Volume 3, Issue 3, Pages 397-403 (March 1999) Molecular Recognition of Fatty Acids by Peroxisome Proliferator–Activated Receptors  H.Eric Xu, Millard H Lambert, Valerie G Montana, Derek J Parks, Steven G Blanchard, Peter J Brown, Daniel D Sternbach, Jürgen M Lehmann, G.Bruce Wisely, Timothy M Willson, Steven A Kliewer, Michael V Milburn  Molecular Cell  Volume 3, Issue 3, Pages 397-403 (March 1999) DOI: 10.1016/S1097-2765(00)80467-0

Figure 1 The Apo PPARδ Crystal Structure (a and b) Two views differing by 90° of the structure of the apo PPARδ LBD (amino acids 210–476) are presented in a solid render. The three layers of alpha-helical sandwich are shown in red, purple, and blue, respectively. Beta strands are shown in yellow and the loops in white. (c) Worm drawing of the PPARδ backbone with a Connolly surface of the unoccupied van der Waals space in the ligand-binding site. The unoccupied space was calculated by fitting water molecules into the hydrophobic pocket of the protein. The total volume of the pocket is approximately 1300 Å3. The backbone is colored according the temperature factor profiles of the polypeptide backbone atoms. (d) The channel providing access to the ligand-binding pocket is shown by a surface presentation of the protein. The surface is colored according to electrostatic potential (blue, positive; red, negative; white, neutral). Molecular Cell 1999 3, 397-403DOI: (10.1016/S1097-2765(00)80467-0)

Figure 2 The PPARδ–EPA Cocrystal Structure (a) Structure of the PPARδ–EPA complex. The PPARδ polypeptide backbone is shown as a yellow ribbon. The carbon atoms of EPA in the tail-up or tail-down configurations are shown in purple and green, respectively. The acid oxygen atoms are shown in red. (b) Interactions between the EPA molecules and residues of the PPARδ LBD. Hydrogen bonds are indicated by solid arrows and hydrophobic interactions are indicated by dashed arrows. Yellow amino acids and boxes correspond to those residues that are conserved in all three PPAR subtypes, and white amino acids and boxes correspond to those that are not conserved between PPAR α, γ, and δ. (c) Electron density map for the alternative conformations of the EPA molecule. The map was calculated with 2Fo − Fc coefficients and contoured at 1.0 sigma. The EPA hydrocarbon chains are colored in green. (d) Quantum mechanical energy surface for the 7-carbon repeating unit from the EPA hydrocarbon chain. Conformations with the lowest energy are colored blue, with higher energies colored according to the scale, where energies are given in kcal/mole. The black dots show the actual conformations of the four copies of the repeating unit in each of the four EPA molecules from the crystal structure. Molecular Cell 1999 3, 397-403DOI: (10.1016/S1097-2765(00)80467-0)

Figure 3 The PPARδ–GW2433 Cocrystal Structure (a) Structure of the PPARδ–GW2433 complex. The PPARδ backbone is represented by the yellow ribbon, and GW2433 is represented with sticks and is color coded as follows: carbon, cyan; oxygen, red; nitrogen, blue; green, chlorine; and orange, fluorine. (b) Superposition of the structures of GW2433 and EPA bound to PPARδ. The surface of the pocket is represented with white dots, and the compounds are color coded as in (a) and in Figure 2A. (c) Chemical structures of the compounds described in this study. (d) Superposition of the TZD headgroup from the PPARγ rosiglitazone cocrystal structure (Nolte et al. 1998) with the carboxylic acid headgroup from the EPA PPARδ cocrystal structure. PPARγ (blue, carbon) and PPARδ (yellow, carbon) amino acid side chains are denoted in different colors. The polar headgroups form the same key hydrogen bonds in PPARγ and PPARδ that are essential for stabilizing the coactivator motif–binding pocket. Molecular Cell 1999 3, 397-403DOI: (10.1016/S1097-2765(00)80467-0)