Difference Between Pantoprazole and Omeprazole

Pantoprazole and Omeprazole are two drugs coming under the drug class category of proton pump inhibitors. Proton pumps are situated in mitochondrial membranes, which mean they are in almost all cells. The importance of these drugs is that they selectively inhibit proton pumps in the stomach lining. The mechanism of action is to selectively inhibit H+/K+ ATPase enzyme in gastric parietal cells. In the sense of organic chemistry, both these drugs are benzimidazoles containing substituted benzene ring and imidazole ring.


Pantoprazole also known by the trade name Protonix is a proton pump inhibitor. Its empirical formula is C16H14F2N3NaOS x 1.5 H2O and has a molecular weight of 432.4. This drug is prescribed to treat complications related to excessive acid secretion in the stomach such as damage to esophagus and Zollinger-Ellison syndrome. However, this drug cannot render immediate relief from heartburns. When taking the drug prescriptions should be followed accurately. The tablet should be taken 30 minutes before meals. The pill should be swallowed as a whole without chewing because it may damage the coating which is designed to protect the stomach. Granular suspension should be taken only with apple juice. Sometimes the granular suspension is delivered through nasogastric feeding tube. There are a number of harmful effects of the drug.

Animal studies have shown the chronic usage of Pantoprazole may cause stomach cancers although it is not confirmed with humans up to date. Tendency to increase bone fracture in hips, wrists, and spine is also found through clinical studies. Long term usage has shown to decrease the Vitamin B12 absorption and, therefore, cause B12 deficiency. Apart from all the harmful effects the drug also has various side effects associated. Uneven and fast heart rate, muscle weakness, diarrhea, coughing and choking, headache and troubles in memory are some of the serious side effects. In addition weight change, stomach pain, insomnia is also experienced.

Pantoprazole should not be taken if one is allergic to the drug. It should not be taken while under medication of other benzimidazole drugs. If a person is taking HIV AIDS medicine, ampicillin, blood thinner, water pills, iron tablets, diabetes medicine, it is important to seek medical advice before taking Pantoprazole.


Omeprazole is also a proton pump inhibitor. It is also known by the trade names Prilosec and Zegerid. The empirical formula of omeprazole is C17H19N3O3S and has a molecular weight of 345.42. Omeprazole is also prescribed for complications related with excess acid secretion in the stomach. It is used to treat damaged esophagus and gastroesophageal reflux disease (GERD). Sometimes omeprazole is prescribed along with antibiotics to treat ulcers caused by Helicobacter pylori infections.

Side effects, effects due to prolonged use and other medication which should be generally avoided are quite similar for the two drugs.

Pantoprazole vs Omeprazole

• Pantoprazole has a molecular weight of 432.4 and Omeprazole has a molecular weight of 345.42.

• The drugs are structurally different due to the various substituents and is indicated by Pantoprazole having empirical formula C16H14F2N3NaO4 S x 1.5 H2O and Omeprazole having the empirical formula C17H19N3O3S.