Figure 2.

Binding interactions of compound 8302 with BRD4 throughout the molecular simulation. Primary receptor ligand interactions (hydrogen bonds, hydrophobic, ionic, water bridges) of 8302 for the duration of the MD simulation with BRD4(1). The top panel shows the total number of specific contacts the protein makes with the ligand over the course of the trajectory. The bottom panel shows which residues interact with the ligand over the simulation time. Some residues make more than one specific contact with the ligand, which is represented by a darker shade of orange, according to the scale to the right of the plot. The visualizations were generated using the Desmond simulation interactions diagram component.