Record Information
Version 1.0
Update Date 1/22/2018 12:54:53 PM
Metabolite IDPAMDB000219
Identification
Name: dCTP
Description:Deoxycytidine triphosphate (dCTP) is a cytidine nucleotide triphosphate that is used whenever DNA is synthesized, such as in the polymerase chain reaction. e.g.:
Structure
Thumb
Synonyms:
  • 2'-Deoxycytidine-5'-triphosphate
  • 2'-Deoxycytidine-5'-triphosphoric acid
  • DCTP
  • Deoxy-CTP
  • Deoxycytidine-triphosphate
  • Deoxycytidine-triphosphoric acid
Chemical Formula: C9H16N3O13P3
Average Molecular Weight: 467.1569
Monoisotopic Molecular Weight: 466.989597149
InChI Key: RGWHQCVHVJXOKC-SHYZEUOFSA-N
InChI:InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
CAS number: 2056-98-6
IUPAC Name:({[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid
Traditional IUPAC Name: dCTP
SMILES:NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O1
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct Parent Pyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydropyrimidine
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-3
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility11.8 mg/mLALOGPS
logP-0.52ALOGPS
logP-3.6ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)0.95ChemAxon
pKa (Strongest Basic)-0.05ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area247.97 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity85.65 m3·mol-1ChemAxon
Polarizability35.21 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-939cbd147b029e517cc1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2911000000-f4b496ca2bd6dcb38361View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-4900000000-a5e5fd690ddf51310279View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00xu-4110900000-42349a9362c5d3d7c6efView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-057r-9540100000-7a06dee6889dcffec4e9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-056r-9610000000-0a85daf50b374c5ac8baView in MoNA
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Brzezianska E, Zdzieszynska M, Gos R, Lewinski A: [Genetic analysis of rhodopsin and peripherin genes in patients with autosomal dominant retinitis pigmentosa (adRP) in Polish families] Klin Oczna. 2004;106(6):743-8. Pubmed: 15787173
  • Choi JY, Guengerich FP: Adduct size limits efficient and error-free bypass across bulky N2-guanine DNA lesions by human DNA polymerase eta. J Mol Biol. 2005 Sep 9;352(1):72-90. Pubmed: 16061253
  • Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • 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
  • Moriarty TJ, Marie-Egyptienne DT, Autexier C: Regulation of 5' template usage and incorporation of noncognate nucleotides by human telomerase. RNA. 2005 Sep;11(9):1448-60. Pubmed: 16120835
  • van 't Wout AB: Gene expression profiling of HIV-1 infection using cDNA microarrays. Methods Mol Biol. 2005;304:455-9. Pubmed: 16061997
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Yamauchi T, Ueda T: A sensitive new method for clinically monitoring cytarabine concentrations at the DNA level in leukemic cells. Biochem Pharmacol. 2005 Jun 15;69(12):1795-803. Epub 2005 Apr 26. Pubmed: 15935150
Synthesis Reference: Hinz M; Gottschling D; Eritja R; Seliger H Synthesis and properties of 2'-deoxycytidine triphosphate carrying c-myc tag sequence. Nucleosides, nucleotides & nucleic acids (2000), 19(10-12), 1543-52.
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16311
HMDB IDHMDB00998
Pubchem Compound ID625
Kegg IDC00458
ChemSpider ID58601
WikipediadCTP
BioCyc IDDCTP
EcoCyc IDDCTP
Ligand ExpoDCP

Enzymes

General function:
Involved in nucleic acid binding
Specific function:
In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity. It is able to utilize nicked circular duplex DNA as a template and can unwind the parental DNA strand from its template
Gene Name:
polA
Locus Tag:
PA5493
Molecular weight:
99.8 kDa
Reactions
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
General function:
Involved in DNA binding
Specific function:
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease
Gene Name:
dnaQ
Locus Tag:
PA1816
Molecular weight:
26.8 kDa
Reactions
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
General function:
Involved in nucleotide binding
Specific function:
The gamma chain seems to interact with the delta subunit to transfer the beta subunit on the DNA
Gene Name:
dnaX
Locus Tag:
PA1532
Molecular weight:
73.3 kDa
Reactions
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate
Gene Name:
ndk
Locus Tag:
PA3807
Molecular weight:
15.6 kDa
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
General function:
Involved in DNA binding
Specific function:
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP- independent) along duplex DNA
Gene Name:
dnaN
Locus Tag:
PA0002
Molecular weight:
40.7 kDa
Reactions
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
General function:
Involved in [formate-C-acetyltransferase]-activating enzyme activity
Specific function:
Activation of anaerobic ribonucleoside-triphosphate reductase under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine
Gene Name:
nrdG
Locus Tag:
PA1919
Molecular weight:
25.7 kDa
General function:
Involved in nucleoside-triphosphate diphosphatase activity
Specific function:
Specific function unknown
Gene Name:
mazG
Locus Tag:
PA0935
Molecular weight:
31.2 kDa
Reactions
ATP + H(2)O = AMP + diphosphate.
General function:
Involved in 3'-5' exonuclease activity
Specific function:
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase
Gene Name:
dnaE
Locus Tag:
PA3640
Molecular weight:
130.9 kDa
Reactions
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
General function:
Involved in DNA binding
Specific function:
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The delta subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA
Gene Name:
holA
Locus Tag:
PA3989
Molecular weight:
37.4 kDa
Reactions
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
General function:
Involved in DNA binding
Specific function:
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity
Gene Name:
holB
Locus Tag:
PA2961
Molecular weight:
35.7 kDa
Reactions
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
General function:
Involved in catalytic activity
Specific function:
2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin
Gene Name:
nrdD
Locus Tag:
PA1920
Molecular weight:
76.1 kDa
Reactions
2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin.
General function:
Involved in DNA binding
Specific function:
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity
Gene Name:
holC
Locus Tag:
PA3832
Molecular weight:
16.1 kDa
Reactions
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
General function:
Involved in ATP binding
Specific function:
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth
Gene Name:
adk
Locus Tag:
PA3686
Molecular weight:
23.1 kDa
Reactions
ATP + AMP = 2 ADP.