One of the protein structures that resulted in successful treatments is the example of the HIV-Protease:
HIV protease structure was used in designing anti-retroviral protease inhibitors that, as a component of Highly Active Anti-Retroviral Therapy (HAART), have added many high-quality years to the lives of HIV infected individuals. While HAART greatly extends life in HIV infected patients, it is not a cure, and these patients may eventually succumb to AIDS. For more, please see AIDS Before Protease Inhibitors & HIV Protease Inhibitors: A Breakthrough.
As this is such a prime example of how protein structures contribute to medicine, I commonly refer to it when confronted with the question: “That weird bio-something stuff you are doing there – What is it actually good for?”
Here is a movie of (un-)docking the inhibitor Ritonavir to HIV protease – I rendered it in PyMOL based on Morph-data of Conformational Changes for the exhibition “Mensch-Mikrobe” of the Robert Koch Institute.