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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:53:30 UTC
Update Date2021-09-26 22:56:13 UTC
HMDB IDHMDB0246881
Secondary Accession NumbersNone
Metabolite Identification
Common Name5'-Deoxy-5'-fluorouridine
Description5'-Deoxy-5'-fluorouridine 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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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. Based on a literature review very few articles have been published on 5'-Deoxy-5'-fluorouridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5'-deoxy-5'-fluorouridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5'-Deoxy-5'-fluorouridine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
SynonymsNot Available
Chemical FormulaC9H11FN2O5
Average Molecular Weight246.194
Monoisotopic Molecular Weight246.065199625
IUPAC Name1-[5-(fluoromethyl)-3,4-dihydroxyoxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name1-[5-(fluoromethyl)-3,4-dihydroxyoxolan-2-yl]-3H-pyrimidine-2,4-dione
CAS Registry NumberNot Available
SMILES
OC1C(O)C(OC1CF)N1C=CC(=O)NC1=O
InChI Identifier
InChI=1S/C9H11FN2O5/c10-3-4-6(14)7(15)8(17-4)12-2-1-5(13)11-9(12)16/h1-2,4,6-8,14-15H,3H2,(H,11,13,16)
InChI KeyJIWIXZJAAUQOCE-UHFFFAOYSA-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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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
  • N-glycosyl compound
  • Glycosyl compound
  • Pentose monosaccharide
  • Pyrimidone
  • Pyrimidine
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Urea
  • Secondary alcohol
  • Lactam
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organofluoride
  • Organohalogen compound
  • Alkyl halide
  • Alkyl fluoride
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.2ALOGPS
logP-1.5ChemAxon
logS-0.31ALOGPS
pKa (Strongest Acidic)9.85ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area99.1 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity50.87 m³·mol⁻¹ChemAxon
Polarizability21.29 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
DeepCCS[M+H]+143.29830932474
DeepCCS[M-H]-140.90330932474
DeepCCS[M-2H]-176.16830932474
DeepCCS[M+Na]+150.73730932474
AllCCS[M+H]+155.132859911
AllCCS[M+H-H2O]+151.332859911
AllCCS[M+NH4]+158.632859911
AllCCS[M+Na]+159.632859911
AllCCS[M-H]-151.332859911
AllCCS[M+Na-2H]-151.232859911
AllCCS[M+HCOO]-151.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5'-Deoxy-5'-fluorouridineOC1C(O)C(OC1CF)N1C=CC(=O)NC1=O3176.1Standard polar33892256
5'-Deoxy-5'-fluorouridineOC1C(O)C(OC1CF)N1C=CC(=O)NC1=O2285.3Standard non polar33892256
5'-Deoxy-5'-fluorouridineOC1C(O)C(OC1CF)N1C=CC(=O)NC1=O2251.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5'-Deoxy-5'-fluorouridine,3TMS,isomer #1C[Si](C)(C)OC1C(CF)OC(N2C=CC(=O)N([Si](C)(C)C)C2=O)C1O[Si](C)(C)C2314.1Semi standard non polar33892256
5'-Deoxy-5'-fluorouridine,3TMS,isomer #1C[Si](C)(C)OC1C(CF)OC(N2C=CC(=O)N([Si](C)(C)C)C2=O)C1O[Si](C)(C)C2307.2Standard non polar33892256
5'-Deoxy-5'-fluorouridine,3TMS,isomer #1C[Si](C)(C)OC1C(CF)OC(N2C=CC(=O)N([Si](C)(C)C)C2=O)C1O[Si](C)(C)C2324.6Standard polar33892256
5'-Deoxy-5'-fluorouridine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1C(CF)OC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C1O[Si](C)(C)C(C)(C)C3021.3Semi standard non polar33892256
5'-Deoxy-5'-fluorouridine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1C(CF)OC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C1O[Si](C)(C)C(C)(C)C2887.4Standard non polar33892256
5'-Deoxy-5'-fluorouridine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1C(CF)OC(N2C=CC(=O)N([Si](C)(C)C(C)(C)C)C2=O)C1O[Si](C)(C)C(C)(C)C2668.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-056r-9320000000-fbb2abccab1cbc454cbc2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5'-Deoxy-5'-fluorouridine GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5'-Deoxy-5'-fluorouridine 10V, Positive-QTOFsplash10-000i-2910000000-206469ce5df5433da6152021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5'-Deoxy-5'-fluorouridine 20V, Positive-QTOFsplash10-03dj-2920000000-e0191688fed25b8c64262021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5'-Deoxy-5'-fluorouridine 40V, Positive-QTOFsplash10-03dj-9500000000-f0f86eb5af973e54f0852021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5'-Deoxy-5'-fluorouridine 10V, Negative-QTOFsplash10-0gxt-1950000000-f8bcada99fc39ec7e96e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5'-Deoxy-5'-fluorouridine 20V, Negative-QTOFsplash10-02dl-6900000000-8e6027ed3a8d3021d89a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5'-Deoxy-5'-fluorouridine 40V, Negative-QTOFsplash10-0006-9400000000-53ac1301fcc9091abb392021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID255844
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound289972
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]