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. 2014 Jun 2;5(7):727-9.
doi: 10.1021/ml500220a. eCollection 2014 Jul 10.

Protein-ligand cocrystal structures: we can do better

Charles H Reynolds  1
Affiliations

Protein-ligand cocrystal structures: we can do better

Charles H Reynolds. ACS Med Chem Lett. .

Abstract

There is a large body of evidence that many protein-ligand cocrystal structures contain poorly refined ligand geometries. These errors result in bound structures that have nonideal bond lengths and angles, are strained, contain improbable conformations, and have bad protein-ligand contacts. Many of these problems can be greatly reduced with better refinement models.

Keywords: Protein−ligand cocrystal; bound ligand strain; structure refinement; structure-based design; structure-induced fit.

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Figures

Figure 1
Figure 1
Comparison of ligand structures in (a) 3qad, (b) the revised structure 3rzf, and (c) the 3rzf ligand after minimization outside the protein using the MMFF force field in MOE (Chemical Computing Group).
See this image and copyright information in PMC

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