Figure 2. Characterization of VPC-18005 binding to the ERG-ETS domain.
(A) Chemical structure of VPC-18005, in the isomeric form used for docking. The R-isomer is calculated to have the most favorable binding energy. (Molecular weight = 318 g/mol at pH 7). (B) A space-filling representation of the predicted VPC-18005 binding pose within the ERG-ETS domain pocket (orange = carbon, blue = nitrogen, red = oxygen, yellow = sulfur). (C) Protein residues that are predicted to interact with VPC-18005 at the ERG-ETS domain. The red dotted lines indicate hydrogen bonds, and the green lines represent non-polar packing interactions. (D) Amide chemical shift perturbations resulting from the addition of a 10 fold molar excess of VPC-18005 to the ERG-ETS domain (derived from Supplementary Figure 5). Coloured bars denote significant changes (magenta ≥ mean + standard deviation, cyan ≥ mean). The secondary structure of the EGR-ETS domain is shown at the bottom. (E) Amino acid residues exhibiting significant chemical shift perturbations were mapped to their corresponding locations on the ERG-ETS domain (same colour code as in D). (F) 1H-NMR monitored titration of VPC-18005 (sharp signals) with increasing concentrations (red through purple) of the ERG-ETS domain (broad signals). Signals from 1H nuclei directly bonded to the indicated chemical moieties shift and broaden upon binding the protein.