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Record Information
Version2.0
Creation Date2012-05-31 14:44:26 -0600
Update Date2015-06-03 17:20:00 -0600
Secondary Accession Numbers
  • ECMDB20429
Identification
Name:Hydroxymethyl-dCTP
DescriptionHydroxymethyl-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
Thumb
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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine deoxyribonucleotides
Direct ParentPyrimidine 2'-deoxyribonucleoside triphosphates
Alternative Parents
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 FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility25.4 g/LALOGPS
logP-0.93ALOGPS
logP-3ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)0.9ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area270.9 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity98.43 m³·mol⁻¹ChemAxon
Polarizability36.82 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0005-0000900000-f5536b55ddc13d94bbceView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-0000900000-c569b84173439425ffc9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udj-4970200000-e0c108b251c44281b906View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-5000900000-21b05ce984968c17db04View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-4100900000-30737f8e792799861469View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0016-9100000000-2a0c9edd03583b06c252View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView 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
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25201516
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDCPD0-1346
EcoCyc IDCPD0-1346