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Record Information
Version3.6
Creation Date2013-05-17 01:00:16 UTC
Update Date2017-03-02 22:05:02 UTC
HMDB IDHMDB60405
Secondary Accession NumbersNone
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 These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom.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
StatusExpected but not Quantified
Origin
  • Drug metabolite
Biofunction
  • Waste products
ApplicationNot Available
Cellular locationsNot Available
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 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count1ChemAxon
Refractivity64.62 m3·mol-1ChemAxon
Polarizability21.59 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular LocationsNot Available
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • Kidney
  • Liver
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableNormal
  • Not Applicable
details
UrineExpected but not QuantifiedNot ApplicableNot AvailableNot AvailableNormal
  • Not Applicable
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
NuGOwiki LinkHMDB60405
Metagene LinkHMDB60405
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, Consortium U: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [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