Record Information
Version2.0
Creation Date2012-05-31 13:47:56 -0600
Update Date2015-09-13 12:56:10 -0600
Secondary Accession Numbers
  • ECMDB01227
Identification
Name:5-Thymidylic acid
Description5-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
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
Weight:Average: 322.2085
Monoisotopic: 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
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
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Reactions:
SMPDB Pathways:
One Carbon Pool by Folate IPW001735 ThumbThumb?image type=greyscaleThumb?image type=simple
One carbon pool by folatePW000773 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
salvage pathways of pyrimidine deoxyribonucleotidesPW002061 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • formylTHF biosynthesis I 1CMET2-PWY
  • pyrimidine deoxyribonucleotides de novo biosynthesis I PWY0-166
  • salvage pathways of pyrimidine deoxyribonucleotides PWY0-181
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-01u0-0961000000-4380a23f8bec3c2dd015View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-03k9-0940000000-6238904f1b1f293aaf3aView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-01u0-0961000000-4380a23f8bec3c2dd015View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-03k9-0940000000-6238904f1b1f293aaf3aView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9500000000-ca4d82d816839360b115View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0002-9621000000-1a0c588cd8f192b77565View in MoNA
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
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004i-9703000000-452b674ca61adb40209bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-b932c025cbc139ba930bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4900000000-ae144ce0df705b85f237View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-5900000000-9f2e5ba96fb24ff28b7fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9766000000-855dcb81a8d160218e77View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9200000000-f9116de370dd3211ece6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-0953b010bfa0e123afa7View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
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

General function:
Involved in hydrolase activity
Specific function:
Degradation of external UDP-glucose to uridine monophosphate and glucose-1-phosphate, which can then be used by the cell
Gene Name:
ushA
Uniprot ID:
P07024
Molecular weight:
60824
Reactions
UDP-sugar + H(2)O = UMP + alpha-D-aldose 1-phosphate.
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
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
Uniprot ID:
P0A720
Molecular weight:
23783
Reactions
ATP + dTMP = ADP + dTDP.
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 E.coli in stationary growth phase
Gene Name:
surE
Uniprot ID:
P0A840
Molecular weight:
26900
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.
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
Uniprot ID:
P0A884
Molecular weight:
30480
Reactions
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP.
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows high phosphatase activity toward three nucleoside 5'-monophosphates, UMP, dUMP, and dTMP, and very low activity against TDP, IMP, UDP, GMP, dGMP, AMP, dAMP, and 6- phosphogluconate. Is strictly specific to substrates with 5'- phosphates and shows no activity against nucleoside 2'- or 3'- monophosphates. Might be involved in the pyrimidine nucleotide substrate cycles
Gene Name:
yjjG
Uniprot ID:
P0A8Y1
Molecular weight:
25300
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
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
Uniprot ID:
P0AE22
Molecular weight:
26103
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.
General function:
Involved in nucleoside-triphosphate diphosphatase activity
Specific function:
Specific function unknown
Gene Name:
mazG
Uniprot ID:
P0AEY3
Molecular weight:
30412
Reactions
ATP + H(2)O = AMP + diphosphate.
General function:
Involved in thymidine kinase activity
Specific function:
Phosphorylates both thymidine and deoxyuridine
Gene Name:
tdk
Uniprot ID:
P23331
Molecular weight:
23456
Reactions
ATP + thymidine = ADP + thymidine 5'-phosphate.
General function:
Involved in hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Specific function:
Catalyzes the hydrolysis of nucleoside triphosphates, with a preference for pyrimidine deoxynucleoside triphosphates (dUTP, dTTP and dCTP)
Gene Name:
nudI
Uniprot ID:
P52006
Molecular weight:
16371
Reactions
Nucleoside triphosphate + H(2)O = nucleoside monophosphate + diphosphate.
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows strict specificity toward deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. Might be involved in the regulation of all dNTP pools in E.coli
Gene Name:
yfbR
Uniprot ID:
P76491
Molecular weight:
22708
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.

Transporters

General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368