Fig. 4.

MD simulations results for AJAY-4. a The alignments of AJAY-4 between before MD (orange) and after MD (blue). b The distances between AJAY-4 and APE-1, the H-bond distances between active compound AJAY-4 and Arg177/His309 remained stable. We also performed the MD simulations for inhibitor AJAY-15, as shown in Fig. 3S. However, the distances between inactive compound AJAY-15 and Arg177/His309 fluctuated greatly. More detail can be found in Fig. 3S. We suggest that Arg177 and His309 play key roles in the recognitions of inhibitors