Fig. 3
Molecular dynamics (MD) simulations of apixaban bound to factor Xa variants. Root-mean-square deviations (RMSDs) of atomic positions of the apixaban ligand during independent 750 ns MD simulations of apixaban binding to either P. textilis isoform FXa (Iso FXa, five independent MD simulations (a–e)) or to human FXa (four independent MD simulations (f–i)) are presented as block averages over 10 ns intervals. The corresponding single standard deviation interval is indicated (gray density). For each independent simulation, the molecular configurations at 750 ns are depicted, in which apixaban (green), the 99-loop (magenta), the isoform FXa extended 99-loop region PQKAYKFDL (yellow), and the catalytic triad residues (red) are highlighted. Molecular configurations at 250 and 500 ns of each simulation are compared with those at 750 ns in Supplementary Fig. 4
