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Figure 3.
Figure 3: Clomipramine-binding site. a, Stereo view, with
clomipramine and leucine carbon atoms depicted in yellow, sodium
ions in purple and two water molecules in red. Residues whose
interactions with clomipramine are hydrophobic, polar (Q34) or
ionic (D401) are coloured grey, orange and pink, respectively.
Atoms depicted as spheres interact through either a hydrogen
bond or a salt bridge. b, F[o]–F[c] simulated annealing omit
map, contoured at 3.0  ,
of D404 and R30, depicting the direct salt bridge between the
guanidium of R30 and the carboxylate of D404, with displacement
of two water molecules (compare to overlay in d). Distances
(Å) are shown along dashed lines. c, F[o]–F[c] simulated
annealing omit map, contoured at 3.0 ,
of the tip of EL4 (residues A317–N321), illustrating the
movement 'up' of A319 in the LeuT–clomipramine crystal
structure (compare to overlay in d). d, Same view as in a with
residues from the original LeuT structure (PDB ID 2A65) overlaid
(in green with two water molecules between D404 and R30 in cyan)
onto those from the LeuT–clomipramine crystal structure (in
pink with the two displaced waters in red and labelled as H[2]O
(CMI)). e, CPK rendering of clomipramine, R30 and F253
illustrating how the positively charged guanidium group is
sandwiched between the aromatic rings of clomipramine and F253.
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