Fig. 5. Drug-free ABLE has a preorganized structure with an open binding site competent for binding.

(A) A slice through a surface representation of the 1.3-Å resolution structure of unliganded ABLE shows an open binding cavity. (B) Same slice, shown for the structure of apixaban-bound ABLE. (C) The Cα atom backbone superposition of unliganded and liganded ABLE. Colored squares surrounding the structure correspond to panels in (G), (H), and (I), looking down from the top. (D) The binding site of drug-free ABLE shows nine buried, crystallographic waters (red spheres, occupancy > 0.9) involved in an extensive H-bonded network with binding-site residues Tyr⁶, Gln¹⁴, Tyr⁴⁶, and His⁴⁹. The 2mFo-DFc electron density map of drug-free ABLE is contoured at 1 σ. An acetate (Act) group from the crystallization condition H-bonds with His⁴⁹. His⁴⁹ and Tyr⁴⁶ are observed with alternate rotamers. (E) Same view as in (D) but with the addition of the corresponding residues from the apixaban-bound structure, after an all-Cα-atom backbone superposition. The 1-σ 2mFo-DFc electron density (purple) of apixaban from the drug-bound structure shows where the crystallographic waters bind in the ligand-free structure relative to the bound structure. A water (shown as an orange sphere) mediates the H-bond between Tyr⁴⁶ and apixaban. This water is not observed in the unliganded structure. (F) Binding of apixaban in the drug-bound structure displaces all of the nine buried waters in the drug-free structure. Stick renderings, as well as the surface background, show the binding site of the ABLE-apixaban complex. (G and H) Binding-site overlay of liganded (orange, apixaban purple) and unliganded (cyan) ABLE shows preorganized rotamers. (I) The remote folding core contains identical rotamers in drug-free and drug-bound ABLE, predisposing the drug-free protein for binding.