PDBsum entry 3htd

Hydrolase

PDB id: 3htd

Contents

Protein chain

163 a.a.

Ligands

PO4

JZ5

BME ×2

Waters ×331

References listed in PDB file

Key reference

Title

Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.

Authors

S.E.Boyce, D.L.Mobley, G.J.Rocklin, A.P.Graves, K.A.Dill, B.K.Shoichet.

Ref.

J Mol Biol, 2009, 394, 747-763. [DOI no: 10.1016/j.jmb.2009.09.049]

PubMed id

19782087

Abstract

We present a combined experimental and modeling study of organic ligand molecules binding to a slightly polar engineered cavity site in T4 lysozyme (L99A/M102Q). For modeling, we computed alchemical absolute binding free energies. These were blind tests performed prospectively on 13 diverse, previously untested candidate ligand molecules. We predicted that eight compounds would bind to the cavity and five would not; 11 of 13 predictions were correct at this level. The RMS error to the measurable absolute binding energies was 1.8 kcal/mol. In addition, we computed "relative" binding free energies for six phenol derivatives starting from two known ligands: phenol and catechol. The average RMS error in the relative free energy prediction was 2.5 kcal/mol (phenol) and 1.1 kcal/mol (catechol). To understand these results at atomic resolution, we obtained x-ray co-complex structures for nine of the diverse ligands and for all six phenol analogs. The average RMSD of the predicted pose to the experiment was 2.0 A (diverse set), 1.8 A (phenol-derived predictions), and 1.2 A (catechol-derived predictions). We found that predicting accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site. Unanticipated binding modes, multiple ligand binding, and protein conformational change all proved challenging for the free energy methods. We believe that these results can help guide future improvements in physics-based absolute binding free energy methods.

Figure 1.
Fig. 1. (a) T4 Lysozyme L99A/M102Q binding site shown in complex with phenol and one ordered water molecule.^23 (b) Unwinding of helix F upon binding of certain ligands (cyan) yields an enlarged binding site relative to apo (orange).

Figure 6.
Fig. 6. Crystallographic orientations of the reference ligands phenol (orange; PDB ID 1LI2) and catechol (cyan; PDB ID 1XEP) overlaid on the apo reference structure (gray; PDB ID 1LGU). The two alternate hydroxyl positions are labeled A and B.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 394, 747-763) copyright 2009.