Chymotrypsin (EC 3.4.21.1, chymotrypsins A and B, alpha-chymar ophth, avazyme, chymar, chymotest, enzeon, quimar, quimotrase, alpha-chymar, alpha-chymotrypsin A, alpha-chymotrypsin) is a digestive enzyme component of pancreatic juice acting in the duodenum where it performs proteolysis, the breakdown of proteins and polypeptides. Chymotrypsin preferentially cleaves peptide amide bonds where the carboxyl side of the amide bond (the P₁ position) is a large hydrophobic amino acid (tyrosine, tryptophan, and phenylalanine). These amino acids contain an aromatic ring in their sidechain that fits into a 'hydrophobic pocket' (the S₁ position) of the enzyme. It is activated in the presence of trypsin. The hydrophobic and shape complementarity between the peptide substrate P₁ sidechain and the enzyme S₁ binding cavity accounts for the substrate specificity of this enzyme. Chymotrypsin also hydrolyzes other amide bonds in peptides at slower rates, particularly those containing leucine and methionine at the P₁ position.

Structurally, it is the archetypal structure for its superfamily, the PA clan of proteases.

Chymotrypsin is synthesized in the pancreas by protein biosynthesis as a called chymotrypsinogen that is enzymatically inactive. Trypsin activates chymotrypsinogen by cleaving peptidic bonds in positions Arg15 - Ile16 and produces π-Chymotrypsin. In turn, aminic group (-NH3⁺) of the Ile16 residue interacts with the side chain of Glu194, producing the "oxyanion hole" and the hydrophobic "S1 pocket". Moreover, Chymotrypsin induces its own activation by cleaving in positions 14-15, 146-147 and 148-149, producing α-Chymotrypsin (which is more active and stable than π-Chymotrypsin). The resulting molecule is a three-polypeptide molecule interconnected via disulfide bonds.

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