Often, pharmaceutical researchers want to try to treat diseases by learning how to alter (turn on or turn off) signaling pathways within certain cells in the body. They might want to develop an artificial agonist of a pathway, or a molecule that turns on the pathway. Alternatively, they might want to develop an artificial antagonist, which turns the pathway off.
To do this, it's critical to understand the structure of the body's own agonists/antagonists. The 3D structure of these molecules is what allows them to bind to receptors, enabling them to activate or inactivate the pathway. A receptor has its own specific 3D shape at its binding sight that is compatible with only certain molecules- the receptor and signalling molecule need to have compatible 3D structures or they won't fit together. Scientists can use this knowledge of molecular structure to engineer molecules that manipulate the pathway.