Human Metabolome Database Version 3.5

Showing metabocard for Deoxyuridine (HMDB00012)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:07:45 -0700
HMDB ID HMDB00012
Secondary Accession Numbers None
Metabolite Identification
Common Name Deoxyuridine
Description 2'-Deoxyuridine is a naturally occurring nucleoside. It is similar in chemical structure to uridine, but without the 2'-hydroxyl group. It is considered to be an antimetabolite that is converted to deoxyuridine triphosphate during DNA synthesis. Laboratory suppression of deoxyuridine is used to diagnose megaloblastic anemia due to vitamin B12 and folate deficiencies.
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. 1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  2. 1-(2-Deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  3. 1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  4. 1-(2-Deoxy-beta-delta-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  5. 1-(2-Deoxy-D-erythro-pentofuranosyl)uracil
  6. 1-(2-Deoxy-delta-erythro-pentofuranosyl)uracil
  7. 2'-Deoxyuridine
  8. 2'-Desoxyuridine
  9. Deoxyribose uracil
  10. Desoxyuridine
  11. Uracil deoxyriboside
  12. Uracil desoxyuridine
Chemical Formula C9H12N2O5
Average Molecular Weight 228.202
Monoisotopic Molecular Weight 228.074621504
IUPAC Name 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name deoxyuridine
CAS Registry Number 951-78-0
SMILES OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O
InChI Identifier InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1
InChI Key MXHRCPNRJAMMIM-SHYZEUOFSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Pyrimidine Nucleosides and Analogues
Sub Class Pyrimidine 2'-deoxyribonucleosides and Analogues
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • Deoxyribonucleosides(KEGG)
  • Organic Compounds
  • pyrimidine 2'-deoxyribonucleoside(ChEBI)
Substituents
  • Hydropyrimidine
  • Oxolane
  • Primary Alcohol
  • Pyrimidine
  • Pyrimidone
  • Secondary Alcohol
Direct Parent Pyrimidine 2'-deoxyribonucleosides and Analogues
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • DNA component
Application Not Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Nucleus
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 167 °C Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP -1.51 BALZARINI,JM ET AL. (1989)
Predicted Properties
Property Value Source
Water Solubility 90.6 g/L ALOGPS
LogP -1.49 ALOGPS
LogP -1.5 ChemAxon
LogS -0.40 ALOGPS
pKa (strongest acidic) 9.71 ChemAxon
pKa (strongest basic) -3 ChemAxon
Hydrogen Acceptor Count 5 ChemAxon
Hydrogen Donor Count 3 ChemAxon
Polar Surface Area 99.1 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 51.05 ChemAxon
Polarizability 21.06 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 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 GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies )
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies )
MS/MS Spectrum GC-MS
MS/MS Spectrum GC-MS
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • Muscle
  • Bladder
  • Bone Marrow
  • Fibroblasts
  • Intestine
  • Lymphocyte
  • Most Tissues
  • Neuron
  • Pancreas
  • Placenta
  • Testes
  • Prostate
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
0.052 (0.049-0.056) uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
0.200 (0.100-0.300) uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
0.6 +/- 0.6 uM Adult (>18 years old) Both Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
0 - 0.1 uM Adult (>18 years old) Both Normal
Urine Detected and Quantified
1.00 (0.00-2.00) umol/mmol creatinine Adult (>18 years old) Both Normal
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 FDB021870
KNApSAcK ID Not Available
Chemspider ID 13118 Link_out
KEGG Compound ID C00526 Link_out
BioCyc ID DEOXYURIDINE Link_out
BiGG ID 35251 Link_out
Wikipedia Link Deoxyuridine Link_out
NuGOwiki Link HMDB00012 Link_out
Metagene Link HMDB00012 Link_out
METLIN ID 5086 Link_out
PubChem Compound 13712 Link_out
PDB ID DUR Link_out
ChEBI ID 16450 Link_out
References
Synthesis Reference Huang, Haoqiang; Chu, Chung K. A practical synthesis of 2'-deoxyuridine from uridine. Synthetic Communications (1990), 20(7), 1039-46.
Material Safety Data Sheet (MSDS) Download (PDF)
General References
  1. Li KM, Rivory LP, Clarke SJ: Rapid quantitation of plasma 2'-deoxyuridine by high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry and its application to pharmacodynamic studies in cancer patients. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Jun 5;820(1):121-30. Epub 2005 Apr 19. Pubmed: 15866500 Link_out
  2. Di Stefano G, Busi C, Derenzini M, Trere D, Fiume L: Conjugation of 5-fluoro-2'-deoxyuridine with lactosaminated poly-l-lysine to reduce extrahepatic toxicity in the treatment of hepatocarcinomas. Ital J Gastroenterol Hepatol. 1998 Apr;30(2):173-7. Pubmed: 9675653 Link_out
  3. Reidy JA: Deoxyuridine increases folate-sensitive fragile site expression in human lymphocytes. Am J Med Genet. 1987 Jan;26(1):1-5. Pubmed: 3812550 Link_out
  4. Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. Pubmed: 6656991 Link_out
  5. Huong PL, Kolk AH, Eggelte TA, Verstijnen CP, Gilis H, Hendriks JT: Measurement of antigen specific lymphocyte proliferation using 5-bromo-deoxyuridine incorporation. An easy and low cost alternative to radioactive thymidine incorporation. J Immunol Methods. 1991 Jul 5;140(2):243-8. Pubmed: 1906076 Link_out
  6. Kanazawa S, Herbert V: Detection of folate deficiency in alcoholism using the peripheral blood lymphocyte deoxyuridine suppression test. J Nutr Sci Vitaminol (Tokyo). 1986 Jun;32(3):251-7. Pubmed: 3761048 Link_out
  7. Zittoun J, Zittoun R: Modern clinical testing strategies in cobalamin and folate deficiency. Semin Hematol. 1999 Jan;36(1):35-46. Pubmed: 9930567 Link_out
  8. Fairbanks LD, Marinaki AM, Carrey EA, Hammans SR, Duley JA: Deoxyuridine accumulation in urine in thymidine phosphorylase deficiency (MNGIE). J Inherit Metab Dis. 2002 Nov;25(7):603-4. Pubmed: 12638947 Link_out
  9. Remacha A, Barcelo MJ, Pastor M, Ubeda J, Espadaler M, Gimferrer E: The deoxyuridine suppression test in peripheral lymphocytes. Eur J Haematol. 1990 Mar;44(3):196-200. Pubmed: 2328792 Link_out
  10. Galanis E, Goldberg R, Reid J, Atherton P, Sloan J, Pitot H, Rubin J, Adjei AA, Burch P, Safgren SL, Witzig TE, Ames MM, Erlichman C: Phase I trial of sequential administration of raltitrexed (Tomudex) and 5-iodo-2'-deoxyuridine (IdUrd). Ann Oncol. 2001 May;12(5):701-7. Pubmed: 11432631 Link_out
  11. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411 Link_out
  12. Akhrem, A.A. et al., Org. Magn. Reson., 1979, 12, 247, (cmr)
  13. Fox, J.J. et al., Adv. Carbohydr. Chem., 1959, 14, 283, (rev)
  14. Rimerman, R.A. et al., J. Chromatogr., B: Biomed. Appl., 1993, 619, 29-35, (5'-triphosphate)
  15. Schinazi, R.F. et al., J. Med. Chem., 1978, 21, 1141, (synth, acid)
  16. Barr, P.J. et al., Tetrahedron, 1980, 36, 1269, (cryst struct)
  17. Ludwig, J. et al., Synthesis, 1982, 32-34, (5'-phosphate)
  18. Dematte, N. et al., Comp. Biochem. Physiol., B: Comp. Biochem., 1986, 84, 11, (isol, acid)
  19. Rahman, A. et al., Acta Cryst. B, 1972, 28, 2260, (cryst struct)
  20. Sakema, S. et al., Comp. Biochem. Physiol., B: Comp. Biochem., 1985, 82, 107-109, (isol)
  21. Aldrich Library of FT-IR Spectra, 1st edn., 1985, 2, 816A, (ir)
  22. Kikugawa, K. et al., Chem. Pharm. Bull., 1969, 17, 785, (synth, deriv)
  23. Sprecher, C.A. et al., Biopolymers, 1977, 16, 2243, (cd)
  24. Komori, T. et al., Annalen, 1980, 653-668, (isol)
  25. Aldrich Library of 13C and 1H FT NMR Spectra, 1992, 3, 374B, (nmr)
  26. Hruska, F.E. et al., Can. J. Chem., 1974, 52, 497, (conformn, pmr)
  27. U.S. Pat., 1966, 3 280 104, CA, 66, 38207y
  28. Lidgren, G. et al., J. Nat. Prod., 1988, 51, 1277-1280, (2'-Deoxy-3-methyluridine)

Enzymes
Name: AID
Reactions: Not Available
Gene Name: AID
Uniprot ID: Q546Y9 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Purine nucleoside phosphorylase
Reactions:
Deoxyuridine + Phosphoric acid unknown Uracil + Deoxyribose 1-phosphate details
Gene Name: PNP
Uniprot ID: P00491 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Thymidine kinase, cytosolic
Reactions:
Adenosine triphosphate + Deoxyuridine unknown ADP + dUMP details
Gene Name: TK1
Uniprot ID: P04183 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Thymidine kinase 2, mitochondrial
Reactions:
Adenosine triphosphate + Deoxyuridine unknown ADP + dUMP details
Gene Name: TK2
Uniprot ID: O00142 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Thymidine phosphorylase
Reactions:
Deoxyuridine + Phosphoric acid unknown Uracil + Deoxyribose 1-phosphate details
Gene Name: TYMP
Uniprot ID: P19971 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytidine deaminase
Reactions:
Deoxycytidine + Water unknown Deoxyuridine + Ammonia details
Gene Name: CDA
Uniprot ID: P32320 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Uridine-cytidine kinase-like 1
Reactions: Not Available
Gene Name: UCKL1
Uniprot ID: Q9NWZ5 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
Name: DNA dC->dU-editing enzyme APOBEC-3G
Reactions:
Deoxycytidine + Water unknown Deoxyuridine + Ammonia details
Gene Name: APOBEC3G
Uniprot ID: Q9HC16 Link_out
Protein Sequence: FASTA