Pepsin enzyme. Computer graphic of the protein- digesting enzyme pepsin. It is a protease enzyme that is secreted as part of gastric juice into the stomach in an inactive form known as pepsinogen. When it comes into contact with hydrochloric acid it is converted into the active form that hydrolyses proteins into smaller polypeptides (peptones). The active site of the enzyme is the cleft at centre left. The molecule's secondary structure consists of coiled or folded units, seen as green & yellow cylinders (alpha helices) and red arrows (beta or pleated sheets), which give the molecule energetic stability.