A summary of the most common chemical descriptors (InChI Key and SMILES codes) for Gemcitabine are summarized together with 3D and 2D structures and relevant physico-chemical properties.

What is the Gemcitabine?

The molecule Gemcitabine presents a molecular formula of C9H11F2N3O4 and its IUPAC name is 4-amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one.

Gemcitabine (Gemzar) is a chemotherapy medication used to treat a number of types of cancer. This drug works by interfering with the growth of cancer cells and slowing their spread in the body. Gemcitabine is used to treat pancreatic cancer, non-small cell lung cancer, breast cancer, and ovarian cancer. It is usually given as an intravenous (IV) infusion. Common side effects of gemcitabine include fatigue, nausea, vomiting, and low blood cell counts..

3D structure

Cartesian coordinates

Geometry of Gemcitabine in x, y and z coordinates (Å units) to copy/paste elsewhere. Generated with Open Babel software.

2D drawing


Gemcitabine SDUQYLNIPVEERB-QPPQHZFASA-N chemical compound 2D structure molecule svg


Molecule descriptors

IUPAC name4-amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
InChI codeInChI=1S/C9H11F2N3O4/c10-9(11)6(16)4(3-15)18-7(9)14-2-1-5(12)13-8(14)17/h1-2,4,6-7,15-16H,3H2,(H2,12,13,17)/t4-,6-,7-/m1/s1

Other names (synonyms)

IUPAC nomenclature provides a standardized method for naming chemical compounds. Although this system is widely used in chemistry, many chemical compounds have also other names commonly used in different contexts. These synonyms can come from a variety of sources and are used for a variety of purposes.

One common source of synonyms for chemical compounds is the common or trivial names, assigned on the basis of appearance, properties, or origin of the molecule.

Another source of synonyms are historical or obsolete names employed in the past, however replaced nowadays by more modern or standardized names.

In addition to common and historical names, chemical compounds may also have synonyms that are specific to a particular field or industry.

  • 1-(2-deoxy-2,2-difluoro-
  • 103882-84-4
  • 2',2'-DiF-dC
  • 2',2'-Difluorodeoxycytidine
  • 2',2'-difluoro-2'-deoxycytidine
  • 2'-Deoxy-.beta.-D-2',2'-difluorocytidine
  • 2'-Deoxy-2',2'-difluorocytidine
  • 2'deoxy-2',2'-difluorocytidine
  • 2`-Deoxy-2`,2`-difluorocytidine
  • 2vpp
  • 4-Amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
  • 4-Amino-1-[3,3-difluoro-4-hydroxy-5-(hydroxymethyl) tetrahydrofuran-2-yl]-1H-pyrimidin-2-one
  • 4-amino-1-((2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)pyrimidin-2(1H)-one
  • 4-amino-1-((2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-one
  • 4-amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
  • 4-amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2-one
  • 4pd5
  • 882G844
  • 95058-81-4
  • 95058-81-4 (free base)
  • A-D-erythropentofuranosyl)cytosine
  • AB01274777-01
  • AB01274777-02
  • AB01274777_05
  • AB01274777_06
  • B76N6SBZ8R
  • BCP9000721
  • BCPP000219
  • BDBM429521
  • C07650
  • CCG-221183
  • CCRIS 8984
  • CS-0643
  • Cytidine, 2'-deoxy-2',2'-difluoro-
  • Cytidine, 2'-deoxy-2',2'-difluoro-2'-Deoxy-.beta.-D-2',2'-difluorocytidine
  • D02368
  • DB00441
  • DL-215
  • Folfugem
  • G0544
  • GS-3582
  • GTPL4793
  • Gamcitabine
  • GemLip
  • Gemcel
  • Gemcitabina
  • Gemcitabine
  • Gemcitabine (USAN/INN)
  • Gemcitabine free base
  • Gemcitabinum
  • Gemzar (hydrochloride)
  • HMS2089P10
  • HMS3715N07
  • HSDB 7567
  • HY-17026
  • J-001056
  • LY 188011
  • LY-188011
  • LY188011
  • MFCD00869720
  • NCGC00168784-02
  • NCGC00168784-08
  • NCGC00168784-12
  • NSC 613327
  • NSC-613327
  • Q414143
  • SR-05000001491
  • SR-05000001491-1
  • SR-05000001491-2
  • SW199649-2
  • Z1741982024
  • Zefei
  • dFdC
  • gemcitabine
  • gemcitabine (Gemzar)
  • med.21724, Compound Gemcitabine
  • s1714

Reference codes for other databases

There exist several different chemical codes commonly used in orded to identify molecules:
  • ZINC18279854
  • AKOS015920303
  • BRD-K15108141-001-04-1
  • DTXSID3040487
  • CHEMBL888
  • CHEBI:175901
  • SCHEMBL4295

Physico-Chemical properties

IUPAC name4-amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
Molecular formulaC9H11F2N3O4
Molecular weight263.198
Melting point (ºC)
Boiling point (ºC)
Density (g/cm3)
Molar refractivity54.83
Topological polar surface area110.6

LogP and topological polar surface area (TPSA) values were estimated using Open Babel software.

The n-octanol/water partition coeficient (Kow) data is applied in toxicology and drug research. Kow values are used, to guess the environmental fate of persistent organic pollutants. High partition coefficients values, tend to accumulate in the fatty tissue of organisms. Molecules with a log(Kow) (or LogP) greater than 5 are considered to bioaccumulate.

TPSA values are the sum of the surface area over all polar atoms or molecules, mainly oxygen and nitrogen, also including hydrogen atoms.

In medicinal chemistry, TPSA is used to assess the ability of a drug to permeabilise cells.

For molecules to penetrate the blood-brain barrier (and act on receptors in the central nervous system), TPSA values below 90 Å2 are required. Thus, molecules with a polar surface area greater than 140 Å2 tend to be poorly permeable to cell membranes.