Consider a chemical reaction in which substrate S is converted to product P , by an enzyme E . The least stable species on the reaction pathway is called the transition state . Enzymes bind their substrates more tightly in the transition state than in their normal states, ie the transition state ES is stabilized. A very large number of types of chemical reactions are involved in an organism's metabolic processes, catalyzed by many different enzymes. The Enzyme Structures Database at University College London .
Active sites are the clefts or crevices to which the substrate binds.
In many cases water is excluded from these clefts, which may have a largely hydrophobic surface, although there will usually be a number of polar side chains which effect the binding and catalysis of the substrate. In some cases water molecules are reactants. The binding of a substrate to its active site is often likened to a key fitting a lock. Only a small proportion of the enzyme's volume constitutes the active site, and therefore only a small fraction of the residues of the polypeptide chain are in contact with the substrate. The residues which constitute the active site are often not close to each other in the primary sequence, but the tertiary fold brings them close together in three-dimensional space.