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dGTP (YMDB00744)

Identification
YMDB IDYMDB00744
NamedGTP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionDeoxyguanosine triphosphate (dGTP) is a nucleotide precursor used in cells for DNA synthesis. DNA usually exists as a double-stranded structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotides having the bases: adenine, cytosine, guanine, and thymine. A nucleotide is a mono-, di-, or triphosphate deoxyribonucleoside; that is, a deoxyribose sugar is attached to one, two, or three phosphates. Chemical interaction of these nucleotides forms phosphodiester linkages, creating the phosphate-deoxyribose backbone of the DNA double helix with the bases pointing inward. Nucleotides (bases) are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine, and cytosine pairs with guanine. [Wikipedia]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2-deoxyguanosine 5-triphosphate
  • 2'-Deoxyguanosine 5'-triphosphate
  • 2'-Deoxyguanosine triphosphate
  • deoxyguanosine 5-triphosphate
  • Deoxyguanosine 5'-triphosphate
  • deoxyguanosine triphosphate
  • DGT
  • dGTP
  • 2'-Deoxyguanosine 5'-triphosphoric acid
  • Deoxyguanosine 5'-triphosphoric acid
  • Deoxyguanosine triphosphoric acid
  • Deoxy-GTP
  • Deoxyguanosine triphosphate, 3H-labeled
CAS number2564-35-4
WeightAverage: 507.181
Monoisotopic: 506.995745159
InChI KeyHAAZLUGHYHWQIW-KVQBGUIXSA-N
InChIInChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
IUPAC Name({[({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid
Traditional IUPAC NamedGTP
Chemical FormulaC10H16N5O13P3
SMILESNC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O2)C(=O)N1
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside triphosphates. These are purine nucleotides with triphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine deoxyribonucleotides
Direct ParentPurine 2'-deoxyribonucleoside triphosphates
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside triphosphate
  • Imidazopyrimidine
  • Purine
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Pyrimidine
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility5.59 g/LALOGPS
logP-0.61ALOGPS
logP-3.2ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)1.03ChemAxon
pKa (Strongest Basic)0.33ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area274.58 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity95.73 m³·mol⁻¹ChemAxon
Polarizability39.09 ųChemAxon
Number of Rings3ChemAxon
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
purine nucleotides de novo biosynthesisPW002478 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Purine metabolismec00230 Map00230
Pyrimidine metabolismec00240 Map00240
SMPDB Reactions
dGDP + Adenosine triphosphate → ADP + dGTP
GTP + a reduced flavodoxin → dGTP + an oxidized flavodoxin + water
KEGG Reactions
Adenosine triphosphate + dGDP ↔ ADP + dGTP
water + dGTP → phosphate + hydron + dGDP
GTP + thioredoxin dithiol → thioredoxin disulfide + water + dGTP
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
15 ± 0 µM YEPD mediumaerobicBaker's yeastPMID: 14573610
Conversion Details Here
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-054n-9663300000-69b95474f5eb453321beJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0002-9630410000-325219a8d4bf19fde6eeJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0a6r-3900000000-2b39865e9630ea05d80dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0000090000-d8f04ae52811ac8ce0f8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-0910430000-fa9d3bf4f37e0cb50b28JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0910100000-0b4a31d8c636c368a5aeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-1158073094ef9de8ec75JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0900000000-4330d672c10b6546947eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0330290000-f951ce7240e0b3c9bb63JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fb9-7940100000-9f33838fecee36769f00JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-056r-9710000000-e1ba8d1db7700c321064JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900010000-d7e37dbd2de5a9544178JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-361a2474138028086bb3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0962000000-1d07cae94f51a1051829JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0200090000-0515f993040e10903acdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9200000000-7e8bf9b83b4109faf2c6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-4b46e4586c2a8edbe158JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • 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
  • Muller, E. G. (1994). "Deoxyribonucleotides are maintained at normal levels in a yeast thioredoxin mutant defective in DNA synthesis." J Biol Chem 269:24466-24471.7929110
  • Koc, A., Wheeler, L. J., Mathews, C. K., Merrill, G. F. (2004). "Hydroxyurea arrests DNA replication by a mechanism that preserves basal dNTP pools." J Biol Chem 279:223-230.14573610
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID16497
HMDB IDHMDB01440
Pubchem Compound ID65103
Kegg IDC00286
ChemSpider ID24785582
FOODB IDFDB022623
WikipediaDeoxyguanosine_triphosphate
BioCyc IDDGTP

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. 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
3. 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