FIGURE 5.

A, distances between a ligand and the six putative binding residues. The pairs between the phosphorus atoms (P1, P4, and P5) of PI(4,5)P₂ and the side chain atoms (CZ of Arg⁸⁰, Arg⁸² and NZ of Lys¹⁸², Lys¹⁸⁵, Lys¹⁸⁷, and Lys¹⁸⁸) are visualized by solid, dashed, and dotted lines. The distances of these pairs were used to cluster accepted poses. B, Kir 2.1–3SPI subunit A and D shown in yellow and silver ribbon, respectively, with the crystallographic PI(4,5)P₂ bound to the subunit A shown in sphere translucently. An overlay of a single representative pose from each cluster of seven different C1-PIP ligands stacked on the Kir2.1–3SPI surface clearly indicates that these ligand bind primarily within two clusters. C, number of accepted poses within cluster 1 (red) and cluster 2 (blue) for each PIP. For each PIP, 96–99% of poses reside in cluster 1. D, average binding energy for poses in cluster 1 (red) and cluster 2 (blue) for each PIP docked to Kir2.1–3SPI.