2.0 2012-05-31 14:44:26 -0600 2015-06-03 17:20:00 -0600 ECMDB20429 M2MDB001250 Hydroxymethyl-dCTP Hydroxymethyl-dCTP is a member of the chemical class known as Pyrimidine 2'-deoxyribonucleoside Triphosphates. These are pyrimidine nucleotides with a triphosphate group linked to the ribose moiety lacking an hydroxyl group at position 2. Hydroxymethyl-dCTP is a hydroxylated pyrimidine which appears when E. coli has been infected with T4 phage. The T4 phage enzyme Deoxycytidylate 5-hydroxymethyltransferase gives rise to the novel phage-specific pyrimidine DNA base, 5-hydroxymethylcytosine. Hydroxymethyl-dCTP is an intermediate in the synthesis or breakdown of phage-modified DNA. [PMID: 4525160; 10064578] 5'-Hydroxymethyl-dCTP 5-Hydroxymethyl-dCTP C10H14N2O15P3 495.1438 494.960702324 1-[(2S,4S,5S)-4-hydroxy-5-({[hydroxy({[hydroxy(phosphonatooxy)phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-2-yl]-5-(hydroxymethyl)-2-oxo-1,2-dihydropyrimidin-4-olate 1-[(2S,4S,5S)-4-hydroxy-5-[({hydroxy[hydroxy(phosphonatooxy)phosphoryl]oxyphosphoryl}oxy)methyl]oxolan-2-yl]-5-(hydroxymethyl)-2-oxopyrimidin-4-olate [H][C@]1(O)C[C@]([H])(O[C@@]1([H])COP(O)(=O)OP(O)(=O)OP([O-])([O-])=O)N1C=C(CO)C([O-])=NC1=O InChI=1S/C10H17N2O15P3/c13-3-5-2-12(10(16)11-9(5)15)8-1-6(14)7(25-8)4-24-29(20,21)27-30(22,23)26-28(17,18)19/h2,6-8,13-14H,1,3-4H2,(H,20,21)(H,22,23)(H,11,15,16)(H2,17,18,19)/p-3/t6-,7-,8-/m0/s1 RLHFVRMIEVOHOR-FXQIFTODSA-K Cytoplasm Periplasm logp -0.93 ALOGPS logs -1.33 ALOGPS solubility 2.54e+01 g/l ALOGPS logp -3 ChemAxon pka_strongest_acidic 0.9 ChemAxon pka_strongest_basic -2.8 ChemAxon iupac 1-[(2S,4S,5S)-4-hydroxy-5-({[hydroxy({[hydroxy(phosphonatooxy)phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-2-yl]-5-(hydroxymethyl)-2-oxo-1,2-dihydropyrimidin-4-olate ChemAxon average_mass 495.1438 ChemAxon mono_mass 494.960702324 ChemAxon smiles [H][C@]1(O)C[C@]([H])(O[C@@]1([H])COP(O)(=O)OP(O)(=O)OP([O-])([O-])=O)N1C=C(CO)C([O-])=NC1=O ChemAxon formula C10H14N2O15P3 ChemAxon inchi InChI=1S/C10H17N2O15P3/c13-3-5-2-12(10(16)11-9(5)15)8-1-6(14)7(25-8)4-24-29(20,21)27-30(22,23)26-28(17,18)19/h2,6-8,13-14H,1,3-4H2,(H,20,21)(H,22,23)(H,11,15,16)(H2,17,18,19)/p-3/t6-,7-,8-/m0/s1 ChemAxon inchikey RLHFVRMIEVOHOR-FXQIFTODSA-K ChemAxon polar_surface_area 270.9 ChemAxon refractivity 98.43 ChemAxon polarizability 36.82 ChemAxon rotatable_bond_count 9 ChemAxon acceptor_count 13 ChemAxon donor_count 4 ChemAxon physiological_charge -3 ChemAxon formal_charge -3 ChemAxon Specdb::NmrOneD 268288 Specdb::NmrOneD 268289 Specdb::NmrOneD 268290 Specdb::NmrOneD 268291 Specdb::NmrOneD 268292 Specdb::NmrOneD 268293 Specdb::NmrOneD 268294 Specdb::NmrOneD 268295 Specdb::NmrOneD 268296 Specdb::NmrOneD 268297 Specdb::NmrOneD 268298 Specdb::NmrOneD 268299 Specdb::NmrOneD 268300 Specdb::NmrOneD 268301 Specdb::NmrOneD 268302 Specdb::NmrOneD 268303 Specdb::NmrOneD 268304 Specdb::NmrOneD 268305 Specdb::NmrOneD 268306 Specdb::NmrOneD 268307 Specdb::MsMs 23825 Specdb::MsMs 23826 Specdb::MsMs 23827 Specdb::MsMs 30623 Specdb::MsMs 30624 Specdb::MsMs 30625 25201516 CPD0-1346 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 Wovcha, M. G., Tomich, P. K., Chiu, C. S., Greenberg, G. R. (1973). "Direct participation of dCMP hydroxymethylase in synthesis of bacteriophage T4 DNA." Proc Natl Acad Sci U S A 70:2196-2200. 4525160