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dTDP (YMDB00205)

Identification
YMDB IDYMDB00205
NamedTDP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptiondTDP, also known as deoxy-TDP, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. dTDP is an extremely weak basic (essentially neutral) compound (based on its pKa). dTDP exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • Deoxy-tdp
  • Deoxythymidine 5'-diphosphate
  • dTDP
  • TDP
  • Thymidine 5'-diphosphate
  • Thymidine 5'-pyrophosphate
  • 2'-Deoxyribosylthymine 5'-(trihydrogen diphosphate)
  • THYMIDINE-5'- diphosphATE
  • 2'-Deoxyribosylthymine 5'-(trihydrogen diphosphoric acid)
  • Deoxythymidine 5'-diphosphoric acid
  • Thymidine 5'-diphosphoric acid
  • Thymidine 5'-pyrophosphoric acid
  • THYMIDINE-5'- diphosphoric acid
CAS number491-97-4
WeightAverage: 402.1884
Monoisotopic: 402.022932388
InChI KeyUJLXYODCHAELLY-XLPZGREQSA-N
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
IUPAC Name{[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy}phosphonic acid
Traditional IUPAC NamedTDP
Chemical FormulaC10H16N2O11P2
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])O[H])N1C([H])=C(C(=O)N([H])C1=O)C([H])([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate 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 diphosphates
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside diphosphate
  • Organic pyrophosphate
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Lactam
  • Urea
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • 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 Solubility6.94 g/LALOGPS
logP-0.87ALOGPS
logP-1.7ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area192.16 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity77.16 m³·mol⁻¹ChemAxon
Polarizability32.12 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
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
Adenosine triphosphate + dTDP → ADP + dTTP
KEGG Reactions
Adenosine triphosphate + 5-Thymidylic acid ↔ dTDP + ADP
dTDP + Adenosine triphosphate ↔ dTTP + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004m-6922000000-78987adf8e4b2b4baa77JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00dm-9341200000-af3e3a557688731137d2JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0kdi-9720700000-003f87d03143415a6bf9JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-f02dc55e07c9935275d9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4901000000-bc16523808594ec9a806JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-5900000000-2199218952cf36a3e3a2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-2607900000-696f76b41235895dc296JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9801000000-9bc55b2280dfcf3aed1dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-d33e29452de0777eaa0dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-1100900000-bedafc8a6d3579ef1476JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9102100000-8cad78608dae5988a8c1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-0ff3218786dbaaac7deaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0920500000-ccf96f505a327015ed67JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2910000000-857f636dcd89f8378f36JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-2910000000-b95a62414e3f309b00bbJSpectraViewer
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
Synthesis Reference:Rupprath, Carsten; Kopp, Maren; Hirtz, Dennis; Mueller, Rolf; Elling, Lothar. An enzyme module system for in situ regeneration of deoxythymidine 5'-diphosphate (dTDP)-activated deoxy sugars. Advanced Synthesis & Catalysis (2007), 349(8+9), 1489-149
External Links:
ResourceLink
CHEBI ID18075
HMDB IDHMDB01274
Pubchem Compound ID164628
Kegg IDC00363
ChemSpider ID24604727
FOODB IDFDB022528
WikipediadTDP
BioCyc IDTDP

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. Thymidylate kinase
General function:
Involved in thymidylate kinase activity
Specific function:
Catalyzes the conversion of dTMP to dTDP
Gene Name:
CDC8
Uniprot ID:
P00572
Molecular weight:
24687.19922
Reactions
ATP + dTMP → ADP + dTDP.