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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2013-02-09 00:07:45 UTC
HMDB IDHMDB00012
Secondary Accession NumbersNone
Metabolite Identification
Common NameDeoxyuridine
Description2'-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
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 FormulaC9H12N2O5
Average Molecular Weight228.202
Monoisotopic Molecular Weight228.074621504
IUPAC Name1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Namedeoxyuridine
CAS Registry Number951-78-0
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 KeyMXHRCPNRJAMMIM-SHYZEUOFSA-N
Chemical Taxonomy
KingdomOrganic Compounds
Super ClassNucleosides, Nucleotides, and Analogues
ClassPyrimidine Nucleosides and Analogues
Sub ClassPyrimidine 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 ParentPyrimidine 2'-deoxyribonucleosides and Analogues
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • DNA component
ApplicationNot Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point167 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-1.51BALZARINI,JM ET AL. (1989)
Predicted Properties
PropertyValueSource
water solubility90.6 g/LALOGPS
logP-1.5ALOGPS
logP-1.5ChemAxon
logS-0.4ALOGPS
pKa (strongest acidic)9.71ChemAxon
pKa (strongest basic)-3ChemAxon
physiological charge0ChemAxon
hydrogen acceptor count5ChemAxon
hydrogen donor count3ChemAxon
polar surface area99.1ChemAxon
rotatable bond count2ChemAxon
refractivity51.05ChemAxon
polarizability21.06ChemAxon
Spectra
SpectraGC-MSMS/MS1D NMR2D NMR
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • Bladder
  • Bone Marrow
  • Fibroblasts
  • Intestine
  • Lymphocyte
  • Most Tissues
  • Muscle
  • Neuron
  • Pancreas
  • Placenta
  • Prostate
  • Testes
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046map00240
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.052 (0.049-0.056) uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.200 (0.100-0.300) uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.6 +/- 0.6 uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0 - 0.1 uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified1.00 (0.00-2.00) umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
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 IDFDB021870
KNApSAcK IDNot Available
Chemspider ID13118
KEGG Compound IDC00526
BioCyc IDDEOXYURIDINE
BiGG ID35251
Wikipedia LinkDeoxyuridine
NuGOwiki LinkHMDB00012
Metagene LinkHMDB00012
METLIN ID5086
PubChem Compound13712
PDB IDDUR
ChEBI ID16450
References
Synthesis ReferenceHuang, 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
  2. 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
  3. 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
  4. Reidy JA: Deoxyuridine increases folate-sensitive fragile site expression in human lymphocytes. Am J Med Genet. 1987 Jan;26(1):1-5. Pubmed: 3812550
  5. 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
  6. 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
  7. 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
  8. Zittoun J, Zittoun R: Modern clinical testing strategies in cobalamin and folate deficiency. Semin Hematol. 1999 Jan;36(1):35-46. Pubmed: 9930567
  9. 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
  10. 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
  11. 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
  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

General function:
Involved in zinc ion binding
Specific function:
Not Available
Gene Name:
AID
Uniprot ID:
Q546Y9
Molecular weight:
23953.3
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:
PNP
Uniprot ID:
P00491
Molecular weight:
32117.69
Reactions
Deoxyuridine + Phosphoric acid → Uracil + Deoxyribose 1-phosphatedetails
General function:
Nucleotide transport and metabolism
Specific function:
Not Available
Gene Name:
TK1
Uniprot ID:
P04183
Molecular weight:
25468.455
Reactions
Adenosine triphosphate + Deoxyuridine → ADP + dUMPdetails
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 + Deoxyuridine → ADP + dUMPdetails
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
TYMP
Uniprot ID:
P19971
Molecular weight:
49954.965
Reactions
Deoxyuridine + Phosphoric acid → Uracil + Deoxyribose 1-phosphatedetails
General function:
Involved in zinc ion binding
Specific function:
This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Gene Name:
CDA
Uniprot ID:
P32320
Molecular weight:
16184.545
Reactions
Deoxycytidine + Water → Deoxyuridine + Ammoniadetails
General function:
Involved in ATP binding
Specific function:
May contribute to UTP accumulation needed for blast transformation and proliferation.
Gene Name:
UCKL1
Uniprot ID:
Q9NWZ5
Molecular weight:
59465.77
General function:
Involved in ATP binding
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q8IZR3
Molecular weight:
35439.6
General function:
Not Available
Specific function:
DNA deaminase (cytidine deaminase) that mediates a form of innate resistance to retroviral infections (at least to HIV-1 infection) by triggering G-to-A hypermutation in the newly synthesized viral DNA. The replacements C-to-U in the minus strand DNA of HIV-1 during reverse transcription, leads to G-to-A transitions in the plus strand. The inhibition of viral replication is either due to the degradation of the minus strand before its integration or to the lethality of the hypermutations. Modification of both DNA strands is not excluded. This antiviral activity is neutralized by the virion infectivity factor (VIF), that prevents the incorporation of APOBEC3G into progeny HIV-1 virions by both inhibiting its translation and/or by inducing its ubiquitination and subsequent degradation by the 26S proteasome. May also prevent the transposition of a subset of retroelements. Binds a variety of RNAs, but does not display detectable APOB, NF1 and NAT1 mRNA editing.
Gene Name:
APOBEC3G
Uniprot ID:
Q9HC16
Molecular weight:
11822.52
Reactions
Deoxycytidine + Water → Deoxyuridine + Ammoniadetails