Deoxyuridine (PAMDB000002)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000002
Identification
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.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 1-(2-Deoxy-b-D-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-b-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-b-delta-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-b-delta-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-b-δ-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-b-δ-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  • 1-(2-Deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  • 1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  • 1-(2-Deoxy-beta-delta-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione
  • 1-(2-Deoxy-D-erythro-pentofuranosyl)uracil
  • 1-(2-Deoxy-delta-erythro-pentofuranosyl)uracil
  • 1-(2-Deoxy-β-D-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-β-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-β-δ-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-β-δ-ribofuranosyl)-2,4(1H,3H)-pyrimidinedione
  • 1-(2-Deoxy-δ-erythro-pentofuranosyl)uracil
  • 2'-Deoxyuridine
  • 2'-Desoxyuridine
  • Deoxyribose uracil
  • Desoxyuridine
  • DUri
  • Uracil deoxyriboside
  • Uracil desoxyuridine
Chemical Formula: C9H12N2O5
Average Molecular Weight: 228.202
Monoisotopic Molecular Weight: 228.074621504
InChI Key: MXHRCPNRJAMMIM-SHYZEUOFSA-N
InChI: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
CAS number: 951-78-0
IUPAC Name:1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name: 2'-deoxyuridine
SMILES:OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct Parent Pyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Pyrimidone
  • Pyrimidine
  • Hydropyrimidine
  • Saccharide
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Urea
  • Secondary alcohol
  • Lactam
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: 167 °C
Experimental Properties:
PropertyValueSource
LogP:-1.51 [BALZARINI,JM ET AL. (1989)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility90.6 mg/mLALOGPS
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 Area99.1 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity51.05 m3·mol-1ChemAxon
Polarizability21.06 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
dUMP + Water > Deoxyuridine + Phosphate
Deoxyuridine + Phosphate <> Deoxyribose 1-phosphate + Uracil
Adenosine triphosphate + Deoxyuridine > ADP + dUMP + Hydrogen ion
Deoxycytidine + Hydrogen ion + Water > Deoxyuridine + Ammonium
Adenosine triphosphate + Deoxyuridine <> ADP + dUMP
Deoxycytidine + Water <> Deoxyuridine + Ammonia
Deoxyuridine + Phosphate <> deoxyribose-1-phosphate + Uracil
Cytidine + Water + Deoxycytidine <> Uridine + Ammonia + Deoxyuridine
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0udi-0900000000-c680f47a48626bc1de41View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0udi-0900000000-13135426d5efdf47090cView in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0v4i-2910000000-b0c82cef369c86d585bcView in MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0udi-2900000000-c2cdba9e46defe05a225View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-1900000000-6610506190427bbb3b6cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03di-9800000000-af237f79161aa13a5893View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-022d-9100000000-a06cdd7ea870d049c8a9View in MoNA
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Akhrem, A.A. et al., Org. Magn. Reson., 1979, 12, 247, (cmr)
  • Aldrich Library of 13C and 1H FT NMR Spectra, 1992, 3, 374B, (nmr)
  • Aldrich Library of FT-IR Spectra, 1st edn., 1985, 2, 816A, (ir)
  • Barr, P.J. et al., Tetrahedron, 1980, 36, 1269, (cryst struct)
  • Dematte, N. et al., Comp. Biochem. Physiol., B: Comp. Biochem., 1986, 84, 11, (isol, acid)
  • 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
  • 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
  • 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
  • Fox, J.J. et al., Adv. Carbohydr. Chem., 1959, 14, 283, (rev)
  • 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
  • Hruska, F.E. et al., Can. J. Chem., 1974, 52, 497, (conformn, pmr)
  • 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
  • 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
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Kikugawa, K. et al., Chem. Pharm. Bull., 1969, 17, 785, (synth, deriv)
  • Komori, T. et al., Annalen, 1980, 653-668, (isol)
  • 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
  • Lidgren, G. et al., J. Nat. Prod., 1988, 51, 1277-1280, (2'-Deoxy-3-methyluridine)
  • Ludwig, J. et al., Synthesis, 1982, 32-34, (5'-phosphate)
  • Rahman, A. et al., Acta Cryst. B, 1972, 28, 2260, (cryst struct)
  • Reidy JA: Deoxyuridine increases folate-sensitive fragile site expression in human lymphocytes. Am J Med Genet. 1987 Jan;26(1):1-5. Pubmed: 3812550
  • 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
  • Rimerman, R.A. et al., J. Chromatogr., B: Biomed. Appl., 1993, 619, 29-35, (5'-triphosphate)
  • Sakema, S. et al., Comp. Biochem. Physiol., B: Comp. Biochem., 1985, 82, 107-109, (isol)
  • Schinazi, R.F. et al., J. Med. Chem., 1978, 21, 1141, (synth, acid)
  • Sprecher, C.A. et al., Biopolymers, 1977, 16, 2243, (cd)
  • 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
  • U.S. Pat., 1966, 3 280 104, CA, 66, 38207y
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
  • Zittoun J, Zittoun R: Modern clinical testing strategies in cobalamin and folate deficiency. Semin Hematol. 1999 Jan;36(1):35-46. Pubmed: 9930567
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)
External Links:
ResourceLink
CHEBI ID16450
HMDB IDHMDB00012
Pubchem Compound ID13712
Kegg IDC00526
ChemSpider ID13118
WikipediaDeoxyuridine
BioCyc IDDEOXYURIDINE
EcoCyc IDDEOXYURIDINE
Ligand ExpoDUR

Enzymes

Protein Details
• Multifunctional protein surE
General function:
Involved in hydrolase activity
Specific function:
Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'- monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain- length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs. Also plays a significant physiological role in stress-response and is required for the survival of Pseudomonas aeruginosa in stationary growth phase
Gene Name:
surE
Locus Tag:
PA3625
Molecular weight:
26.4 kDa
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate.
Protein Details
• Class B acid phosphatase
General function:
Involved in acid phosphatase activity
Specific function:
Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:
aphA
Locus Tag:
PA1409
Molecular weight:
38 kDa
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.

Transporters