Showing metabocard for 5-Thymidylic acid (BMDB0001227)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (4) Show 4 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:42:45 UTC
Update Date2020-05-21 16:29:01 UTC
BMDB IDBMDB0001227
Secondary Accession Numbers
  • BMDB01227
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. 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. Within cattle, 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; which is mediated by the enzyme thymidylate synthase. In addition, 5-thymidylic acid can be converted into dTDP through its interaction with the enzyme thymidylate synthase. In cattle, 5-thymidylic acid is involved in the metabolic pathway called the pyrimidine metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
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
StatusDetected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Lysosome
  • Mitochondria
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
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
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
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-2233c579a23110abe895View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-9af792986db292f0d8d1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9010000000-9936ff7b595382418b7cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9200000000-5c7a9e2c6c970eec2d92View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-edfd7498bf3ebaedbb4bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-001i-9000000000-9dafb0586b1aadb8475dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-001i-9100000000-b286ae95b38725486f5bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-c716e9bc2009f1adb3aeView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-ec3ffc3673cc769d3a0eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-004i-8900000000-90b7e520ce562f39a280View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-004i-7900000000-a01024a3e21d2de7f133View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-004j-5900000000-57620f7a2b0abf78c220View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-004i-8900000000-b0b0ac82c08ccb2ea84eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-006t-0905000000-49f5a9d8a112c369032dView 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 Spectrum (1D, 500 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, D2O, experimental)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
2D NMR[1H, 1H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Lysosome
  • Mitochondria
Biospecimen Locations
  • Fibroblasts
  • Mammary Gland
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FibroblastsExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0001227
DrugBank IDDB01643
Phenol Explorer Compound IDNot Available
FooDB IDFDB030840
KNApSAcK IDC00019637
Chemspider ID9319
KEGG Compound IDC00364
BioCyc IDTMP
BiGG ID34753
Wikipedia LinkThymidine_monophosphate
METLIN ID6092
PubChem Compound9700
PDB IDNot Available
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)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Cytosolic purine 5'-nucleotidase
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:
O46411
Molecular weight:
64841.0
Reactions
5-Thymidylic acid + Water → Thymidine + Hydrogen phosphatedetails
Enzyme Details
2. Thymidylate synthase
General function:
Nucleotide transport and metabolism
Specific function:
Contributes to the de novo mitochondrial thymidylate biosynthesis pathway.
Gene Name:
TYMS
Uniprot ID:
Q2TA32
Molecular weight:
39785.0
Reactions
dUMP + 5,10-Methylene-THF → 5-Thymidylic acid + Dihydrofolic aciddetails
5-Thymidylic acid + Adenosine triphosphate → dTDP + ADPdetails
Enzyme Details
3. Calcium activated nucleotidase 1
General function:
Not Available
Specific function:
Not Available
Gene Name:
CANT1
Uniprot ID:
E1BGL5
Molecular weight:
44706.0
Reactions
dTDP + Water → 5-Thymidylic acid + Hydrogen phosphatedetails
Enzyme Details
4. Thymidine kinase, cytosolic
General function:
Not Available
Specific function:
Not Available
Gene Name:
TK1
Uniprot ID:
A5D7R8
Molecular weight:
26377.0
Reactions
Thymidine + Adenosine triphosphate → 5-Thymidylic acid + ADPdetails