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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-07-04 18:58:38 UTC
Update Date2021-09-14 15:44:46 UTC
HMDB IDHMDB0060774
Secondary Accession Numbers
  • HMDB60774
Metabolite Identification
Common Name5-Carboxy-2'-deoxyuridine
Description5-Carboxy-2'-deoxyuridine 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. 5-Carboxy-2'-deoxyuridine is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-Carboxy-2'-deoxyuridine is a metabolite of trifluridine. Trifluridine (also called trifluorothymidine or TFT) is an anti-herpesvirus antiviral drug, used primarily on the eye. The brand is now owned by Monarch Pharmaceuticals, which is wholly owned by King Pharmaceuticals. It was sold under the trade name, Viroptic, by Glaxo Wellcome, now merged into GlaxoSmithKline.
Structure
Data?1563866103
SynonymsNot Available
Chemical FormulaC10H12N2O7
Average Molecular Weight272.2115
Monoisotopic Molecular Weight272.064450748
IUPAC Name4-hydroxy-1-[(2S,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid
Traditional Name4-hydroxy-1-[(2S,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-oxopyrimidine-5-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC[C@H]1O[C@@H](C[C@@H]1O)N1C=C(C(O)=O)C(O)=NC1=O
InChI Identifier
InChI=1S/C10H12N2O7/c13-3-6-5(14)1-7(19-6)12-2-4(9(16)17)8(15)11-10(12)18/h2,5-7,13-14H,1,3H2,(H,16,17)(H,11,15,18)/t5-,6+,7-/m0/s1
InChI KeyGAGYTXTVUMXAOC-XVMARJQXSA-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
  • Hydropyrimidine carboxylic acid derivative
  • Pyrimidine-5-carboxylic acid
  • Pyrimidine-5-carboxylic acid or derivatives
  • Pyrimidone
  • Hydropyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Lactam
  • Urea
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organopnictogen compound
  • Primary alcohol
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location

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
Water Solubility9.54 g/LALOGPS
logP-1.7ALOGPS
logP-1.6ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)2.94ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area139.89 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity57.45 m³·mol⁻¹ChemAxon
Polarizability24.11 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]+163.15431661259
DarkChem[M-H]-158.39631661259
DeepCCS[M+H]+160.48130932474
DeepCCS[M-H]-158.12330932474
DeepCCS[M-2H]-191.84530932474
DeepCCS[M+Na]+167.07230932474
AllCCS[M+H]+159.432859911
AllCCS[M+H-H2O]+155.832859911
AllCCS[M+NH4]+162.732859911
AllCCS[M+Na]+163.632859911
AllCCS[M-H]-157.132859911
AllCCS[M+Na-2H]-156.932859911
AllCCS[M+HCOO]-156.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Carboxy-2'-deoxyuridineOC[C@H]1O[C@@H](C[C@@H]1O)N1C=C(C(O)=O)C(O)=NC1=O3702.8Standard polar33892256
5-Carboxy-2'-deoxyuridineOC[C@H]1O[C@@H](C[C@@H]1O)N1C=C(C(O)=O)C(O)=NC1=O2345.2Standard non polar33892256
5-Carboxy-2'-deoxyuridineOC[C@H]1O[C@@H](C[C@@H]1O)N1C=C(C(O)=O)C(O)=NC1=O2718.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5-Carboxy-2'-deoxyuridine,1TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O)C(O)=NC2=O)C[C@@H]1O2548.1Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,1TMS,isomer #2C[Si](C)(C)O[C@H]1C[C@@H](N2C=C(C(=O)O)C(O)=NC2=O)O[C@@H]1CO2583.8Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,1TMS,isomer #3C[Si](C)(C)OC(=O)C1=CN([C@@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N=C1O2545.8Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,1TMS,isomer #4C[Si](C)(C)OC1=NC(=O)N([C@@H]2C[C@H](O)[C@@H](CO)O2)C=C1C(=O)O2542.0Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O[Si](C)(C)C)C(O)=NC2=O)C[C@@H]1O2512.3Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TMS,isomer #2C[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O)C(O[Si](C)(C)C)=NC2=O)C[C@@H]1O2509.3Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TMS,isomer #3C[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O)C(O)=NC2=O)C[C@@H]1O[Si](C)(C)C2508.5Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TMS,isomer #4C[Si](C)(C)OC(=O)C1=CN([C@@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C(=O)N=C1O2531.6Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TMS,isomer #5C[Si](C)(C)OC1=NC(=O)N([C@@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C=C1C(=O)O2512.2Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TMS,isomer #6C[Si](C)(C)OC(=O)C1=CN([C@@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N=C1O[Si](C)(C)C2507.4Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,3TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O[Si](C)(C)C)C(O[Si](C)(C)C)=NC2=O)C[C@@H]1O2511.9Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,3TMS,isomer #2C[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O[Si](C)(C)C)C(O)=NC2=O)C[C@@H]1O[Si](C)(C)C2487.5Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,3TMS,isomer #3C[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O)C(O[Si](C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C2486.8Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,3TMS,isomer #4C[Si](C)(C)OC(=O)C1=CN([C@@H]2C[C@H](O[Si](C)(C)C)[C@@H](CO)O2)C(=O)N=C1O[Si](C)(C)C2531.8Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,4TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O[Si](C)(C)C)C(O[Si](C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C2526.0Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O)C(O)=NC2=O)C[C@@H]1O2812.9Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H]1C[C@@H](N2C=C(C(=O)O)C(O)=NC2=O)O[C@@H]1CO2822.6Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(=O)C1=CN([C@@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N=C1O2782.4Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC1=NC(=O)N([C@@H]2C[C@H](O)[C@@H](CO)O2)C=C1C(=O)O2761.9Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O[Si](C)(C)C(C)(C)C)C(O)=NC2=O)C[C@@H]1O2966.7Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O)C(O[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O2966.6Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O)C(O)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C3011.6Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)C1=CN([C@@H]2C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C(=O)N=C1O3003.4Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)OC1=NC(=O)N([C@@H]2C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C=C1C(=O)O2989.3Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)OC(=O)C1=CN([C@@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C2942.2Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O3146.7Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O[Si](C)(C)C(C)(C)C)C(O)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C3197.1Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O)C(O[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C3190.6Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)C1=CN([C@@H]2C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O2)C(=O)N=C1O[Si](C)(C)C(C)(C)C3184.9Semi standard non polar33892256
5-Carboxy-2'-deoxyuridine,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@H](N2C=C(C(=O)O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)=NC2=O)C[C@@H]1O[Si](C)(C)C(C)(C)C3368.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-Carboxy-2'-deoxyuridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-9150000000-2946360e0e25245c068c2017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Carboxy-2'-deoxyuridine GC-MS (4 TMS) - 70eV, Positivesplash10-0fdk-7630970000-117d98baf16585de770b2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Carboxy-2'-deoxyuridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 10V, Positive-QTOFsplash10-0a4i-0900000000-8dcdbe4fcfcf7a6956cb2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 20V, Positive-QTOFsplash10-08g0-0930000000-9ee8a94b476d98a3a8c32017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 40V, Positive-QTOFsplash10-0a4i-3900000000-9ecf758850c12eb66ff82017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 10V, Negative-QTOFsplash10-00bi-0490000000-64cf18129521933ef7ba2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 20V, Negative-QTOFsplash10-053i-1930000000-c909ceba26c11bd00a6f2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 40V, Negative-QTOFsplash10-03di-3900000000-931397545a462bf568062017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 10V, Positive-QTOFsplash10-0ab9-0940000000-cdfc60660b28e1eeee7d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 20V, Positive-QTOFsplash10-000i-0900000000-9593d082c851d2af5c1a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 40V, Positive-QTOFsplash10-06s9-1900000000-3c073d3e3469f89a92f02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 10V, Negative-QTOFsplash10-00di-0490000000-c1e941310a4160ade1f72021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 20V, Negative-QTOFsplash10-08g0-1910000000-0de3c739cc69cb102f022021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Carboxy-2'-deoxyuridine 40V, Negative-QTOFsplash10-000f-6900000000-eaec1bdad7fc9f8adb6b2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView 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 IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound189023
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 ReferencesNot Available