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5-Thymidylic acid (YMDB00162)

Identification
YMDB IDYMDB00162
Name5-Thymidylic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description5-Thymidylic acid, also known as TMP or thymidylate, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleoside monophosphates. These are pyrimidine nucleotides with a monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. 5-Thymidylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-Thymidylic acid exists in all living species, ranging from bacteria to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2'-Deoxythymidine 5'-monophosphate
  • 5-Methyl-dUMP
  • 5'-dTMP
  • 5'-Thymidylate
  • 5'-Thymidylic acid
  • 5'-TMP
  • Deoxy TMP
  • Deoxyribosylthymine monophosphate
  • Deoxythymidine 5'-monophosphate
  • Deoxythymidine 5'-phosphate
  • Deoxythymidine monophosphate
  • Deoxythymidylate
  • Deoxythymidylic acid
  • Deoxythymydilate
  • Deoxythymydilic acid
  • DTMP
  • Thymidine 5'-monophosphate
  • Thymidine 5'-phosphate
  • Thymidine 5'-phosphorate
  • Thymidine 5'-phosphoric acid
  • Thymidine 5'MP
  • Thymidine mononucleotide
  • Thymidine monophosphate
  • Thymidine phosphate
  • Thymidine-5'-monophosphorate
  • Thymidine-5'-monophosphoric acid
  • Thymidylate
  • Thymidylic acid
  • (DT)1
  • Ribothymidine 5'-monophosphate
  • Thymidine 5'-(dihydrogen phosphate)
  • THYMIDINE-5'-phosphATE
  • TMP
  • Deoxyribosylthymine monophosphoric acid
  • Ribothymidine 5'-monophosphoric acid
  • Thymidine 5'-(dihydrogen phosphoric acid)
  • Thymidine monophosphoric acid
  • Thymidine-5'-monophosphate
  • THYMIDINE-5'-phosphoric acid
  • Deoxythymidine 5'-phosphoric acid
  • 5-Thymidylate
  • Thymidylic acids
  • Acids, thymidylic
  • Acid, thymidylic
  • monoPhosphate, thymidine
CAS number365-07-1
WeightAverage: 322.2085
Monoisotopic: 322.056601978
InChI KeyGYOZYWVXFNDGLU-XLPZGREQSA-N
InChIInChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
IUPAC Name{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Namethymidylate
Chemical FormulaC10H15N2O8P
SMILES[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([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 monophosphates. These are pyrimidine nucleotides with a monophosphate 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 monophosphates
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside monophosphate
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Lactam
  • Secondary alcohol
  • Urea
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • 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 Solubility6.78 g/LALOGPS
logP-1.4ALOGPS
logP-1.2ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area145.63 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity66.28 m³·mol⁻¹ChemAxon
Polarizability27.46 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
One Carbon Pool by Folate IPW002468 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB Reactions
Dihydrofolic acid + 5-Thymidylic acid → 5,10-Methylene-THF + dUMP
dUMP + 5,10-methenyltetrahydrofolate mono-L-glutamate → Dihydrofolic acid + 5-Thymidylic acid
KEGG Reactions
water + 5-Thymidylic acid → phosphate + Thymidine
Adenosine triphosphate + 5-Thymidylic acid ↔ dTDP + ADP
Adenosine triphosphate + Thymidine → hydron + ADP + 5-Thymidylic acid
dUMP + 5,10-Methylene-THF → 5-Thymidylic acid + Dihydrofolic acid
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-01u0-0961000000-4380a23f8bec3c2dd015JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-03k9-0940000000-6238904f1b1f293aaf3aJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-01u0-0961000000-4380a23f8bec3c2dd015JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-03k9-0940000000-6238904f1b1f293aaf3aJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9500000000-ca4d82d816839360b115JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0002-9621000000-1a0c588cd8f192b77565JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-001i-9110000000-a45c0d5a58cdb0e5fee4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9000000000-624fe22ca203d0e6430eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-001i-9000000000-0c23943cc868acaaeda4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-004i-9703000000-452b674ca61adb40209bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004i-9703000000-452b674ca61adb40209bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-2233c579a23110abe895JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-9af792986db292f0d8d1JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9010000000-9936ff7b595382418b7cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9200000000-5c7a9e2c6c970eec2d92JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-edfd7498bf3ebaedbb4bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9000000000-9dafb0586b1aadb8475dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9100000000-b286ae95b38725486f5bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-c716e9bc2009f1adb3aeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-ec3ffc3673cc769d3a0eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-004i-8900000000-90b7e520ce562f39a280JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-004i-7900000000-a01024a3e21d2de7f133JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-004j-5900000000-57620f7a2b0abf78c220JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-004i-8900000000-b0b0ac82c08ccb2ea84eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-006t-0905000000-49f5a9d8a112c369032dJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-b932c025cbc139ba930bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4900000000-ae144ce0df705b85f237JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-5900000000-9f2e5ba96fb24ff28b7fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9766000000-855dcb81a8d160218e77JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9200000000-f9116de370dd3211ece6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-0953b010bfa0e123afa7JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H 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
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:
  • 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
  • Nookaew, I., Jewett, M. C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., Bhumiratana, S. (2008). "The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism." BMC Syst Biol 2:71.18687109
  • Jong, A. Y., Campbell, J. L. (1984). "Characterization of Saccharomyces cerevisiae thymidylate kinase, the CDC8 gene product. General properties, kinetic analysis, and subcellular localization." J Biol Chem 259:14394-14398.6094555
  • Jong, A. Y., Kuo, C. L., Campbell, J. L. (1984). "The CDC8 gene of yeast encodes thymidylate kinase." J Biol Chem 259:11052-11059.6088527
Synthesis Reference:Scarano, E. Enzymic formation of thymidylic acid from 5-methyl-5'-deoxycytidylic acid. Bollettino - Societa Italiana di Biologia Sperimentale (1958), 34 945.
External Links:
ResourceLink
CHEBI ID17013
HMDB IDHMDB01227
Pubchem Compound ID9700
Kegg IDC00364
ChemSpider ID23217524
FOODB IDFDB030840
WikipediadTMP
BioCyc IDTMP

Enzymes

Protein Details
1. Thymidylate synthase
General function:
Involved in thymidylate synthase activity
Specific function:
Required for both nuclear and mitochondrial DNA synthesis
Gene Name:
TMP1
Uniprot ID:
P06785
Molecular weight:
35046.89844
Reactions
5,10-methylenetetrahydrofolate + dUMP → dihydrofolate + dTMP.
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.