2.0 2012-05-31 14:44:23 -0600 2015-06-03 17:20:00 -0600 ECMDB20428 M2MDB001249 Hydroxymethyl-dCDP Hydroxymethyl-dCDP is a member of the chemical class known as Pyrimidine 2'-deoxyribonucleoside Diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking an hydroxyl group at position 2. Hydroxymethyl-dCDP 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-dCDP is an intermediate in the synthesis or breakdown of phage-modified DNA. [PMID: 4525160; 10064578] 5'-Hydroxymethyl-dCDP 5-Hydroxymethyl-dCDP C10H13N2O12P2 415.1639 414.994371914 1-[(2S,4S,5S)-4-hydroxy-5-({[hydroxy(phosphonatooxy)phosphoryl]oxy}methyl)oxolan-2-yl]-5-(hydroxymethyl)-2-oxo-1,2-dihydropyrimidin-4-olate 1-[(2S,4S,5S)-4-hydroxy-5-({[hydroxy(phosphonatooxy)phosphoryl]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-])=O)N1C=C(CO)C([O-])=NC1=O InChI=1S/C10H16N2O12P2/c13-3-5-2-12(10(16)11-9(5)15)8-1-6(14)7(23-8)4-22-26(20,21)24-25(17,18)19/h2,6-8,13-14H,1,3-4H2,(H,20,21)(H,11,15,16)(H2,17,18,19)/p-3/t6-,7-,8-/m0/s1 JEXKSGKPLHRGPO-FXQIFTODSA-K Cytoplasm Periplasm logp -1.67 ALOGPS logs -1.28 ALOGPS solubility 2.47e+01 g/l ALOGPS logp -2.6 ChemAxon pka_strongest_acidic 1.77 ChemAxon pka_strongest_basic -2.8 ChemAxon iupac 1-[(2S,4S,5S)-4-hydroxy-5-({[hydroxy(phosphonatooxy)phosphoryl]oxy}methyl)oxolan-2-yl]-5-(hydroxymethyl)-2-oxo-1,2-dihydropyrimidin-4-olate ChemAxon average_mass 415.1639 ChemAxon mono_mass 414.994371914 ChemAxon smiles [H][C@]1(O)C[C@]([H])(O[C@@]1([H])COP(O)(=O)OP([O-])([O-])=O)N1C=C(CO)C([O-])=NC1=O ChemAxon formula C10H13N2O12P2 ChemAxon inchi InChI=1S/C10H16N2O12P2/c13-3-5-2-12(10(16)11-9(5)15)8-1-6(14)7(23-8)4-22-26(20,21)24-25(17,18)19/h2,6-8,13-14H,1,3-4H2,(H,20,21)(H,11,15,16)(H2,17,18,19)/p-3/t6-,7-,8-/m0/s1 ChemAxon inchikey JEXKSGKPLHRGPO-FXQIFTODSA-K ChemAxon polar_surface_area 224.37 ChemAxon refractivity 87.56 ChemAxon polarizability 32.33 ChemAxon rotatable_bond_count 7 ChemAxon acceptor_count 11 ChemAxon donor_count 3 ChemAxon physiological_charge -2 ChemAxon formal_charge -3 ChemAxon Specdb::NmrOneD 254308 Specdb::NmrOneD 254309 Specdb::NmrOneD 254310 Specdb::NmrOneD 254311 Specdb::NmrOneD 254312 Specdb::NmrOneD 254313 Specdb::NmrOneD 254314 Specdb::NmrOneD 254315 Specdb::NmrOneD 254316 Specdb::NmrOneD 254317 Specdb::NmrOneD 254318 Specdb::NmrOneD 254319 Specdb::NmrOneD 254320 Specdb::NmrOneD 254321 Specdb::NmrOneD 254322 Specdb::NmrOneD 254323 Specdb::NmrOneD 254324 Specdb::NmrOneD 254325 Specdb::NmrOneD 254326 Specdb::NmrOneD 254327 Specdb::MsMs 27047 Specdb::MsMs 27048 Specdb::MsMs 27049 Specdb::MsMs 33605 Specdb::MsMs 33606 Specdb::MsMs 33607 25202010 CPD0-1345 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