Structural analysis of c-Kit2 G-quadruplex in the presence of a benzimidazole derivative

1D 1H titration of c-Kit2 with a benzimidale derivative (namely, BPBA) in 5 mM K-phosphate buffer (pH 7.0), 20 mM KCl in 95% H2O, 5% D2O at 25 °C. 

2D NOESY (300 ms) for c-Kit2/BPBA (1:2 molar ratio) in 5 mM K-phosphate buffer (pH 7.0), 20 mM KCl in 95% H2O, 5% D2O at 25 °C (600 and 800 MHz), and at 40 °C (600 MHz); in 5 mM K-phosphate buffer (pH 7.0), 20 mM KCl in 100% D2O, the spectrum at 25 °C (600 MHz).

2D TOCSY (80 ms) for c-Kit2/BPBA (1:2 molar ratio) in 5 mM K-phosphate buffer (pH 7.0), 20 mM KCl in 95% H2O, 5% D2O at 40 °C (600 MHz). 

COSY and TOCSY for BPBA in 100% DMSO-d6.COSY and TOCSY for BPBA in 5 mM K-phosphate buffer (pH 7.0), 20 mM KCl in 90% H2O, 10% DMSO-d6.PDB files for the 10 lowest energy structures obtained for c-Kit2 in the presence of ligand;

Four PDB cluster structures from restrained SA calculations with time-averaged NOE restraints, using COM-based r⁻⁶ averaging to model ligand pseudosymmetry and binding at the G-quadruplex 5′-end;NMR NOE distance restraints used for restrained SA calculations, including ambiguous COM-based restraints with r⁻⁶ averaging (AMBER igroup, ir6=1).