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Record Information
Version4.0
Creation Date2013-05-17 01:00:16 UTC
Update Date2017-09-27 08:43:46 UTC
HMDB IDHMDB0060405
Secondary Accession Numbers
  • HMDB60405
Metabolite Identification
Common Name5'-Deoxy-5-fluorocytidine
Description5'-Deoxy-5-fluorocytidine is a metabolite of capecitabine. Capecitabine (Xeloda, Roche) is an orally-administered chemotherapeutic agent used in the treatment of metastatic breast and colorectal cancers. 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. (Wikipedia)
Structure
Thumb
SynonymsNot Available
Chemical FormulaC9H12FN3O4
Average Molecular Weight245.2077
Monoisotopic Molecular Weight245.081184092
IUPAC Name(2R,3R,4S,5R)-2-(5-fluoro-2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-5-methyloxolane-3,4-diol
Traditional Name5'-deoxy-5-fluorocytidine
CAS Registry NumberNot Available
SMILES
C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(F)C(=N)N=C1O
InChI Identifier
InChI=1S/C9H12FN3O4/c1-3-5(14)6(15)8(17-3)13-2-4(10)7(11)12-9(13)16/h2-3,5-6,8,14-15H,1H3,(H2,11,12,16)/t3-,5-,6-,8-/m1/s1
InChI KeyYSNABXSEHNLERR-ZIYNGMLESA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities 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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub Class5'-deoxyribonucleosides
Direct Parent5'-deoxyribonucleosides
Alternative Parents
Substituents
  • 5'-deoxyribonucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Aminopyrimidine
  • Halopyrimidine
  • Pyrimidone
  • Aryl fluoride
  • Aryl halide
  • Hydropyrimidine
  • Primary aromatic amine
  • Pyrimidine
  • Imidolactam
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organofluoride
  • Organohalogen compound
  • Amine
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Organonitrogen compound
  • Organooxygen compound
  • Primary amine
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Biological Location:

  Biofluid and excreta:

  Organ and components:

Source:

Role

Biological role:

Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.64 g/LALOGPS
logP-0.93ALOGPS
logP-0.57ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)8.81ChemAxon
pKa (Strongest Basic)0.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area109.37 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity64.62 m³·mol⁻¹ChemAxon
Polarizability21.59 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0910000000-032e0321a8c4aeee72f0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-0900000000-ce61dba9f0b0828ec936View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0w3c-7900000000-2cd6e57546558d390a81View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002f-0890000000-8f685d78656ff605ad37View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-5930000000-f165a2b6eba7865e3cc9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9300000000-68e982d847d196912136View in MoNA
Biological Properties
Cellular LocationsNot Available
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • Kidney
  • Liver
PathwaysNot Available
NameSMPDB/PathwhizKEGG
No entries found
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not Quantified Not AvailableNot AvailableNormal
    details
    UrineExpected but not Quantified Not AvailableNot AvailableNormal
      details
      Abnormal Concentrations
      Not Available
      Associated Disorders and Diseases
      Disease ReferencesNone
      Associated OMIM IDsNone
      DrugBank IDNot Available
      DrugBank Metabolite IDNot Available
      Phenol Explorer Compound IDNot Available
      Phenol Explorer Metabolite IDNot Available
      FoodDB IDNot Available
      KNApSAcK IDNot Available
      Chemspider ID8213064
      KEGG Compound IDC16635
      BioCyc IDNot Available
      BiGG IDNot Available
      Wikipedia LinkNot Available
      METLIN IDNot Available
      PubChem Compound10037499
      PDB IDNot Available
      ChEBI 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:
      Lipid transport and metabolism
      Specific function:
      Involved in the detoxification of xenobiotics and in the activation of ester and amide prodrugs. Hydrolyzes aromatic and aliphatic esters, but has no catalytic activity toward amides or a fatty acyl-CoA ester. Hydrolyzes the methyl ester group of cocaine to form benzoylecgonine. Catalyzes the transesterification of cocaine to form cocaethylene. Displays fatty acid ethyl ester synthase activity, catalyzing the ethyl esterification of oleic acid to ethyloleate.
      Gene Name:
      CES1
      Uniprot ID:
      P23141
      Molecular weight:
      62520.62
      Reactions
      Capecitabine + Water → 5'-Deoxy-5-fluorocytidine + 1-Pentanol + Carbon dioxidedetails
      General function:
      Lipid transport and metabolism
      Specific function:
      Involved in the detoxification of xenobiotics and in the activation of ester and amide prodrugs. Shows high catalytic efficiency for hydrolysis of cocaine, 4-methylumbelliferyl acetate, heroin and 6-monoacetylmorphine.
      Gene Name:
      CES2
      Uniprot ID:
      O00748
      Molecular weight:
      68898.39
      Reactions
      Capecitabine + Water → 5'-Deoxy-5-fluorocytidine + 1-Pentanol + Carbon dioxidedetails
      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