Model cavities to test
molecular docking and protein–ligand
interactions. These cavities range from the L99A cavity in T4 lysozyme
(represented by PDB 181L(28)), which binds exclusively apolar, hydrophobic
ligands, to the W191G cavity in cytochrome C peroxidase (CCP) (represented
by PDB 1AES(73)). Intermediate to these are the more polar T4
lysozyme cavities L99A/M102Q (PDB 1LI2), which adds a polar glutamine residue
to the cavity and L99A/M102E† (PDB 3GUN(55)), which
adds a neutral glutamic acid, and L99A/M102H† (PDB 4EKQ(37)), the focus of this study, which adds a histidine residue
to the cavity. These intermediate cavities bind both nonpolar and
polar, hydrogen-bond donating ligands.