AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
Fig 8
Comparison of side-chain conformations between apo, holo, and successfully docked solution.
This figure provides a pairwise comparison of the conformations of the apo (4EK3), holo complex (1YKR), and the 1YKR ligand docked solution with the 12 flexible receptor side-chains displayed as ball-and-sticks. A) Apo vs. holo: The native bound ligand is displayed as sticks with green carbon atoms along with a partially transparent green molecular surface. The 2 lysine side-chains in the apo conformation severely overlap with the space occupied by the ligand. B) Docked vs. apo. The docked solution is shown with purple carbon atoms and partially transparent ligand molecular surface. The apo structure is shown with orange carbon atoms. All 12 side-chains in the docked solution adopt conformations different from the initial apo conformation. Most of them settle for conformations corresponding to small adjustments while others adopt substantially different conformations to resolve steric clashes (Lys33 and Lys89). C) The docked solution (purple carbon atoms) is shown with the holo receptor (green carbon atoms). The ligand is docked perfectly (RMSD from the crystallographic structure is 0.34Å) and the receptor side-chains changed their conformations to accommodate the ligand binding in the correct binding mode.