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Characterization of the ligand binding pockets within the-simulation systems.

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posted on 24.06.2013 by Ralf C. Kling, Harald Lanig, Timothy Clark, Peter Gmeiner

(A) Extracellular view into the binding pocket of β2AR (blue ribbons). Residues involved in ligand binding are shown as blue sticks, whereas the ligand BI167107 is represented as orange sticks. (C) Side view into the binding pockets of the D2Down/UpR-models. Helices TM3, TM4 and TM5 are shown as ribbons (green: D2DownR; red: D2UpR), the other parts of the receptors are removed for clarity. Residues that stabilize dopamine in its binding pocket are represented as sticks. The different conformations of dopamine (green and red sticks) within the D2DownR- and D2UpR-simulations are depicted. (B, D) Schematic representation of interactions between the ligands BI167107 (B) and dopamine (D) and residues from β2AR and D2Down/UpR, respectively.