Human Metabolome Database Version 3.5

Showing metabocard for 5-Thymidylic acid (HMDB01227)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-05-29 13:30:50 -0600
HMDB ID HMDB01227
Secondary Accession Numbers None
Metabolite Identification
Common 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. In mammalian cells, thymidine deprivation induces chromosome aberrations such as chromatid breaks, chromatid interchanges, and chromosome fragmentation. (PMID 3888175 Link_out).
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. 2'-Deoxythymidine 5'-monophosphate
  2. 5'-dTMP
  3. 5'-Thymidylate
  4. 5'-Thymidylic acid
  5. 5'-TMP
  6. 5-Methyl-dUMP
  7. Deoxy TMP
  8. Deoxyribosylthymine monophosphate
  9. Deoxythymidine 5'-monophosphate
  10. Deoxythymidine 5'-phosphate
  11. Deoxythymidine monophosphate
  12. Deoxythymidylate
  13. Deoxythymidylic acid
  14. Deoxythymydilate
  15. Deoxythymydilic acid
  16. dTMP
  17. Thymidine 5'-monophosphate
  18. Thymidine 5'-phosphate
  19. Thymidine 5'-phosphorate
  20. Thymidine 5'-phosphoric acid
  21. Thymidine 5'MP
  22. Thymidine mononucleotide
  23. Thymidine monophosphate
  24. Thymidine phosphate
  25. Thymidine-5'-monophosphorate
  26. Thymidine-5'-monophosphoric acid
  27. Thymidylate
  28. Thymidylic acid
Chemical Formula C10H15N2O8P
Average Molecular Weight 322.2085
Monoisotopic Molecular Weight 322.056601978
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 IUPAC Name [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3H-pyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid
CAS Registry Number 365-07-1
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 Key GYOZYWVXFNDGLU-XLPZGREQSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Pyrimidine Nucleotides
Sub Class Pyrimidine Deoxyribonucleotides
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • Deoxyribonucleotides(KEGG)
  • Pyrimidine Deoxyribonucleotides
  • thymidine 5'-monophosphate(ChEBI)
Substituents
  • Hydropyrimidine
  • Organic Hypophosphite
  • Organic Phosphite
  • Oxolane
  • Phosphoric Acid Ester
  • Pyrimidine
  • Pyrimidone
  • Secondary Alcohol
Direct Parent Pyrimidine 2'-deoxyribonucleoside Monophosphates
Ontology
Status Expected and Not Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
  • DNA component
Application Not Available
Cellular locations
  • Mitochondria
  • Lysosome
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 6.78 g/L ALOGPS
LogP -1.37 ALOGPS
LogP -1.2 ChemAxon
LogS -1.68 ALOGPS
pKa (strongest acidic) 1.23 ChemAxon
pKa (strongest basic) -3.2 ChemAxon
Hydrogen Acceptor Count 7 ChemAxon
Hydrogen Donor Count 4 ChemAxon
Polar Surface Area 145.63 A2 ChemAxon
Rotatable Bond Count 4 ChemAxon
Refractivity 66.28 ChemAxon
Polarizability 27.58 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -2 ChemAxon
Spectra
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum LC-ESI-QTOF (UPLC Q-Tof Premier, Waters)
[1H,1H] 2D NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Mitochondria
  • Lysosome
Biofluid Locations Not Available
Tissue Location
  • Fibroblasts
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID Not Available
DrugBank Metabolite ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB022499
KNApSAcK ID Not Available
Chemspider ID 9319 Link_out
KEGG Compound ID C00364 Link_out
BioCyc ID TMP Link_out
BiGG ID 34753 Link_out
Wikipedia Link dTMP Link_out
NuGOwiki Link HMDB01227 Link_out
Metagene Link HMDB01227 Link_out
METLIN ID 6092 Link_out
PubChem Compound 9700 Link_out
PDB ID DT Link_out
ChEBI ID 17013 Link_out
References
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)
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 Link_out
  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 Link_out
  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 Link_out
  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 Link_out

Enzymes
Name: 5'-nucleotidase
Reactions:
5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
Gene Name: NT5E
Uniprot ID: P21589 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytosolic 5'-nucleotidase 1B
Reactions:
5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
Gene Name: NT5C1B
Uniprot ID: Q96P26 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytosolic 5'-nucleotidase 1A
Reactions:
5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
Gene Name: NT5C1A
Uniprot ID: Q9BXI3 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 5'(3')-deoxyribonucleotidase, cytosolic type
Reactions:
5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
Gene Name: NT5C
Uniprot ID: Q8TCD5 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 5'(3')-deoxyribonucleotidase, mitochondrial
Reactions:
5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
Gene Name: NT5M
Uniprot ID: Q9NPB1 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Thymidylate kinase
Reactions:
Adenosine triphosphate + 5-Thymidylic acid unknown ADP + dTDP details
Gene Name: DTYMK
Uniprot ID: P23919 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 1
Reactions:
dTDP + Water unknown 5-Thymidylic acid + Phosphoric acid details
Gene Name: ENTPD1
Uniprot ID: P49961 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Soluble calcium-activated nucleotidase 1
Reactions: Not Available
Gene Name: CANT1
Uniprot ID: Q8WVQ1 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 3
Reactions:
dTDP + Water unknown 5-Thymidylic acid + Phosphoric acid details
Gene Name: ENTPD3
Uniprot ID: O75355 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytosolic 5'-nucleotidase 3
Reactions:
5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
Gene Name: NT5C3
Uniprot ID: Q9H0P0 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytosolic purine 5'-nucleotidase
Reactions:
5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
Gene Name: NT5C2
Uniprot ID: P49902 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Thymidine kinase, cytosolic
Reactions:
Adenosine triphosphate + Thymidine unknown ADP + 5-Thymidylic acid details
Gene Name: TK1
Uniprot ID: P04183 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Thymidine kinase 2, mitochondrial
Reactions:
Adenosine triphosphate + Thymidine unknown ADP + 5-Thymidylic acid details
Gene Name: TK2
Uniprot ID: O00142 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Thymidylate synthase
Reactions:
5,10-Methylene-THF + dUMP unknown Dihydrofolic acid + 5-Thymidylic acid details
Gene Name: TYMS
Uniprot ID: P04818 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleoside triphosphate diphosphohydrolase 8
Reactions:
dTDP + Water unknown 5-Thymidylic acid + Phosphoric acid details
Gene Name: ENTPD8
Uniprot ID: Q5MY95 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Thymidine kinase
Reactions: Not Available
Gene Name: Not Available
Uniprot ID: Q8IZR3 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA