5-Thymidylic acid (PAMDB000303)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000303
Identification
Name: 5-Thymidylic acid
Description:5-Thymidylic acid is a thymine nucleotide. Also known as thymidine monophosphate, and abbreviated TMP, is a nucleotide that is found in DNA. It is an ester of phosphoric acid with the nucleoside thymidine. TMP consists of a phosphate group, esterified to the the pentose sugar deoxyribose moiety, and the nucleobase thymine.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 2'-Deoxythymidine 5'-monophosphate
  • 2'-Deoxythymidine 5'-monophosphoric acid
  • 5'-dTMP
  • 5'-Thymidylate
  • 5'-Thymidylic acid
  • 5'-TMP
  • 5-Methyl-dUMP
  • 5-Thymidylate
  • Deoxy TMP
  • Deoxyribosylthymine monophosphate
  • Deoxyribosylthymine monophosphoric acid
  • Deoxythymidine 5'-monophosphate
  • Deoxythymidine 5'-monophosphoric acid
  • Deoxythymidine 5'-phosphate
  • Deoxythymidine 5'-phosphoric acid
  • Deoxythymidine monophosphate
  • Deoxythymidine monophosphoric acid
  • Deoxythymidylate
  • Deoxythymidylic acid
  • Deoxythymydilate
  • Deoxythymydilic acid
  • DTMP
  • T
  • Thymidine 5'-monophosphate
  • Thymidine 5'-monophosphoric acid
  • Thymidine 5'-phosphate
  • Thymidine 5'-phosphorate
  • Thymidine 5'-phosphoric acid
  • Thymidine 5'MP
  • Thymidine mononucleotide
  • Thymidine monophosphate
  • Thymidine monophosphoric acid
  • Thymidine phosphate
  • Thymidine phosphoric acid
  • Thymidine-5'-monophosphate
  • Thymidine-5'-monophosphorate
  • Thymidine-5'-monophosphoric acid
  • Thymidine-5'-phosphate
  • Thymidine-5'-phosphoric acid
  • Thymidine-phosphate
  • Thymidine-phosphoric acid
  • Thymidylate
  • Thymidylic acid
  • TMP
Chemical Formula: C10H15N2O8P
Average Molecular Weight: 322.2085
Monoisotopic Molecular Weight: 322.056601978
InChI Key: GYOZYWVXFNDGLU-XLPZGREQSA-N
InChI:InChI=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
CAS number: 365-07-1
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 Name: thymidylate
SMILES:CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(O)=O)O2)C(=O)NC1=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidine deoxyribonucleotides. These are pyrimidine nucleotides where the purine moiety is linked to a ribose lacking a hydroxyl group at one or more positions.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleotides
Sub ClassPyrimidine deoxyribonucleotides
Direct Parent Pyrimidine deoxyribonucleotides
Alternative Parents
Substituents
  • Pyrimidine deoxyribonucleotide
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Urea
  • Secondary alcohol
  • Lactam
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility6.78 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity66.28 m3·mol-1ChemAxon
Polarizability27.56 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
5-Thymidylic acid + Water > Phosphate + Thymidine
Thymidine 5'-triphosphate + Water > 5-Thymidylic acid + Hydrogen ion + Pyrophosphate
Adenosine triphosphate + 5-Thymidylic acid <> ADP + dTDP
Adenosine triphosphate + Thymidine <> ADP + 5-Thymidylic acid + Hydrogen ion
dUMP + 5,10-Methylene-THF <> Dihydrofolic acid + 5-Thymidylic acid
Adenosine triphosphate + Thymidine <> ADP + 5-Thymidylic acid
Dihydrofolic acid + 5-Thymidylic acid + Dihydrofolic acid > 5,10-Methylene-THF + dUMP + 5,10-Methylene-THF
dUMP + 5,10-methenyltetrahydrofolate mono-L-glutamate + 5,10-methenyltetrahydrofolate mono-L-glutamate > Dihydrofolic acid + 5-Thymidylic acid + Dihydrofolic acid
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-001i-9110000000-a45c0d5a58cdb0e5fee4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9000000000-624fe22ca203d0e6430eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-001i-9000000000-0c23943cc868acaaeda4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-004i-9703000000-452b674ca61adb40209bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Gribaudo G, Riera L, Caposio P, Maley F, Landolfo S: Human cytomegalovirus requires cellular deoxycytidylate deaminase for replication in quiescent cells. J Gen Virol. 2003 Jun;84(Pt 6):1437-41. Pubmed: 12771412
  • Gribaudo G, Riera L, Lembo D, De Andrea M, Gariglio M, Rudge TL, Johnson LF, Landolfo S: Murine cytomegalovirus stimulates cellular thymidylate synthase gene expression in quiescent cells and requires the enzyme for replication. J Virol. 2000 Jun;74(11):4979-87. Pubmed: 10799571
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Seno T, Ayusawa D, Shimizu K, Koyama H, Takeishi K, Hori T: Thymineless death and genetic events in mammalian cells. Basic Life Sci. 1985;31:241-63. Pubmed: 3888175
  • Terai C, Carson DA: Pyrimidine nucleotide and nucleic acid synthesis in human monocytes and macrophages. Exp Cell Res. 1991 Apr;193(2):375-81. Pubmed: 1706277
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference: Scarano, E. Enzymic formation of thymidylic acid from 5-methyl-5'-deoxycytidylic acid. Bollettino - Societa Italiana di Biologia Sperimentale (1958), 34 945.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID17013
HMDB IDHMDB01227
Pubchem Compound ID9700
Kegg IDC00364
ChemSpider ID9319
WikipediadTMP
BioCyc IDTMP
EcoCyc IDTMP
Ligand ExpoTMP

Enzymes

Protein Details
• Thymidylate kinase
General function:
Involved in thymidylate kinase activity
Specific function:
Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth
Gene Name:
tmk
Locus Tag:
PA2962
Molecular weight:
23.1 kDa
Reactions
ATP + dTMP = ADP + dTDP.
Protein Details
• Multifunctional protein surE
General function:
Involved in hydrolase activity
Specific function:
Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'- monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain- length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. Also plays a significant physiological role in stress-response and is required for the survival of Pseudomonas aeruginosa in stationary growth phase
Gene Name:
surE
Locus Tag:
PA3625
Molecular weight:
26.4 kDa
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.
Protein Details
• Thymidylate synthase
General function:
Involved in thymidylate synthase activity
Specific function:
Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation
Gene Name:
thyA
Locus Tag:
PA0342
Molecular weight:
30 kDa
Reactions
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP.
Protein Details
• Class B acid phosphatase
General function:
Involved in acid phosphatase activity
Specific function:
Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:
aphA
Locus Tag:
PA1409
Molecular weight:
38 kDa
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.
Protein Details
• Protein mazG
General function:
Involved in nucleoside-triphosphate diphosphatase activity
Specific function:
Specific function unknown
Gene Name:
mazG
Locus Tag:
PA0935
Molecular weight:
31.2 kDa
Reactions
ATP + H(2)O = AMP + diphosphate.

Transporters