Figure 6. Orientation and positioning of arylamide compounds in the hDM2 binding pocket at 10 ps intervals.

Four of five simulations sample in the same region of space, whereas simulation c does not. Ether oxygens from anti-parallel conformations of Phe-Nap-ⁱPr are projected onto a plane defined by Cα atoms from Tyrosine 56, Methione 62 and Valine 93. Data points are color-coded depending on which ether oxygen they belong to: R₁ (Blue); R₂ (Green); and R₃ (Red). Data was plotted at 10 ps intervals starting after 4 ns of data collection. Values at t = 0 ps are plotted with diamonds. Graphs show images of starting conformation relative to the high affinity p53 helix and data from: a) conformation 1; b) conformation 2; c) conformation 3; d) conformation 7; and e) conformation 8.