Extended Data Fig. 2. Comparisons between DNA-PKcs and mTOR in complex with ligands.

a, Comparison of ATPγS-Mg²⁺₂ binding in the ligand binding grooves of DNA-PKcs and mTOR (PDB entry: 4JSP)¹². The PIKK regulatory domain (PRD) of mTOR is lifted and removed completely from the substrate-binding site while the PRD of DNA-PKcs still docks there, although it is lifted compared to apo DNA-PKcs. DNA-PKcs/ATPγS-Mg²⁺₂ complex is coloured grey while mTOR/ATPγS-Mg²⁺₂ is coloured orange. PRDs of DNA-PKcs and mTOR are circled in dashed lines. b, Close-up view of the ligand-binding pocket of DNA-PKcs and mTOR. Residues contributing to the pocket are highly conserved between DNA-PKcs and mTOR. The major differences lie in the p-loop, including residue composition and loop conformation. The residues that differ are labeled in the figure. Compared to that of mTOR, the p-loop of DNA-PKcs is positioned more inward and closer to the C-lobe, leaving a narrower channel for the ligands to enter. Moreover, DNA-PKcs p-loop pushes the ligands more toward the C-lobe as the ribose moiety and the phosphate groups of ATPγS-Mg²⁺₂ rotate towards the C-lobe compared to those of mTOR. The adenine moieties overlay well as the deep hydrophobic pockets are highly structurally similar. c, Comparison of mTOR in complex with specific inhibitor Torin2 (PDB code: 4JSX) and pp242 (PDB code: 4JT5) and DNA-PKcs in complex with specific inhibitor AZD7648 and M3814 and close-up view. The major differences are in the p-loop conformations. Moreover, among the few residues that differ, Met3729 of DNA-PKcs is more extended compared to the Ile2163 of mTOR at the equivalent position and acts as the gatekeeper. Moreover, it affects the conformation of DNA-PKcs p-loop when different ligands bind. DNA-PKcs in complex with AZD7648 is coloured purple, DNA-PKcs in complex with M3814 is coloured cyan, mTOR in complex with Torin2 is coloured salmon and mTOR in complex with pp242 is coloured olive.