Figure 5.

The docked pose of 20a in the binding site of Tdp1 as predicted by the ChemPLP scoring function. (A) The predicted configuration is shown in the ball-and-stick format and the adjacent amino acid residues are depicted in the stick format; the hydrogen atoms are not shown for clarity. The amino acids forming the pocket accommodating the adamantine cage are Tyr204, His263, Lys269, Asn283, Ser399, His493 and Lys495; the lipophilic cleft occupied by the aliphatic monoterpene is made up by Pro461, Gly498 and Try590. (B) The protein surface is rendered; blue depicts regions with a partial positive charge on the surface; red depicts regions with a partial negative charge and grey shows neutral areas. The ligand occupies the catalytic binding pocket, blocking access to it.