The best predicted binding poses of ligands in the CD45 active site.

Abstract

<p>The best predicted binding poses for peroxy acid C14 (panel A) and hydrogen peroxide (panel B) in the CD45 active site. The receptor was based on the CD45 D1 domain from PDB structure 1YGU <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052495#pone.0052495-Nam1" target="_blank">[20]</a>, with residues mutated to correspond to a CD45 reference sequence (UniProtKB accession number P08575) using the SWISS-MODEL web server <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052495#pone.0052495-Arnold1" target="_blank">[11]</a>. The docking was performed with the AutoDock Vina version 1.1.1 software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052495#pone.0052495-Trott1" target="_blank">[15]</a> using a rigid receptor and a binding box centered on the CD45 phosphatase active site. The best binding pose was defined as the pose with the strongest affinity in the largest cluster of poses, with poses clustered with a 1.5 Å RMSD thresholds. Also highlighted are four important residues involved in binding (Tyr683, His822, Arg859 and Gln897) and the catalytic cysteine (Cys853). Predicted hydrogen bonds with a 3.5 Å distance cutoff are shown as green dashed lines. The residues are numbered according the P08575 sequence.</p