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

What is the (-)-Pantoprazole?

The molecule (-)-Pantoprazole presents a molecular formula of C16H15F2N3O4S and its IUPAC name is 6-(difluoromethoxy)-2-[(S)-(3,4-dimethoxypyridin-2-yl)methylsulfinyl]-1H-benzimidazole.

Pantoprazole, sold under the brand name Protonix among others, is a medication used for the treatment of gastric acid-related disorders.[2] This includes erosive esophagitis, peptic ulcer disease, gastroesophageal reflux disease (GERD), and Zollinger–Ellison syndrome.[2] It is taken by mouth or by injection into a vein.[2].

Common side effects include headache, diarrhea, constipation, and nausea.[2] Serious side effects may include low blood magnesium, C. difficile-associated diarrhea, and pneumonia.[2] Use in pregnancy may result in harm to the baby.[2] Pantoprazole is in the proton pump inhibitor family of medications.[2] It works by inhibiting gastric acid secretion.[2].

Pantoprazole was patented in 1981 and approved for medical use in 1994.[3][4] It exists as a generic medication.[2] In 2018, it was the 171st most commonly prescribed medication in the United States, with more than 6 million prescriptions.[5].

3D structure

Cartesian coordinates

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

2D drawing


(-)-Pantoprazole IQPSEEYGBUAQFF-SANMLTNESA-N chemical compound 2D structure molecule svg


Molecule descriptors

IUPAC name6-(difluoromethoxy)-2-[(S)-(3,4-dimethoxypyridin-2-yl)methylsulfinyl]-1H-benzimidazole
InChI codeInChI=1S/C16H15F2N3O4S/c1-23-13-5-6-19-12(14(13)24-2)8-26(22)16-20-10-4-3-9(25-15(17)18)7-11(10)21-16/h3-7,15H,8H2,1-2H3,(H,20,21)/t26-/m0/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.

  • (-)-Pantoprazole
  • (S)-(-)-Pantoprazole
  • 142678-35-1
  • 1H-Benzimidazole, 6-(difluoromethoxy)-2-((S)-((3,4-dimethoxy-2-pyridinyl)methyl)sulfinyl)-
  • 6-(difluoromethoxy)-2-[(S)-(3,4-dimethoxypyridin-2-yl)methylsulfinyl]-1H-benzimidazole
  • L-Pantoprazole
  • Pantoprazole, S-
  • Q27289440
  • S-(-)-Pantoprazole
  • S-Pantoprazole
  • SX78SGO2TV
  • Zosecta

Reference codes for other databases

There exist several different chemical codes commonly used in orded to identify molecules:
  • ZINC4099200
  • DTXSID201015709
  • CHEMBL3526697
  • SCHEMBL29466

Physico-Chemical properties

IUPAC name6-(difluoromethoxy)-2-[(S)-(3,4-dimethoxypyridin-2-yl)methylsulfinyl]-1H-benzimidazole
Molecular formulaC16H15F2N3O4S
Molecular weight383.37
Melting point (ºC)
Boiling point (ºC)
Density (g/cm3)
Molar refractivity90.36
Topological polar surface area105.5

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.