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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2013-06-15 18:25:01 UTC
Update Date2017-12-20 20:30:53 UTC
HMDB IDHMDB0060638
Secondary Accession Numbers
  • HMDB60638
Metabolite Identification
Common NameGemcitabine triphosphate
DescriptionGemcitabine triphosphate, also known as 2'2'-difluorodeoxycytidine 5'-triphosphate or 2,2-df-ctp, is a member of the class of compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Gemcitabine triphosphate is soluble (in water) and an extremely strong acidic compound (based on its pKa). Gemcitabine triphosphate can be found primarily in blood and urine, as well as in human kidney and liver tissues. Within the cell, gemcitabine triphosphate is primarily located in the cytoplasm. In humans, gemcitabine triphosphate is involved in a couple of metabolic pathways, which include gemcitabine metabolism pathway and gemcitabine pathway. Gemcitabine triphosphate is a metabolite of gemcitabine. Gemcitabine is a nucleoside analog used as chemotherapy. It is marketed as Gemzar by Eli Lilly and Company (Wikipedia).
Structure
Thumb
Synonyms
ValueSource
2'2'-Difluorodeoxycytidine 5'-triphosphateChEMBL
2'2'-Difluorodeoxycytidine 5'-triphosphoric acidGenerator
2',2'-DIFLUORODEOXYCYTIDINE 5'-triphosphoric acidGenerator
2,2-DF-CTPMeSH
Chemical FormulaC9H14F2N3O13P3
Average Molecular Weight503.1379
Monoisotopic Molecular Weight502.970753495
IUPAC Name({[({[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,4-difluoro-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid
Traditional Name({[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-4,4-difluoro-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)C1(F)F
InChI Identifier
InChI=1S/C9H14F2N3O13P3/c10-9(11)6(15)4(25-7(9)14-2-1-5(12)13-8(14)16)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h1-2,4,6-7,15H,3H2,(H,20,21)(H,22,23)(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1
InChI KeyYMOXEIOKAJSRQX-QPPQHZFASA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyrimidones. These are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Imidolactam
  • Alkyl phosphate
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Fluorohydrin
  • Halohydrin
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organofluoride
  • Hydrocarbon derivative
  • Organohalogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Amine
  • Alkyl halide
  • Primary amine
  • Alkyl fluoride
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Source:

Biological location:

Process

Naturally occurring process:

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 Solubility16.9 g/LALOGPS
logP0.33ALOGPS
logP-2.6ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)0.91ChemAxon
pKa (Strongest Basic)-0.69ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area247.97 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity85.87 m³·mol⁻¹ChemAxon
Polarizability35.27 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
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, Positivesplash10-004i-9343200000-7b3d57bbbb4251d57fe2View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-000b-9632200000-45d13b60138a08b7abceView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-41738e3baba1fc22f76aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-c45e47aee60a478ca366View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dj-9500000000-94508e784ffaea6f2470View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-08fr-1910420000-9e045b65f966c904f96dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03fr-9320000000-7f2708b0ad4b3a1728d5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-056r-9310000000-5414877dcbeebc9dc89fView in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue Location
  • Kidney
  • Liver
Pathways
NameSMPDB/PathwhizKEGG
Gemcitabine Action PathwayThumbThumb?image type=greyscaleThumb?image type=simpleNot Available
Gemcitabine Metabolism PathwayThumbThumb?image type=greyscaleThumb?image type=simpleNot Available
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
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
      Phenol Explorer Compound IDNot Available
      FoodDB 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 Compound130659
      PDB IDGTF
      ChEBI IDNot Available
      References
      Synthesis ReferenceNot Available
      Material Safety Data Sheet (MSDS)Not Available
      General ReferencesNot Available