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

What is the (S)-Rabeprazole?

The molecule (S)-Rabeprazole presents a molecular formula of C18H21N3O3S and its IUPAC name is 2-[(S)-[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methylsulfinyl]-1H-benzimidazole.

Rabeprazole, sold under the brand name Aciphex among others, is a medication used to treat stomach ulcers, gastroesophageal reflux disease, and Zollinger–Ellison syndrome. It is also sometimes used to prevent Helicobacter pylori infections. It is taken by mouth..

Common side effects include headache, diarrhea, and abdominal pain. Serious side effects may include low blood magnesium, C. difficile associated diarrhea, and Stevens–Johnson syndrome. Use in pregnancy may harm the baby. Rabeprazole is a proton pump inhibitor and works by decreasing the amount of acid produced in the stomach..

Rabeprazole was patented in 1985 and approved for medical use in 1997. It exists as a generic medication. In 2018, it was the 264th most commonly prescribed medication in the United States, with more than two million prescriptions..

3D structure

Cartesian coordinates

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

2D drawing


(S)-Rabeprazole YREYEVIYCVEVJK-VWLOTQADSA-N chemical compound 2D structure molecule svg


Molecule descriptors

IUPAC name2-[(S)-[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methylsulfinyl]-1H-benzimidazole
InChI codeInChI=1S/C18H21N3O3S/c1-13-16(19-9-8-17(13)24-11-5-10-23-2)12-25(22)18-20-14-6-3-4-7-15(14)21-18/h3-4,6-9H,5,10-12H2,1-2H3,(H,20,21)/t25-/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.

  • (S)-2-(((4-(3-Methoxypropoxy)-3-methylpyridin-2-yl)methyl)sulfinyl)-1H-benzimidazole
  • (S)-Rabeprazole
  • 177795-59-4
  • 1H-Benzimidazole, 2-(((4-(3-methoxypropoxy)-3-methyl-2-pyridinyl)methyl)sulfinyl)-, (S)-
  • 1H-Benzimidazole, 2-((S)-((4-(3-methoxypropoxy)-3-methyl-2-pyridinyl)methyl)sulfinyl)-
  • 2-[(S)-[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methylsulfinyl]-1H-benzimidazole
  • BDBM50409894
  • Q27287158
  • Q9Z21M00M9
  • Rabeprazole, (S)-

Reference codes for other databases

There exist several different chemical codes commonly used in orded to identify molecules:
  • ZINC1530935
  • UNII-Q9Z21M00M9
  • DTXSID90445562
  • CHEMBL1627299
  • SCHEMBL23337

Physico-Chemical properties

IUPAC name2-[(S)-[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methylsulfinyl]-1H-benzimidazole
Molecular formulaC18H21N3O3S
Molecular weight359.443
Melting point (ºC)
Boiling point (ºC)
Density (g/cm3)
Molar refractivity97.75
Topological polar surface area96.3

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.