Fig. 2
Crystal analysis shows how compounds bind and VH competition results. KRASQ61H or KRASG12D protein crystals were soaked with compounds, and X-ray diffraction data were collected for determining the binding modes of the compounds. a KRASQ61H-GppNHp soaked with Abd-2. The expanded view of the binding region of this compound (right hand panel) shows clear electron density (2mFo-DFc maps contoured at 1.0 r.m.s. green) attributed to the benzodioxane and furanyl amide parts of the compound. b, c Crystal structures and electron densities for Abd-3 soaked into KRASQ61H-GppNHp or KRASG12D-GppNHp, respectively. The chlorine atom in Abd-3 is depicted in green. The Abd-3–KRAS interactions differ in two mutants, but the H-bond to a neighbouring molecule in the crystal lattice for G12D means that the Q61H complex is unencumbered by the crystal contacts (b). The switch I/II regions are coloured in red and blue, respectively, are defined here as 30–38 (switch I) and 60–76 (switch II). d Explanation for the competition of compound Abd-2 binding to RAS by steric hindrance. The left-hand panel shows a surface representation of mutant HRASG12V-GppNHp (light blue) and the anti-RAS VH from the Fv depicted in orange. The left-hand panel is the surface representation is the KRASQ61H-GppNHp structure soaked with Abd-2, with anti-RAS VH superimposed on KRASQ61H-GppNHp. The expanded right-hand representation shows the predicted steric hindrance between VH and the compound, in particular VH CDR2 residue K56 (transparent, orange representation). Although the K56 side chain is flexible, it is prevented from rotating away from the clash with Abd-2 by steric hindrance with neighbouring regions of KRAS
