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Human Metabolome Database Version 3.5

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Showing metabocard for dCTP (HMDB00998)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:09:43 -0700
HMDB ID HMDB00998
Secondary Accession Numbers None
Metabolite Identification
Common 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
Download: MOL | SDF | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. 2'-Deoxycytidine-5'-triphosphate
  2. dCTP
  3. Deoxy-CTP
  4. Deoxycytidine-triphosphate
Chemical Formula C9H16N3O13P3
Average Molecular Weight 467.1569
Monoisotopic Molecular Weight 466.989597149
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 IUPAC Name ({[(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxyphosphonic acid
CAS Registry Number 2056-98-6
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 Key RGWHQCVHVJXOKC-SHYZEUOFSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Pyrimidine Nucleotides
Sub Class Pyrimidine Deoxyribonucleotides
Other Descriptors
  • 2'-deoxycytidine phosphate(ChEBI)
  • Aromatic Heteropolycyclic Compounds
  • Deoxyribonucleotides(KEGG)
  • Pyrimidine Deoxyribonucleotides
  • pyrimidine 2'-deoxyribonucleoside 5'-triphosphate(ChEBI)
Substituents
  • Aminopyrimidine
  • Hydropyrimidine
  • Organic Hypophosphite
  • Organic Phosphite
  • Organic Pyrophosphate
  • Oxolane
  • Phosphoric Acid Ester
  • Pyrimidine
  • Pyrimidone
  • Secondary Alcohol
Direct Parent Pyrimidine 2'-deoxyribonucleoside Triphosphates
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction Not Available
Application Not Available
Cellular locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 11.8 g/L ALOGPS
LogP -0.52 ALOGPS
LogP -3.6 ChemAxon
LogS -1.60 ALOGPS
pKa (strongest acidic) 0.95 ChemAxon
pKa (strongest basic) -0.05 ChemAxon
Hydrogen Acceptor Count 12 ChemAxon
Hydrogen Donor Count 6 ChemAxon
Polar Surface Area 247.97 A2 ChemAxon
Rotatable Bond Count 8 ChemAxon
Refractivity 85.65 ChemAxon
Polarizability 35.21 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -3 ChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biofluid Locations
  • Blood
Tissue Location Not Available
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Comments
Blood Detected and Quantified
Article_icon
29.0 +/- 19.0 uM Adult (>18 years old) Both Normal Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB022359
KNApSAcK ID Not Available
Chemspider ID 58601 Link_out
KEGG Compound ID C00458 Link_out
BioCyc ID DCTP Link_out
BiGG ID 35027 Link_out
Wikipedia Link dCTP Link_out
NuGOwiki Link HMDB00998 Link_out
Metagene Link HMDB00998 Link_out
METLIN ID 5929 Link_out
PubChem Compound 65091 Link_out
PDB ID DCP Link_out
ChEBI ID 16311 Link_out
References
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
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 Link_out
  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 Link_out
  3. van 't Wout AB: Gene expression profiling of HIV-1 infection using cDNA microarrays. Methods Mol Biol. 2005;304:455-9. Pubmed: 16061997 Link_out
  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 Link_out
  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 Link_out

Enzymes
Name: Uridine-cytidine kinase 1
Reactions:
    Gene Name: UCK1
    Uniprot ID: Q9HA47 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Nucleoside diphosphate kinase, mitochondrial
    Reactions:
      Gene Name: NME4
      Uniprot ID: O00746 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Nucleoside diphosphate kinase A
      Reactions:
        Gene Name: NME1
        Uniprot ID: P15531 Link_out
        Protein Sequence: FASTA
        Gene Sequence: FASTA
        Name: Nucleoside diphosphate kinase B
        Reactions:
          Gene Name: NME2
          Uniprot ID: P22392 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Nucleoside diphosphate kinase 6
          Reactions:
            Gene Name: NME6
            Uniprot ID: O75414 Link_out
            Protein Sequence: FASTA
            Gene Sequence: FASTA
            Name: DNA polymerase beta
            Reactions:
              Gene Name: POLB
              Uniprot ID: P06746 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: DNA polymerase alpha catalytic subunit
              Reactions:
                Gene Name: POLA1
                Uniprot ID: P09884 Link_out
                Protein Sequence: FASTA
                Gene Sequence: FASTA
                Name: DNA polymerase delta subunit 3
                Reactions:
                  Gene Name: POLD3
                  Uniprot ID: Q15054 Link_out
                  Protein Sequence: FASTA
                  Gene Sequence: FASTA
                  Name: DNA polymerase lambda
                  Reactions:
                    Gene Name: POLL
                    Uniprot ID: Q9UGP5 Link_out
                    Protein Sequence: FASTA
                    Gene Sequence: FASTA
                    Name: DNA polymerase epsilon subunit 4
                    Reactions:
                      Gene Name: POLE4
                      Uniprot ID: Q9NR33 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA
                      Name: DNA polymerase eta
                      Reactions:
                        Gene Name: POLH
                        Uniprot ID: Q9Y253 Link_out
                        Protein Sequence: FASTA
                        Gene Sequence: FASTA
                        Name: DNA polymerase delta catalytic subunit
                        Reactions:
                          Gene Name: POLD1
                          Uniprot ID: P28340 Link_out
                          Protein Sequence: FASTA
                          Gene Sequence: FASTA
                          Name: DNA polymerase zeta catalytic subunit
                          Reactions:
                            Gene Name: REV3L
                            Uniprot ID: O60673 Link_out
                            Protein Sequence: FASTA
                            Gene Sequence: FASTA
                            Name: DNA polymerase epsilon catalytic subunit A
                            Reactions:
                              Gene Name: POLE
                              Uniprot ID: Q07864 Link_out
                              Protein Sequence: FASTA
                              Gene Sequence: FASTA
                              Name: DNA polymerase mu
                              Reactions:
                                Gene Name: POLM
                                Uniprot ID: Q9NP87 Link_out
                                Protein Sequence: FASTA
                                Gene Sequence: FASTA
                                Name: DNA polymerase kappa
                                Reactions:
                                  Gene Name: POLK
                                  Uniprot ID: Q9UBT6 Link_out
                                  Protein Sequence: FASTA
                                  Gene Sequence: FASTA
                                  Name: DNA polymerase epsilon subunit 3
                                  Reactions:
                                    Gene Name: POLE3
                                    Uniprot ID: Q9NRF9 Link_out
                                    Protein Sequence: FASTA
                                    Gene Sequence: FASTA
                                    Name: DNA polymerase subunit gamma-1
                                    Reactions:
                                      Gene Name: POLG
                                      Uniprot ID: P54098 Link_out
                                      Protein Sequence: FASTA
                                      Gene Sequence: FASTA
                                      Name: DNA polymerase iota
                                      Reactions:
                                        Gene Name: POLI
                                        Uniprot ID: Q9UNA4 Link_out
                                        Protein Sequence: FASTA
                                        Gene Sequence: FASTA
                                        Name: DNA polymerase epsilon subunit 2
                                        Reactions:
                                          Gene Name: POLE2
                                          Uniprot ID: P56282 Link_out
                                          Protein Sequence: FASTA
                                          Gene Sequence: FASTA
                                          Name: Uridine-cytidine kinase 2
                                          Reactions:
                                            Gene Name: UCK2
                                            Uniprot ID: Q9BZX2 Link_out
                                            Protein Sequence: FASTA
                                            Gene Sequence: FASTA
                                            Name: Uridine-cytidine kinase-like 1
                                            Reactions:
                                              Gene Name: UCKL1
                                              Uniprot ID: Q9NWZ5 Link_out
                                              Protein Sequence: FASTA
                                              Gene Sequence: FASTA
                                              Name: Myb-binding protein 1A
                                              Reactions:
                                                Gene Name: MYBBP1A
                                                Uniprot ID: Q9BQG0 Link_out
                                                Protein Sequence: FASTA
                                                Gene Sequence: FASTA
                                                Name: DNA polymerase theta
                                                Reactions:
                                                  Gene Name: POLQ
                                                  Uniprot ID: O75417 Link_out
                                                  Protein Sequence: FASTA
                                                  Gene Sequence: FASTA