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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 01:00:20 UTC
Update Date2021-09-14 15:18:57 UTC
HMDB IDHMDB0060406
Secondary Accession Numbers
  • HMDB60406
Metabolite Identification
Common Name5'-Deoxy-5-fluorouridine
Description5'-Deoxy-5-fluorouridine, also known as 5'-DFUR or 5-fluoro-5'-deoxyuridine, belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. 5'-Deoxy-5-fluorouridine is an extremely weak basic (essentially neutral) compound (based on its pKa). 5'-Deoxy-5-fluorouridine is a metabolite of capecitabine. Within humans, 5'-deoxy-5-fluorouridine participates in a number of enzymatic reactions. In particular, 5'-deoxy-5-fluorouridine can be converted into fluorouracil and 5-deoxyribose-1-phosphate through the action of the enzyme thymidine phosphorylase. In addition, 5'-deoxy-5-fluorouridine and meprobamate can be biosynthesized from capecitabine through its interaction with the enzymes liver carboxylesterase 1 and cytidine deaminase. Capecitabine is a prodrug, that is enzymatically converted to 5-fluorouracil in the tumor, where it inhibits DNA synthesis and slows growth of tumor tissue. In humans, 5'-deoxy-5-fluorouridine is involved in capecitabine action pathway. Capecitabine (Xeloda, Roche) is an orally-administered chemotherapeutic agent used in the treatment of metastatic breast and colorectal cancers.
Structure
Data?1563866056
Synonyms
ValueSource
1-(beta-D-5-Desoxyribofuranoxyl)-5-fluoruracilChEBI
5'-DFURChEBI
5'-DFUrdChEBI
5-Fluoro-5'-deoxyuridineChEBI
DoxifluridinaChEBI
DoxifluridinumChEBI
FurtulonChEBI
Ro 21-9738ChEBI
Ro 219738ChEBI
DoxifluridineKegg
1-(b-D-5-Desoxyribofuranoxyl)-5-fluoruracilGenerator
1-(Β-D-5-desoxyribofuranoxyl)-5-fluoruracilGenerator
5'-Deoxy-5'-fluorouridineHMDB
5'-Fluoro-5'-deoxyuridineHMDB
DoxyfluridineHMDB
5'-Deoxy-5-fluorouridineMeSH
Chemical FormulaC9H11FN2O5
Average Molecular Weight246.1924
Monoisotopic Molecular Weight246.065199677
IUPAC Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-methyloxolan-2-yl]-5-fluoro-4-hydroxy-1,2-dihydropyrimidin-2-one
Traditional Namedoxifluridine
CAS Registry NumberNot Available
SMILES
C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(O)=NC1=O
InChI Identifier
InChI=1S/C9H11FN2O5/c1-3-5(13)6(14)8(17-3)12-2-4(10)7(15)11-9(12)16/h2-3,5-6,8,13-14H,1H3,(H,11,15,16)/t3-,5-,6-,8-/m1/s1
InChI KeyZWAOHEXOSAUJHY-ZIYNGMLESA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
Class5'-deoxyribonucleosides
Sub ClassNot Available
Direct Parent5'-deoxyribonucleosides
Alternative Parents
Substituents
  • 5'-deoxyribonucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Halopyrimidine
  • Pyrimidone
  • Aryl fluoride
  • Aryl halide
  • Pyrimidine
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Urea
  • Secondary alcohol
  • 1,2-diol
  • Lactam
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organopnictogen compound
  • Organohalogen compound
  • Organofluoride
  • Organonitrogen compound
  • Organooxygen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Biological role:

Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility5.36 g/LALOGPS
logP-0.82ALOGPS
logP-0.8ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)6.2ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area102.59 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity51.55 m³·mol⁻¹ChemAxon
Polarizability21.06 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Collision Cross Sections

NameAdductTypeData SourceValueReference

Retention Indices

Underivatized

Not Available

Derivatized

DerivativeValueReference
5'-Deoxy-5-fluorouridine,1TMS,#12098.8538https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,1TMS,#22118.824https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,1TMS,#32063.039https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,2TMS,#12098.797https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,2TMS,#22119.8486https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,2TMS,#32111.9548https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,3TMS,#12151.0938https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,1TBDMS,#12352.8936https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,1TBDMS,#22371.5083https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,1TBDMS,#32298.0222https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,2TBDMS,#12572.9504https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,2TBDMS,#22612.307https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,2TBDMS,#32583.4604https://arxiv.org/abs/1905.12712
5'-Deoxy-5-fluorouridine,3TBDMS,#12801.6902https://arxiv.org/abs/1905.12712
Spectra

GC-MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-056u-9210000000-68ddd4a6bcf1d8ff7c3f2017-09-20View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-00tk-6976700000-d826a815dab6401bbc3d2017-10-06View Spectrum

LC-MS/MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0910000000-7e78eab45706c44d825f2016-08-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-1900000000-17e125f0d2b5d65e776e2016-08-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03e9-9400000000-4647ffbb75476b52110a2016-08-01View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004l-5950000000-62edf53c23a7fcae3dde2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-4930000000-e1442f1a62dab8ca8e792016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-583eee0dde55403044a42016-08-03View Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB12947
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC12739
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound18343
PDB IDNot Available
ChEBI ID31521
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

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
5'-Deoxy-5-fluorouridine + Phosphate → Fluorouracil + 5-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
5'-Deoxy-5-fluorocytidine + Water → 5'-Deoxy-5-fluorouridine + Ammoniadetails