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Record Information
Version4.0
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-09-27 06:44:08 UTC
HMDB IDHMDB0000012
Secondary Accession Numbers
  • HMDB00012
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
ValueSource
2-DeoxyuridineChEBI
dUChEBI
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-delta-ribofuranosyl)-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-D-erythro-pentofuranosyl)uracilHMDB
1-(2-Deoxy-delta-erythro-pentofuranosyl)uracilHMDB
2'-DeoxyuridineHMDB
2'-DesoxyuridineHMDB
Deoxyribose uracilHMDB
DesoxyuridineHMDB
Uracil deoxyribosideHMDB
Uracil desoxyuridineHMDB
(beta 1-(2-Deoxyribopyranosyl))thymidineMeSH
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 Name2'-deoxyuridine
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
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
Ontology
Disposition

Biological Location:

  Subcellular:

  Biofluid and excreta:

  Organ and components:

  Tissue and substructures:

  Cell and elements:

    Cell:

Source:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Role

Industrial application:

  Pharmaceutical industry:

Indirect biological role:

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 Area99.1 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity51.05 m³·mol⁻¹ChemAxon
Polarizability21.06 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0udi-0900000000-c680f47a48626bc1de41View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)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
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-0900000000-c680f47a48626bc1de41View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-0900000000-13135426d5efdf47090cView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0v4i-2910000000-b0c82cef369c86d585bcView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0udi-2900000000-c2cdba9e46defe05a225View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-01r7-9610000000-dfaab249ec8e9361b4bfView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0g06-9621000000-32e72b8293f4e226223bView 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 , negativesplash10-001r-0900000000-87d0da98372c9c5a167aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-001r-0900000000-795c89de7cd09998501cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-03di-0910000000-0f40c1aaec53591fe03dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-03di-0900000000-35312c7170aff90afa68View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-004i-0090000000-dd791cff5aab8928952fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Linear Ion Trap , negativesplash10-004i-0090000000-e5c282f6027560386d07View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-001l-5900000000-4660ec5181499087824fView 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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-4e3e387ebbab12abe1fdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-5900000000-e483c01cc3a2bd6439c1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-9800000000-e0e5bb84af10a0c46b95View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0036-8960000000-f6a195e38452cd824d19View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000f-7910000000-8de672c701d38c2dd5d3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kf-9100000000-6e86ecc024dbcde80d90View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue Location
  • Bladder
  • Bone Marrow
  • Fibroblasts
  • Intestine
  • Lymphocyte
  • Most Tissues
  • Muscle
  • Neuron
  • Pancreas
  • Placenta
  • Prostate
  • Testes
Pathways
NameSMPDB/PathwhizKEGG
Beta Ureidopropionase DeficiencyPw000187Pw000187 greyscalePw000187 simpleNot Available
Dihydropyrimidinase DeficiencyPw000189Pw000189 greyscalePw000189 simpleNot Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)Pw000190Pw000190 greyscalePw000190 simpleNot Available
Pyrimidine MetabolismPw000160Pw000160 greyscalePw000160 simpleMap00240
UMP Synthase Deficiency (Orotic Aciduria)Pw000188Pw000188 greyscalePw000188 simpleNot Available
Displaying all 5 entries
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
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedNormal details
UrineDetected and Quantified0-2 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified1.00 (0.00-2.00) umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)BothColorectal Cancer details
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedCrohns disease details
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedUlcerative colitis details
FecesDetected but not Quantified Children (6 - 18 years old)Not SpecifiedUnclassified IBD details
FecesDetected but not Quantified Adult (>18 years old)BothColorectal Cancer details
UrineDetected and Quantified1.195 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
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
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. doi: 10.1038/nature07762. [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