You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-20 20:21:48 UTC
HMDB IDHMDB0000998
Secondary Accession Numbers
  • HMDB00998
Metabolite Identification
Common NamedCTP
DescriptionDctp, also known as 2'-deoxycytidine 5'-triphosphate or deoxy-ctp, is a member of the class of compounds known as pyrimidine 2'-deoxyribonucleoside triphosphates. Pyrimidine 2'-deoxyribonucleoside triphosphates are pyrimidine nucleotides with a triphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. Dctp is soluble (in water) and an extremely strong acidic compound (based on its pKa). Dctp can be found primarily in blood. Within the cell, dctp is primarily located in the cytoplasm, in the mitochondria and in the nucleus. Dctp exists in all living species, ranging from bacteria to humans. In humans, dctp is involved in the pyrimidine metabolism. Dctp is also involved in few metabolic disorders, which include beta ureidopropionase deficiency, dihydropyrimidinase deficiency, MNGIE (mitochondrial neurogastrointestinal encephalopathy), and UMP synthase deficiency (orotic aciduria). 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
ValueSource
2'-Deoxycytidine 5'-triphosphateChEBI
Deoxycytidine 5'-triphosphateChEBI
Deoxycytidine triphosphateChEBI
2'-Deoxycytidine 5'-triphosphoric acidGenerator
Deoxycytidine 5'-triphosphoric acidGenerator
Deoxycytidine triphosphoric acidGenerator
2'-Deoxycytidine-5'-triphosphateHMDB
Deoxy-CTPHMDB
Deoxycytidine-triphosphateHMDB
2'-Deoxycytidine 5'-triphosphate, 3H-labeledMeSH
2'-Deoxycytidine 5'-triphosphate, P-(32)P-labeledMeSH
2'-Deoxycytidine 5'-triphosphate, magnesium saltMeSH
2'-Deoxycytidine 5'-triphosphate, p''-(32)P-labeledMeSH
Chemical FormulaC9H16N3O13P3
Average Molecular Weight467.1569
Monoisotopic Molecular Weight466.989597149
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 NamedCTP
CAS Registry Number2056-98-6
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
InChI Identifier
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
InChI KeyRGWHQCVHVJXOKC-SHYZEUOFSA-N
Chemical Taxonomy
DescriptionThis compound 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
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility11.8 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity85.65 m³·mol⁻¹ChemAxon
Polarizability35.21 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-03di-1900000000-3d90990d3831fc38abb6View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9734200000-676373c19e4530dc2572View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00dm-9207110000-47dd719accdfad2d1bb7View in MoNA
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
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biospecimen Locations
  • Blood
Tissue LocationNot Available
Pathways
NameSMPDB/PathwhizKEGG
Beta Ureidopropionase DeficiencyThumbThumb?image type=greyscaleThumb?image type=simpleNot Available
Dihydropyrimidinase DeficiencyThumbThumb?image type=greyscaleThumb?image type=simpleNot Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)ThumbThumb?image type=greyscaleThumb?image type=simpleNot Available
Pyrimidine MetabolismThumbThumb?image type=greyscaleThumb?image type=simpleMap00240
UMP Synthase Deficiency (Orotic Aciduria)ThumbThumb?image type=greyscaleThumb?image type=simpleNot Available
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified29.0 +/- 19.0 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022359
KNApSAcK IDNot Available
Chemspider ID58601
KEGG Compound IDC00458
BioCyc IDDCTP
BiGG ID35027
Wikipedia LinkNot Available
METLIN ID5929
PubChem Compound65091
PDB IDDCP
ChEBI ID16311
References
Synthesis ReferenceHinz 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
General References
  1. 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 ]
  2. 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 ]
  3. van 't Wout AB: Gene expression profiling of HIV-1 infection using cDNA microarrays. Methods Mol Biol. 2005;304:455-9. [PubMed:16061997 ]
  4. 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 ]
  5. 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 ]

Only showing the first 10 proteins. There are 31 proteins in total.

Enzymes

General function:
Involved in protein binding
Specific function:
Required for optimal DNA polymerase delta activity
Gene Name:
POLD3
Uniprot ID:
Q15054
Molecular weight:
51400.0
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. Inhibitor of p53-induced apoptosis.
Gene Name:
NME6
Uniprot ID:
O75414
Molecular weight:
22002.965
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails
General function:
Involved in ATP binding
Specific function:
May contribute to UTP accumulation needed for blast transformation and proliferation.
Gene Name:
UCKL1
Uniprot ID:
Q9NWZ5
Molecular weight:
59465.77
Reactions
dCTP + Uridine → dCDP + Uridine 5'-monophosphatedetails
dCTP + Cytidine → dCDP + Cytidine monophosphatedetails
General function:
Involved in ATP binding
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:
UCK2
Uniprot ID:
Q9BZX2
Molecular weight:
29298.92
Reactions
dCTP + Uridine → dCDP + Uridine 5'-monophosphatedetails
dCTP + Cytidine → dCDP + Cytidine monophosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination.
Gene Name:
NME1
Uniprot ID:
P15531
Molecular weight:
17148.635
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically (PubMed:8392752). Exhibits histidine protein kinase activity.
Gene Name:
NME2
Uniprot ID:
P22392
Molecular weight:
30136.92
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP (By similarity).
Gene Name:
NME4
Uniprot ID:
O00746
Molecular weight:
20658.45
Reactions
Adenosine triphosphate + dCDP → ADP + dCTPdetails
General function:
Involved in binding
Specific function:
May activate or repress transcription via interactions with sequence specific DNA-binding proteins. Repression may be mediated at least in part by histone deacetylase activity (HDAC activity)
Gene Name:
MYBBP1A
Uniprot ID:
Q9BQG0
Molecular weight:
148853.2
General function:
Involved in DNA binding
Specific function:
Has a DNA polymerase activity on nicked double-stranded DNA and on a singly primed DNA template. The enzyme activity is resistant to aphidicolin, and inhibited by dideoxynucleotides. Exhibites a single-stranded DNA-dependent ATPase activity. Could be involved in the repair of interstrand cross-links.
Gene Name:
POLQ
Uniprot ID:
O75417
Molecular weight:
289616.715
General function:
Involved in damaged DNA binding
Specific function:
Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.
Gene Name:
POLI
Uniprot ID:
Q9UNA4
Molecular weight:
83005.335

Only showing the first 10 proteins. There are 31 proteins in total.