Record Information
Version2.0
Creation Date2012-05-31 09:55:14 -0600
Update Date2015-09-13 12:56:05 -0600
Secondary Accession Numbers
  • ECMDB00012
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
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
Weight:Average: 228.202
Monoisotopic: 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
DescriptionThis compound belongs to the class of chemical entities known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleosides
Direct ParentPyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Pyrimidone
  • Hydropyrimidine
  • Pyrimidine
  • Oxolane
  • Heteroaromatic compound
  • Vinylogous amide
  • Lactam
  • Secondary alcohol
  • Urea
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Primary alcohol
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic 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:
SMPDB Pathways:
Pyrimidine metabolismPW000942 Pw000942Pw000942 greyscalePw000942 simple
pyrimidine deoxyribonucleosides degradationPW002063 Pw002063Pw002063 greyscalePw002063 simple
salvage pathways of pyrimidine deoxyribonucleotidesPW002061 Pw002061Pw002061 greyscalePw002061 simple
KEGG Pathways:
EcoCyc Pathways:
  • pyrimidine deoxyribonucleosides degradation PWY0-1298
  • salvage pathways of pyrimidine deoxyribonucleotides PWY0-181
Concentrations
Not Available
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
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , positivesplash10-001i-0910000000-8cef8299b80deeefe1aeView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , positivesplash10-001i-0900000000-043d88b7ac473889f319View 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

General function:
Involved in hydrolase activity
Specific function:
Degradation of external UDP-glucose to uridine monophosphate and glucose-1-phosphate, which can then be used by the cell
Gene Name:
ushA
Uniprot ID:
P07024
Molecular weight:
60824
Reactions
UDP-sugar + H(2)O = UMP + alpha-D-aldose 1-phosphate.
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis
Gene Name:
deoA
Uniprot ID:
P07650
Molecular weight:
47207
Reactions
Thymidine + phosphate = thymine + 2-deoxy-alpha-D-ribose 1-phosphate.
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 E.coli in stationary growth phase
Gene Name:
surE
Uniprot ID:
P0A840
Molecular weight:
26900
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.
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows high phosphatase activity toward three nucleoside 5'-monophosphates, UMP, dUMP, and dTMP, and very low activity against TDP, IMP, UDP, GMP, dGMP, AMP, dAMP, and 6- phosphogluconate. Is strictly specific to substrates with 5'- phosphates and shows no activity against nucleoside 2'- or 3'- monophosphates. Might be involved in the pyrimidine nucleotide substrate cycles
Gene Name:
yjjG
Uniprot ID:
P0A8Y1
Molecular weight:
25300
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
General function:
Involved in zinc ion binding
Specific function:
This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis
Gene Name:
cdd
Uniprot ID:
P0ABF6
Molecular weight:
31539
Reactions
Cytidine + H(2)O = uridine + NH(3).
General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules
Gene Name:
deoD
Uniprot ID:
P0ABP8
Molecular weight:
25950
Reactions
Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
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
Uniprot ID:
P0AE22
Molecular weight:
26103
Reactions
A phosphate monoester + H(2)O = an alcohol + phosphate.
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1- phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis
Gene Name:
udp
Uniprot ID:
P12758
Molecular weight:
27159
Reactions
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.
General function:
Involved in thymidine kinase activity
Specific function:
Phosphorylates both thymidine and deoxyuridine
Gene Name:
tdk
Uniprot ID:
P23331
Molecular weight:
23456
Reactions
ATP + thymidine = ADP + thymidine 5'-phosphate.
General function:
Involved in catalytic activity
Specific function:
Nucleotidase that shows strict specificity toward deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. Might be involved in the regulation of all dNTP pools in E.coli
Gene Name:
yfbR
Uniprot ID:
P76491
Molecular weight:
22708
Reactions
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate.

Transporters

General function:
Involved in nucleoside:sodium symporter activity
Specific function:
Transports nucleosides with a high affinity except guanosine and deoxyguanosine. Driven by a proton motive force
Gene Name:
nupC
Uniprot ID:
P0AFF2
Molecular weight:
43475
General function:
Involved in nucleoside transmembrane transporter activity
Specific function:
Transports nucleosides with a high affinity. Driven by a proton motive force
Gene Name:
nupG
Uniprot ID:
P0AFF4
Molecular weight:
46389
General function:
Involved in nucleoside:sodium symporter activity
Specific function:
Nucleoside transporter
Gene Name:
nupX
Uniprot ID:
P33021
Molecular weight:
43409
General function:
Involved in nucleoside transmembrane transporter activity
Specific function:
Constitutes the receptor for colicin K and phage T6, and functions as substrate-specific channel for nucleosides and deoxynucleosides
Gene Name:
tsx
Uniprot ID:
P0A927
Molecular weight:
33589