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Record Information
Version4.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-07-23 05:44:48 UTC
HMDB IDHMDB0001227
Secondary Accession Numbers
  • HMDB01227
Metabolite Identification
Common Name5-Thymidylic acid
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. dTMP consists of a phosphate group, the pentose sugar deoxyribose, and the nucleobase thymine. 5-Thymidylic acid is a drug. As a substituent, it is called by the prefix thymidylyl-. Unlike the other deoxyribonucleotides, thymidine monophosphate often does not contain the "deoxy" prefix in its name; nevertheless, its symbol often includes a "d" ("dTMP"). 5-Thymidylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). It is an ester of phosphoric acid with the nucleoside thymidine. 5-Thymidylic acid exists in all living species, ranging from bacteria to humans. Within humans, 5-thymidylic acid participates in a number of enzymatic reactions. In particular, 5-thymidylic acid and dihydrofolic acid can be biosynthesized from dUMP and 5,10-methylene-THF through its interaction with the enzyme thymidylate synthase. In addition, 5-thymidylic acid can be converted into dTDP through its interaction with the enzyme thymidylate synthase. In humans, 5-thymidylic acid is involved in the metabolic disorder called the beta-ureidopropionase deficiency pathway. Outside of the human body, 5-thymidylic acid has been detected, but not quantified in, several different foods, such as rosemaries, epazotes, chinese chives, gooseberries, and coconuts. This could make 5-thymidylic acid a potential biomarker for the consumption of these foods. Dorland’s Illustrated Medical Dictionary provides an explanation of the nomenclature variation at its entry for thymidine.
Structure
Data?1563860688
Synonyms
ValueSource
(DT)1ChEBI
5'-Thymidylic acidChEBI
5'-TMPChEBI
5-Methyl-dUMPChEBI
Deoxyribosylthymine monophosphateChEBI
Ribothymidine 5'-monophosphateChEBI
Thymidine 5'-(dihydrogen phosphate)ChEBI
Thymidine 5'-phosphateChEBI
Thymidine 5'-phosphoric acidChEBI
Thymidine monophosphateChEBI
Thymidine-5'-monophosphoric acidChEBI
THYMIDINE-5'-phosphATEChEBI
ThymidylateChEBI
Thymidylic acidChEBI
TMPChEBI
Deoxythymidine 5'-phosphateKegg
Deoxythymidylic acidKegg
5'-ThymidylateGenerator
Deoxyribosylthymine monophosphoric acidGenerator
Ribothymidine 5'-monophosphoric acidGenerator
Thymidine 5'-(dihydrogen phosphoric acid)Generator
Thymidine monophosphoric acidGenerator
Thymidine-5'-monophosphateGenerator
THYMIDINE-5'-phosphoric acidGenerator
Deoxythymidine 5'-phosphoric acidGenerator
DeoxythymidylateGenerator
5-ThymidylateGenerator
2'-Deoxythymidine 5'-monophosphateHMDB
5'-dTMPHMDB
Deoxy TMPHMDB
Deoxythymidine 5'-monophosphateHMDB
Deoxythymidine monophosphateHMDB
DeoxythymydilateHMDB
Deoxythymydilic acidHMDB
dTMPHMDB
Thymidine 5'-monophosphateHMDB
Thymidine 5'-phosphorateHMDB
Thymidine 5'MPHMDB
Thymidine mononucleotideHMDB
Thymidine phosphateHMDB
Thymidine-5'-monophosphorateHMDB
Thymidylic acidsHMDB
Acids, thymidylicHMDB
Acid, thymidylicHMDB
monoPhosphate, thymidineHMDB
Chemical FormulaC10H15N2O8P
Average Molecular Weight322.2085
Monoisotopic Molecular Weight322.056601978
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 Namethymidylate
CAS Registry Number365-07-1
SMILES
CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(O)=O)O2)C(=O)NC1=O
InChI Identifier
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
InChI KeyGYOZYWVXFNDGLU-XLPZGREQSA-N
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
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
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
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
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
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
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
Biological Properties
Cellular Locations
  • Mitochondria
  • Lysosome
Biospecimen Locations
  • Feces
Tissue Locations
  • Fibroblasts
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)Both
Colorectal cancer
details
FecesDetected but not Quantified Adult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDDB01643
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022499
KNApSAcK IDC00019637
Chemspider ID9319
KEGG Compound IDC00364
BioCyc IDNot Available
BiGG ID34753
Wikipedia LinkThymidine_monophosphate
METLIN ID6092
PubChem Compound9700
PDB IDNot Available
ChEBI ID17013
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceScarano, 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)
General References
  1. 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 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]

Only showing the first 10 proteins. There are 16 proteins in total.

Enzymes

General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:
NT5E
Uniprot ID:
P21589
Molecular weight:
57948.125
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphatedetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Molecular weight:
68803.055
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphatedetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Molecular weight:
41020.145
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphatedetails
General function:
Involved in metal ion binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Molecular weight:
Not Available
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphatedetails
General function:
Involved in phosphatase activity
Specific function:
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Molecular weight:
Not Available
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphatedetails
General function:
Involved in thymidylate kinase activity
Specific function:
Catalyzes the conversion of dTMP to dTDP.
Gene Name:
DTYMK
Uniprot ID:
P23919
Molecular weight:
23819.105
Reactions
Adenosine triphosphate + 5-Thymidylic acid → ADP + dTDPdetails
General function:
Involved in hydrolase activity
Specific function:
In the nervous system, could hydrolyze ATP and other nucleotides to regulate purinergic neurotransmission. Could also be implicated in the prevention of platelet aggregation by hydrolyzing platelet-activating ADP to AMP. Hydrolyzes ATP and ADP equally well.
Gene Name:
ENTPD1
Uniprot ID:
P49961
Molecular weight:
58706.0
Reactions
dTDP + Water → 5-Thymidylic acid + Phosphatedetails
General function:
Involved in calcium ion binding
Specific function:
Calcium-dependent nucleotidase with a preference for UDP. The order of activity with different substrates is UDP > GDP > UTP > GTP. Has very low activity towards ADP and even lower activity towards ATP. Does not hydrolyze AMP and GMP. Involved in proteoglycan synthesis.
Gene Name:
CANT1
Uniprot ID:
Q8WVQ1
Molecular weight:
44839.24
General function:
Involved in hydrolase activity
Specific function:
Has a threefold preference for the hydrolysis of ATP over ADP.
Gene Name:
ENTPD3
Uniprot ID:
O75355
Molecular weight:
59104.76
Reactions
dTDP + Water → 5-Thymidylic acid + Phosphatedetails
General function:
Involved in magnesium ion binding
Specific function:
Can act both as nucleotidase and as phosphotransferase.
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Molecular weight:
33914.91
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphatedetails

Only showing the first 10 proteins. There are 16 proteins in total.