Designing an antivenom in 3D (4)
Designing the antidote
Now that we know the active site, we can search for an antidote.
Exercise 14:
What would be a nice way to elimenate the venom? How would you design an antidote?
Exercise 15:
Open Help > Play help movie > 6.8 Rattle snake poison > OK and watch the movie. Click on Continue when the animation is over. You can keep looking at the molecule. Close the window (and click Yes) to go back to the main Yasara window.
You can see that a small molecule enters the active site and binds to our venom protein. This small molecule is called a ligand, and is made in such a way that it fits nicely in the protein cavity. However, it is made only of carbons, and will therefore not have many strong interactions with the active site.