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. 2014 Mar 6;9(3):e90637. doi: 10.1371/journal.pone.0090637

Figure 4. 2D representation of the docking pose of amarogentin inside the hydrophobic cavity of COX.

Figure 4

(A) The docking pose of amarogentin inside the binding cavity of COX-1 shows that besides forming several van der Waals interactions, amarogentin forms four H-bonds, two with Arg119 and one with Ser352. (B) A total of five H-bonds were also observed in the docked amarogentin-COX-2 complex, one each with Arg106, Ser516, Tyr371, and Met508. Amarogentin formed van der Waals interaction with a several residues along the hydrophobic channel. (Legend: green spheres represent hydrophobic residues; cyan spheres represent residues with polar side chains; red spheres and purple spheres show negatively and positively charged amino acid residues, respectively; solid red lines denote cation- π interaction; dotted purple lines indicate hydrogen bonds with side-chain atoms, with the direction of arrow denoting the acceptor atom; solid green lines indicate π-π interactions; and the grey spheres surrounding the atoms indicate that the atoms are exposed to solvent). The illustrations have been generated using Schrödinger Maestro open-source visualisation package.