Fig. 5: Analysis of distances between the Cβ atom of residue V308 and the Cβ atom of residue F401 of ABL.

a Structural overlay highlighting the distance between residues V308 and F401 in the conformations of states A (PDB ID 6XR6, blue), I₁ (PDB ID 6XR7, orange), and I₂ (PDB ID 6XRG, green) of ABL. Residues are represented by spheres at the Cβ atoms, and the proteins are depicted as ribbons. b Depiction of the spatial positioning of residues V308 and F401 within the ABL kinase state A (PDB ID 6XR6). The sequence annotation is based on UniProt entry P00519, with the ATP binding site, αC-helix, active site, and activation loop colored in teal, violet, red, and magenta, respectively. The protein backbone is rendered as a cartoon, the active site residues as sticks, and the Cβ atoms of residues V308 and F401 as spheres. c Distance distributions between residues V308 and F401 for ABL in complex with 12 different inhibitors. Kernel density estimations (KDE) plots for the distances from 20 measured structures are shown for state A (blue), state I₁ (orange), and state I₂ (green). Predicted distance probability distribution of the apo state, derived from AlphaFold2 (AF2), is depicted as grey bars with a bin width of 0.3 Å. The Ligand-Transformer predicted distance probabilities for the 12 inhibitors are displayed as colored bars with a bin width of 0.19 Å. The mean values of predicted distances are plotted as solid lines, with dashed lines representing the standard deviation. The symbol in the upper right corner denotes which conformational state of ABL the inhibitor selectively binds to as determined by NMR analysis⁴¹.