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Record Information
Version1.0
Creation Date2016-09-30 22:18:25 UTC
Update Date2020-05-21 16:29:01 UTC
BMDB IDBMDB0000012
Secondary Accession Numbers
  • BMDB00012
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. Deoxyuridine is an extremely weak basic (essentially neutral) compound (based on its pKa). Deoxyuridine exists in all living organisms, ranging from bacteria to humans. Deoxyuridine is a potentially toxic compound.
Structure
Thumb
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
StatusDetected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • 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
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
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
  • Mitochondria
  • Nucleus
Biospecimen Locations
  • Bladder
  • Bone Marrow
  • Fibroblasts
  • Intestine
  • Leukocyte
  • Neuron
  • Pancreas
  • Placenta
  • Prostate Tissue
  • Ruminal Fluid
  • Skeletal Muscle
  • Testis
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BladderExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Bone MarrowExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
FibroblastsExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
IntestineExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
LeukocyteExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
NeuronExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
PancreasExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
PlacentaExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Prostate TissueExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Ruminal FluidDetected but not QuantifiedNot ApplicableNot SpecifiedNot Specified
Normal
details
Skeletal MuscleExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
TestisExpected but not QuantifiedNot ApplicableNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Abnormal Concentrations
Not Available
HMDB IDHMDB0000012
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
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)Not Available
General ReferencesNot Available

Enzymes

General function:
Not Available
Specific function:
Not Available
Gene Name:
TK1
Uniprot ID:
A5D7R8
Molecular weight:
26377.0
Reactions
Deoxyuridine + Adenosine triphosphate → dUMP + ADPdetails