615 HMDB11601 4469987 3668400 N3-METHYLCYTOSINE Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. 21097882 van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. 17765195 Alpha-ketoglutarate-dependent dioxygenase AlkB P05050 alkB http://ecmdb.ca/proteins/P05050.xml N3-Methylcytosine + Oxygen + Oxoglutaric acid > Hydrogen ion + Cytosine + Carbon dioxide + Formaldehyde + Succinic acid RXN0-985