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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:44:42 UTC
HMDB IDHMDB0000012
Secondary Accession Numbers
  • HMDB00012
Metabolite Identification
Common NameDeoxyuridine
DescriptionDeoxyuridine, also known as dU, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. It is similar in chemical structure to uridine, but without the 2'-hydroxyl group. Deoxyuridine exists in all living organisms, ranging from bacteria to humans. Within humans, deoxyuridine participates in a number of enzymatic reactions. In particular, deoxyuridine can be biosynthesized from deoxycytidine through its interaction with the enzyme cytidine deaminase. In addition, deoxyuridine can be converted into uracil and deoxyribose 1-phosphate through its interaction with the enzyme thymidine phosphorylase. Deoxyuridine is considered to be an antimetabolite that is converted into deoxyuridine triphosphate during DNA synthesis. Laboratory suppression of deoxyuridine is used to diagnose megaloblastic anemia due to vitamin B12 and folate deficiencies. In humans, deoxyuridine is involved in the metabolic disorder called UMP synthase deficiency (orotic aciduria). Outside of the human body, deoxyuridine has been detected, but not quantified in, several different foods, such as lichee, highbush blueberries, agaves, macadamia nut (M. tetraphylla), and red bell peppers. This could make deoxyuridine a potential biomarker for the consumption of these foods.
Structure
Data?1582752107
Synonyms
ValueSource
2-DeoxyuridineChEBI
dUChEBI
2'-DeoxyuridineKegg
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'-DesoxyuridineHMDB
Deoxyribose uracilHMDB
DesoxyuridineHMDB
Uracil deoxyribosideHMDB
Uracil desoxyuridineHMDB
(beta 1-(2-Deoxyribopyranosyl))thymidineHMDB
DeoxyuridineChEBI
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
Description Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct ParentPyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Pyrimidone
  • Hydropyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Vinylogous amide
  • Lactam
  • Secondary alcohol
  • Urea
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Disposition
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point167 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-1.51BALZARINI,JM ET AL. (1989)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Baker151.64430932474
[M-H]-Not Available149.1http://allccs.zhulab.cn/database/detail?ID=AllCCS00000094
Predicted Molecular 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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+149.9231661259
DarkChem[M-H]-149.08131661259
AllCCS[M+H]+150.79232859911
AllCCS[M-H]-149.61132859911
DeepCCS[M+H]+155.2330932474
DeepCCS[M-H]-152.83530932474
DeepCCS[M-2H]-186.04630932474
DeepCCS[M+Na]+161.14330932474
AllCCS[M+H]+150.832859911
AllCCS[M+H-H2O]+147.032859911
AllCCS[M+NH4]+154.432859911
AllCCS[M+Na]+155.432859911
AllCCS[M-H]-149.632859911
AllCCS[M+Na-2H]-149.732859911
AllCCS[M+HCOO]-149.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
DeoxyuridineOC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O3237.8Standard polar33892256
DeoxyuridineOC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O2205.1Standard non polar33892256
DeoxyuridineOC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=O)NC1=O2386.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Deoxyuridine,1TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O2254.6Semi standard non polar33892256
Deoxyuridine,1TMS,isomer #2C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1CO2287.1Semi standard non polar33892256
Deoxyuridine,1TMS,isomer #3C[Si](C)(C)N1C(=O)C=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C1=O2319.1Semi standard non polar33892256
Deoxyuridine,2TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O[Si](C)(C)C2260.2Semi standard non polar33892256
Deoxyuridine,2TMS,isomer #2C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O2329.4Semi standard non polar33892256
Deoxyuridine,2TMS,isomer #3C[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)O[C@@H]1CO2334.8Semi standard non polar33892256
Deoxyuridine,3TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O[Si](C)(C)C2350.5Semi standard non polar33892256
Deoxyuridine,3TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O[Si](C)(C)C2455.2Standard non polar33892256
Deoxyuridine,3TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C)C2=O)C[C@@H]1O[Si](C)(C)C2627.7Standard polar33892256
Deoxyuridine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O2512.4Semi standard non polar33892256
Deoxyuridine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)[NH]C2=O)O[C@@H]1CO2524.5Semi standard non polar33892256
Deoxyuridine,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)N1C(=O)C=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C1=O2545.3Semi standard non polar33892256
Deoxyuridine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)[NH]C2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C2714.5Semi standard non polar33892256
Deoxyuridine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O2784.0Semi standard non polar33892256
Deoxyuridine,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)O[C@@H]1CO2796.4Semi standard non polar33892256
Deoxyuridine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C3014.6Semi standard non polar33892256
Deoxyuridine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C3067.8Standard non polar33892256
Deoxyuridine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C2903.6Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Deoxyuridine GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0udi-0900000000-c680f47a48626bc1de412014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Deoxyuridine GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0udi-0900000000-13135426d5efdf47090c2014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Deoxyuridine GC-MS (3 TMS)splash10-0v4i-2910000000-b0c82cef369c86d585bc2014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Deoxyuridine GC-MS (3 TMS)splash10-0udi-2900000000-c2cdba9e46defe05a2252014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Deoxyuridine GC-EI-TOF (Non-derivatized)splash10-0udi-0900000000-c680f47a48626bc1de412017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Deoxyuridine GC-EI-TOF (Non-derivatized)splash10-0udi-0900000000-13135426d5efdf47090c2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Deoxyuridine GC-MS (Non-derivatized)splash10-0v4i-2910000000-b0c82cef369c86d585bc2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Deoxyuridine GC-MS (Non-derivatized)splash10-0udi-2900000000-c2cdba9e46defe05a2252017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-01r7-9610000000-dfaab249ec8e9361b4bf2017-08-28Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (2 TMS) - 70eV, Positivesplash10-0g06-9621000000-32e72b8293f4e226223b2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Deoxyuridine GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-03di-1900000000-6610506190427bbb3b6c2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-03di-9800000000-af237f79161aa13a58932012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-022d-9100000000-a06cdd7ea870d049c8a92012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Linear Ion Trap , negative-QTOFsplash10-001r-0900000000-87d0da98372c9c5a167a2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Linear Ion Trap , negative-QTOFsplash10-001r-0900000000-795c89de7cd09998501c2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Linear Ion Trap , negative-QTOFsplash10-03di-0910000000-0f40c1aaec53591fe03d2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Linear Ion Trap , negative-QTOFsplash10-03di-0900000000-35312c7170aff90afa682017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Linear Ion Trap , negative-QTOFsplash10-004i-0090000000-dd791cff5aab8928952f2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Linear Ion Trap , negative-QTOFsplash10-004i-0090000000-e5c282f6027560386d072017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine , negative-QTOFsplash10-001l-5900000000-4660ec5181499087824f2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Linear Ion Trap , positive-QTOFsplash10-001i-0910000000-8cef8299b80deeefe1ae2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine Linear Ion Trap , positive-QTOFsplash10-001i-0900000000-043d88b7ac473889f3192017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine 20V, Negative-QTOFsplash10-0006-9100000000-5731c423bed1902e4aa12021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine 10V, Negative-QTOFsplash10-000x-9820000000-29ea64a90c8736117d032021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine 40V, Positive-QTOFsplash10-006t-9400000000-edbb071fcbfdfc740d5c2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine 10V, Positive-QTOFsplash10-03di-2910000000-76f9f11531932d11318e2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine 20V, Positive-QTOFsplash10-03di-4900000000-996ec7312bb565deb6f82021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine 35V, Negative-QTOFsplash10-001i-0900000000-45855a2f2673a9e095e82021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Deoxyuridine 40V, Positive-QTOFsplash10-006w-9100000000-75bb83f5ee43bb79add32021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyuridine 10V, Positive-QTOFsplash10-03di-1900000000-4e3e387ebbab12abe1fd2017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyuridine 20V, Positive-QTOFsplash10-03di-5900000000-e483c01cc3a2bd6439c12017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyuridine 40V, Positive-QTOFsplash10-03di-9800000000-e0e5bb84af10a0c46b952017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyuridine 10V, Negative-QTOFsplash10-0036-8960000000-f6a195e38452cd824d192017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyuridine 20V, Negative-QTOFsplash10-000f-7910000000-8de672c701d38c2dd5d32017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Deoxyuridine 40V, Negative-QTOFsplash10-00kf-9100000000-6e86ecc024dbcde80d902017-07-26Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue Locations
  • Bladder
  • Bone Marrow
  • Fibroblasts
  • Intestine
  • Leukocyte
  • Neuron
  • Pancreas
  • Placenta
  • Prostate
  • Skeletal Muscle
  • Testis
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified<0.1 uMAdult (>18 years old)Not SpecifiedNormal details
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 QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified0-2 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified<0.3 umol/mmol creatinineInfant (0-1 year old)Both
Normal
details
UrineDetected and Quantified1.00 (0.00-2.00) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified<1 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified20 uMAdult (>18 years old)MaleThymidine phosphorylase deficiency details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer
details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedCrohns disease details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedUlcerative colitis details
FecesDetected but not QuantifiedNot QuantifiedChildren (6 - 18 years old)Not SpecifiedUnclassified IBD details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
UrineDetected and Quantified1.195 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
details
UrineDetected and Quantified51 umol/mmol creatinineAdult (>18 years old)MaleThymidine phosphorylase deficiency details
Associated Disorders and Diseases
Disease References
Thymidine phosphorylase deficiency
  1. Bakker JA, Schlesser P, Smeets HJ, Francois B, Bierau J: Biochemical abnormalities in a patient with thymidine phosphorylase deficiency with fatal outcome. J Inherit Metab Dis. 2010 Dec;33 Suppl 3:S139-43. doi: 10.1007/s10545-010-9049-y. Epub 2010 Feb 12. [PubMed:20151198 ]
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  2. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  3. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Crohn's disease
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Ulcerative colitis
  1. Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDDB02256
Phenol Explorer Compound IDNot Available
FooDB IDFDB021870
KNApSAcK IDC00019697
Chemspider ID13118
KEGG Compound IDC00526
BioCyc IDDEOXYURIDINE
BiGG ID35251
Wikipedia LinkDeoxyuridine
METLIN ID5086
PubChem Compound13712
PDB IDNot Available
ChEBI ID16450
Food Biomarker OntologyNot Available
VMH IDDURI
MarkerDB IDMDB00000006
Good Scents IDNot Available
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. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
  13. (). Akhrem, A.A. et al., Org. Magn. Reson., 1979, 12, 247, (cmr). .
  14. (). Fox, J.J. et al., Adv. Carbohydr. Chem., 1959, 14, 283, (rev). .
  15. (). Rimerman, R.A. et al., J. Chromatogr., B: Biomed. Appl., 1993, 619, 29-35, (5'-triphosphate). .
  16. (). Schinazi, R.F. et al., J. Med. Chem., 1978, 21, 1141, (synth, acid). .
  17. (). Barr, P.J. et al., Tetrahedron, 1980, 36, 1269, (cryst struct). .
  18. (). Ludwig, J. et al., Synthesis, 1982, 32-34, (5'-phosphate). .
  19. (). Dematte, N. et al., Comp. Biochem. Physiol., B: Comp. Biochem., 1986, 84, 11, (isol, acid). .
  20. (). Rahman, A. et al., Acta Cryst. B, 1972, 28, 2260, (cryst struct). .
  21. (). Sakema, S. et al., Comp. Biochem. Physiol., B: Comp. Biochem., 1985, 82, 107-109, (isol). .
  22. (). Aldrich Library of FT-IR Spectra, 1st edn., 1985, 2, 816A, (ir). .
  23. (). Kikugawa, K. et al., Chem. Pharm. Bull., 1969, 17, 785, (synth, deriv). .
  24. (). Sprecher, C.A. et al., Biopolymers, 1977, 16, 2243, (cd). .
  25. (). Komori, T. et al., Annalen, 1980, 653-668, (isol). .
  26. (). Aldrich Library of 13C and 1H FT NMR Spectra, 1992, 3, 374B, (nmr). .
  27. (). Hruska, F.E. et al., Can. J. Chem., 1974, 52, 497, (conformn, pmr). .
  28. (). U.S. Pat., 1966, 3 280 104, CA, 66, 38207y. .
  29. (). 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 + Phosphate → 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 + Phosphate → 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