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Record Information
Version4.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-07 01:23:27 UTC
HMDB IDHMDB0001227
Secondary Accession Numbers
  • HMDB01227
Metabolite Identification
Common Name5-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. In mammalian cells, thymidine deprivation induces chromosome aberrations such as chromatid breaks, chromatid interchanges, and chromosome fragmentation. (PMID 3888175 ).
Structure
Thumb
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
5-ThymidylateGenerator
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
2'-Deoxythymidine 5'-monophosphateHMDB
5'-dTMPHMDB
Deoxy TMPHMDB
Deoxythymidine 5'-monophosphateHMDB
Deoxythymidine 5'-phosphateHMDB
Deoxythymidine monophosphateHMDB
DeoxythymidylateHMDB
Deoxythymidylic acidHMDB
DeoxythymydilateHMDB
Deoxythymydilic acidHMDB
dTMPHMDB
Thymidine 5'-monophosphateHMDB
Thymidine 5'-phosphorateHMDB
Thymidine 5'MPHMDB
Thymidine mononucleotideHMDB
Thymidine phosphateHMDB
Thymidine-5'-monophosphorateHMDB
Thymidylic acidsMeSH
Acids, thymidylicMeSH
Acid, thymidylicMeSH
Monophosphate, thymidineMeSH
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
DescriptionThis compound 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

Biological Location:

  Subcellular:

  Cell and elements:

    Cell:

  Biofluid and excreta:

Source:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Role

Industrial application:

  Pharmaceutical industry:

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
Polarizability27.56 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
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
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
Biological Properties
Cellular Locations
  • Mitochondria
  • Lysosome
Biofluid Locations
  • Feces
Tissue Location
  • Fibroblasts
Pathways
NameSMPDB/PathwhizKEGG
Beta Ureidopropionase DeficiencyPw000187Pw000187 greyscalePw000187 simpleNot Available
Dihydropyrimidinase DeficiencyPw000189Pw000189 greyscalePw000189 simpleNot Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)Pw000190Pw000190 greyscalePw000190 simpleNot Available
Pyrimidine MetabolismPw000160Pw000160 greyscalePw000160 simpleMap00240
UMP Synthase Deficiency (Orotic Aciduria)Pw000188Pw000188 greyscalePw000188 simpleNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022499
KNApSAcK IDNot Available
Chemspider ID9319
KEGG Compound IDC00364
BioCyc IDTMP
BiGG ID34753
Wikipedia LinkdTMP
METLIN ID6092
PubChem Compound9700
PDB IDDT
ChEBI ID17013
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 ]

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 + Phosphoric aciddetails
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 + Phosphoric aciddetails
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 + Phosphoric aciddetails
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 + Phosphoric aciddetails
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 + Phosphoric aciddetails
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 + Phosphoric aciddetails
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 + Phosphoric aciddetails
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 + Phosphoric aciddetails
General function:
Involved in 5'-nucleotidase activity
Specific function:
May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:
NT5C2
Uniprot ID:
P49902
Molecular weight:
64969.2
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphoric aciddetails
General function:
Nucleotide transport and metabolism
Specific function:
Not Available
Gene Name:
TK1
Uniprot ID:
P04183
Molecular weight:
25468.455
Reactions
Adenosine triphosphate + Thymidine → ADP + 5-Thymidylic aciddetails
General function:
Involved in ATP binding
Specific function:
Deoxyribonucleoside kinase that phosphorylates thymidine, deoxycytidine, and deoxyuridine. Also phosphorylates anti-viral and anti-cancer nucleoside analogs.
Gene Name:
TK2
Uniprot ID:
O00142
Molecular weight:
27561.495
Reactions
Adenosine triphosphate + Thymidine → ADP + 5-Thymidylic aciddetails
General function:
Involved in thymidylate synthase activity
Specific function:
Contributes to the de novo mitochondrial thymidylate biosynthesis pathway.
Gene Name:
TYMS
Uniprot ID:
P04818
Molecular weight:
35715.65
Reactions
5,10-Methylene-THF + dUMP → Dihydrofolic acid + 5-Thymidylic aciddetails
General function:
Involved in hydrolase activity
Specific function:
Canalicular ectonucleoside NTPDase responsible for the main hepatic NTPDase activity. Ectonucleoside NTPDases catalyze the hydrolysis of gamma- and beta-phosphate residues of nucleotides, playing a central role in concentration of extracellular nucleotides. Has activity toward ATP, ADP, UTP and UDP, but not toward AMP.
Gene Name:
ENTPD8
Uniprot ID:
Q5MY95
Molecular weight:
53903.14
Reactions
dTDP + Water → 5-Thymidylic acid + Phosphoric aciddetails
General function:
Involved in ATP binding
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q8IZR3
Molecular weight:
35439.6