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Record Information
Version	2.0
Creation Date	2012-05-31 14:44:23 -0600
Update Date	2015-06-03 17:20:00 -0600
Secondary Accession Numbers	ECMDB20428
Identification
Name:	Hydroxymethyl-dCDP
Description	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]
Structure	MOLSDFPDBSMILESInChI × Structure for #<Compound:0xab042f94> Close
Synonyms:	5'-Hydroxymethyl-dCDP 5-Hydroxymethyl-dCDP
Chemical Formula:	C10H13N2O12P2
Weight:	Average: 415.1639 Monoisotopic: 414.994371914
InChI Key:	JEXKSGKPLHRGPO-FXQIFTODSA-K
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
CAS number:	Not Available
IUPAC Name:	1-[(2S,4S,5S)-4-hydroxy-5-({[hydroxy(phosphonatooxy)phosphoryl]oxy}methyl)oxolan-2-yl]-5-(hydroxymethyl)-2-oxo-1,2-dihydropyrimidin-4-olate
Traditional IUPAC Name:	1-[(2S,4S,5S)-4-hydroxy-5-({[hydroxy(phosphonatooxy)phosphoryl]oxy}methyl)oxolan-2-yl]-5-(hydroxymethyl)-2-oxopyrimidin-4-olate
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
Chemical Taxonomy
Description	belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
Kingdom	Organic compounds
Super Class	Organic oxygen compounds
Class	Organic oxoanionic compounds
Sub Class	Organic pyrophosphates
Direct Parent	Organic pyrophosphates
Alternative Parents	Pyrimidones Monoalkyl phosphates Hydropyrimidines Tetrahydrofurans Heteroaromatic compounds Secondary alcohols Oxacyclic compounds Azacyclic compounds Primary alcohols Organopnictogen compounds Organonitrogen compounds Organic oxides Hydrocarbon derivatives Aromatic alcohols Organic anions
Substituents	Organic pyrophosphate Monoalkyl phosphate Pyrimidone Alkyl phosphate Pyrimidine Phosphoric acid ester Organic phosphoric acid derivative Hydropyrimidine Heteroaromatic compound Tetrahydrofuran Secondary alcohol Oxacycle Azacycle Organoheterocyclic compound Organic nitrogen compound Organopnictogen compound Organic oxide Hydrocarbon derivative Aromatic alcohol Primary alcohol Organooxygen compound Organonitrogen compound Alcohol Organic anion Aromatic heteromonocyclic compound
Molecular Framework	Aromatic heteromonocyclic compounds
External Descriptors	Not Available
Physical Properties
State:	Not Available
Charge:	-2
Melting point:	Not Available
Experimental Properties:	Property Value Source
Predicted Properties	Property Value Source Water Solubility 24.7 g/L ALOGPS logP -1.7 ALOGPS logP -2.6 ChemAxon logS -1.3 ALOGPS pKa (Strongest Acidic) 1.77 ChemAxon pKa (Strongest Basic) -2.8 ChemAxon Physiological Charge -2 ChemAxon Hydrogen Acceptor Count 11 ChemAxon Hydrogen Donor Count 3 ChemAxon Polar Surface Area 224.37 Ų ChemAxon Rotatable Bond Count 7 ChemAxon Refractivity 87.56 m³·mol⁻¹ ChemAxon Polarizability 32.33 ų ChemAxon Number of Rings 2 ChemAxon Bioavailability 0 ChemAxon Rule of Five Yes ChemAxon Ghose Filter Yes ChemAxon Veber's Rule Yes ChemAxon MDDR-like Rule Yes ChemAxon
Biological Properties
Cellular Locations:	Cytoplasm
Reactions:
SMPDB Pathways:	Not Available
KEGG Pathways:	Not Available
EcoCyc Pathways:	Not Available
Concentrations
	Not Available
Spectra
Spectra:	Spectrum Type Description Splash Key Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Positive splash10-014i-0000900000-07a2f427b5732481b75f View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Positive splash10-01r7-0009200000-3c24ec8c282319fd6410 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Positive splash10-0udi-3971000000-ba82bbb455424008530b View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Negative splash10-03dl-7002900000-0378b8b8f36826ba9f4b View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Negative splash10-08fr-5102900000-5b9dab1acee2e6929fed View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Negative splash10-0006-9000000000-03edadc8f350a656ef97 View in MoNA 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer 1D NMR 13C NMR Spectrum Not Available View in JSpectraViewer 1D NMR 1H NMR Spectrum Not Available View in JSpectraViewer
References
References:	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. Pubmed: 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. Pubmed: 4525160
Synthesis Reference:	Not Available
Material Safety Data Sheet (MSDS)	Not Available
Links
External Links:	Resource Link CHEBI ID Not Available HMDB ID Not Available Pubchem Compound ID 25202010 Kegg ID Not Available ChemSpider ID Not Available Wikipedia ID Not Available BioCyc ID CPD0-1345 EcoCyc ID CPD0-1345