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Record Information
Version	2.0
Creation Date	2012-05-31 14:44:26 -0600
Update Date	2015-06-03 17:20:00 -0600
Secondary Accession Numbers	ECMDB20429
Identification
Name:	Hydroxymethyl-dCTP
Description	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]
Structure	MOLSDFPDBSMILESInChI × Structure for #<Compound:0xa94a4c9c> Close
Synonyms:	5'-Hydroxymethyl-dCTP 5-Hydroxymethyl-dCTP
Chemical Formula:	C10H14N2O15P3
Weight:	Average: 495.1438 Monoisotopic: 494.960702324
InChI Key:	RLHFVRMIEVOHOR-FXQIFTODSA-K
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
CAS number:	Not Available
IUPAC Name:	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
Traditional IUPAC Name:	1-[(2S,4S,5S)-4-hydroxy-5-[({hydroxy[hydroxy(phosphonatooxy)phosphoryl]oxyphosphoryl}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)OP([O-])([O-])=O)N1C=C(CO)C([O-])=NC1=O
Chemical Taxonomy
Description	belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside triphosphates. These are pyrimidine nucleotides with a triphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
Kingdom	Organic compounds
Super Class	Nucleosides, nucleotides, and analogues
Class	Pyrimidine nucleotides
Sub Class	Pyrimidine deoxyribonucleotides
Direct Parent	Pyrimidine 2'-deoxyribonucleoside triphosphates
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	Pyrimidine 2'-deoxyribonucleoside triphosphate 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 Organic oxygen 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:	-3
Melting point:	Not Available
Experimental Properties:	Property Value Source
Predicted Properties	Property Value Source Water Solubility 25.4 g/L ALOGPS logP -0.93 ALOGPS logP -3 ChemAxon logS -1.3 ALOGPS pKa (Strongest Acidic) 0.9 ChemAxon pKa (Strongest Basic) -2.8 ChemAxon Physiological Charge -3 ChemAxon Hydrogen Acceptor Count 13 ChemAxon Hydrogen Donor Count 4 ChemAxon Polar Surface Area 270.9 Ų ChemAxon Rotatable Bond Count 9 ChemAxon Refractivity 98.43 m³·mol⁻¹ ChemAxon Polarizability 36.82 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 splash10-0005-0000900000-f5536b55ddc13d94bbce View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Positive splash10-004i-0000900000-c569b84173439425ffc9 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Positive splash10-0udj-4970200000-e0c108b251c44281b906 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 10V, Negative splash10-0006-5000900000-21b05ce984968c17db04 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 20V, Negative splash10-0006-4100900000-30737f8e792799861469 View in MoNA Predicted LC-MS/MS Predicted LC-MS/MS Spectrum - 40V, Negative splash10-0016-9100000000-2a0c9edd03583b06c252 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 25201516 Kegg ID Not Available ChemSpider ID Not Available Wikipedia ID Not Available BioCyc ID CPD0-1346 EcoCyc ID CPD0-1346