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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. dihydrofolic acid and 5-thymidylic acid can be converted into 5,10-methylene-THF and dUMP; which is catalyzed by the enzyme thymidylate synthase. In yeast, 5-thymidylic acid is involved in the metabolic pathway called the one carbon pool by folate I pathway.
Structure
Thumb
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 acid5,10-Methylene-THF + dUMP
dUMP + 5,10-methenyltetrahydrofolate mono-L-glutamateDihydrofolic acid + 5-Thymidylic acid
KEGG Reactions
water + 5-Thymidylic acidphosphate + Thymidine
Adenosine triphosphate + 5-Thymidylic aciddTDP + ADP
Adenosine triphosphate + Thymidinehydron + ADP + 5-Thymidylic acid
dUMP + 5,10-Methylene-THF5-Thymidylic acid + Dihydrofolic acid
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
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 IDFDB022499
WikipediadTMP
BioCyc IDTMP

Enzymes

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.
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.