Hydrophobic interactions promote the initial coordination of rabeprazole to the zinc cluster. The left shows the structure of the DENR–MCTS1–rabeprazole complex with four possible rabeprazole configurations (highlighted in transparent colours) aligned on the zinc cluster. The inset shows one rabeprazole configuration obtained from MD simulations together with interacting DENR residues. The right shows DENR residues interacting with rabeprazole based on MD simulations of four initial rabeprazole configurations. For every trajectory snapshot, residues with an atom–atom distance below 3.5 A were classified as interacting. Only snapshots with reactive configurations (pyridine N to benzimidazole C distance within 20% of the sum of van der Waals radii) were considered. Data are presented as mean ± s.e.m., based on n = 3 simulations of four different configurations.
