You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Deoxyuridine triphosphate (YMDB00201)

Identification
YMDB IDYMDB00201
NameDeoxyuridine triphosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionDeoxyuridine triphosphate (dUTP) is an intermediate in the metabolism of pyrimidine deoxynucleotides and is essential for the production of dTTP. dUTP is not normal incorperated into DNA. The enzyme dUTP pyrophosphatase (dUTPase), which hydrolyzes dUTP to dUMP, assists in mataining low levels of dUTP. Maintaining low levels of dUTP is essential to preventing the incorperation of dUTP into DNA. [PMID: 8223452]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2'-deoxyuridine 5'-triphosphate
  • 2'-Deoxyuridine-5'-triphosphorate
  • 2'-Deoxyuridine-5'-triphosphoric acid
  • 2'-Deoxyuridine-5'-triphosphoric acid = dUTP
  • Deoxy-utp
  • Deoxyuridine triphosphate
  • Deoxyuridine triphosphic acid
  • Deoxyuridine-5'-Triphosphate
  • dUTP
  • 2'-Deoxyuridine 5'-triphosphoric acid
  • Deoxyuridine triphosphoric acid
  • 2'-Deoxyuridine 5'-(tetrahydrogen triphosphate)
  • 2'-deoxy-UTP
  • 2’-Deoxyuridine 5’-(tetrahydrogen triphosphate)
  • 2’-Deoxyuridine 5’-triphosphate
  • 2’-deoxy-UTP
  • Deoxyuridine 5'-triphosphate
  • Deoxyuridine 5’-triphosphate
CAS number1173-82-6
WeightAverage: 468.1417
Monoisotopic: 467.973612734
InChI KeyAHCYMLUZIRLXAA-SHYZEUOFSA-N
InChIInChI=1S/C9H15N2O14P3/c12-5-3-8(11-2-1-7(13)10-9(11)14)23-6(5)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,20,21)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
IUPAC Name({[({[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid
Traditional IUPAC NamedUTP
Chemical FormulaC9H15N2O14P3
SMILES[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OP(=O)(O[H])O[H])N1C([H])=C([H])C(=O)N([H])C1=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
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydroxypyrimidine
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organopnictogen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility8.63 g/LALOGPS
logP-0.12ALOGPS
logP-2.5ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)0.9ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area238.69 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity83.67 m³·mol⁻¹ChemAxon
Polarizability34.62 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB Reactions
dUDP + Adenosine triphosphate → ADP + Deoxyuridine triphosphate
Deoxyuridine triphosphate + water → phosphate + hydron + dUMP
Uridine triphosphate + a reduced flavodoxin → water + an oxidized flavodoxin + Deoxyuridine triphosphate
dCTP + water + hydron → Ammonium + Deoxyuridine triphosphate
KEGG Reactions
water + hydron + dCTP → Deoxyuridine triphosphate + Ammonium
Deoxyuridine triphosphate + water → Pyrophosphate + dUMP + hydron
Adenosine triphosphate + dUDP ↔ Deoxyuridine triphosphate + ADP
Uridine triphosphate + thioredoxin dithiol → thioredoxin disulfide + Deoxyuridine triphosphate + water
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4j-8963100000-15f9b7594aa45581dcc0JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-05be-9551020000-12e307f13199997c5947JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-014i-0100900000-8e7a148aec1d751cc1c4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0a6r-4911000000-4e7687aefa9b30fe654cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0aor-0913400000-108f05d6274de41c6fbcJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0a4i-1922000000-1891134d52577ca759f0JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9000000000-192f049c7d1787f75c4cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9000000000-57fd03e21769cf32cb69JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-0a4i-1922000000-489aaa48942eed69703bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9000000000-f4b40a8824847f5ca8a7JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-9dfd5f9811270d9aaab8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3911000000-b480c4f463f71544be8fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-2ba3b00121251c9adda0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01b9-3120900000-dedbedae66448a647f3bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-057u-9430100000-0b81cc8084e6bd0f3088JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-056r-9510000000-a72cd2e823cab077b0e1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0003900000-eff09a2f41b2c9e59343JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9715400000-83fd98a60651b67d2aeaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9201000000-c6b0a4a5f0bb84bc1987JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-2900200000-ad484f076fd7c4b32fb9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9701100000-04958af5fb614287d4a0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-0910000000-52122719a1b16858a2a0JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Gadsden, M. H., McIntosh, E. M., Game, J. C., Wilson, P. J., Haynes, R. H. (1993). "dUTP pyrophosphatase is an essential enzyme in Saccharomyces cerevisiae." EMBO J 12:4425-4431.8223452
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID17625
HMDB IDHMDB01191
Pubchem Compound ID689
Kegg IDC00460
ChemSpider ID58580
FOODB IDFDB030842
Wikipedia IDNot Available
BioCyc IDDUTP

Enzymes

Protein Details
1. Nucleoside diphosphate kinase
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. Required for repair of UV radiation- and etoposide-induced DNA damage
Gene Name:
YNK1
Uniprot ID:
P36010
Molecular weight:
17166.59961
Reactions
ATP + nucleoside diphosphate → ADP + nucleoside triphosphate.
Protein Details
2. Deoxycytidylate deaminase
General function:
Involved in zinc ion binding
Specific function:
Supplies the nucleotide substrate for thymidylate synthetase
Gene Name:
DCD1
Uniprot ID:
P06773
Molecular weight:
35645.69922
Reactions
dCMP + H(2)O → dUMP + NH(3).
Protein Details
3. Deoxyuridine 5'-triphosphate nucleotidohydrolase
General function:
Involved in hydrolase activity
Specific function:
This enzyme is involved in nucleotide metabolism:it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA
Gene Name:
DUT1
Uniprot ID:
P33317
Molecular weight:
15307.2002
Reactions
dUTP + H(2)O → dUMP + diphosphate.
Protein Details
4. Thioredoxin-2
General function:
Involved in electron carrier activity
Specific function:
Participates as a hydrogen donor in redox reactions through the reversible oxidation of its active center dithiol to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. It is involved in many cellular processes, including deoxyribonucleotide synthesis, repair of oxidatively damaged proteins, protein folding, sulfur metabolism, and redox homeostasis. Thioredoxin-dependent enzymes include phosphoadenosine-phosphosulfate reductase MET16, alkyl- hydroperoxide reductase DOT5, thioredoxin peroxidases TSA1 and TSA2, alkyl hydroperoxide reductase AHP1, and peroxiredoxin HYR1. Thioredoxin is also involved in protection against reducing stress. As part of the LMA1 complex, it is involved in the facilitation of vesicle fusion such as homotypic vacuole and ER- derived COPII vesicle fusion with the Golgi. This activity does not require the redox mechanism. Through its capacity to inactivate the stress response transcription factor YAP1 and its regulator the hydroperoxide stress sensor HYR1, it is involved in feedback regulation of stress response gene expression upon oxidative stress
Gene Name:
TRX2
Uniprot ID:
P22803
Molecular weight:
11203.7998
Reactions
Protein Details
5. Thioredoxin-1
General function:
Involved in electron carrier activity
Specific function:
Participates as a hydrogen donor in redox reactions through the reversible oxidation of its active center dithiol to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. It is involved in many cellular processes, including deoxyribonucleotide synthesis, repair of oxidatively damaged proteins, protein folding, sulfur metabolism, and redox homeostasis. Thioredoxin-dependent enzymes include phosphoadenosine-phosphosulfate reductase MET16, alkyl- hydroperoxide reductase DOT5, thioredoxin peroxidases TSA1 and TSA2, alkyl hydroperoxide reductase AHP1, and peroxiredoxin HYR1. Thioredoxin is also involved in protection against reducing stress. As part of the LMA1 complex, it is involved in the facilitation of vesicle fusion such as homotypic vacuole and ER- derived COPII vesicle fusion with the Golgi. This activity does not require the redox mechanism
Gene Name:
TRX1
Uniprot ID:
P22217
Molecular weight:
11234.90039
Reactions