1OWZ

T4 Lysozyme Cavity Mutant L99A/M102Q Bound With 4-FluoroPhenEthyl Alcohol

DOI: 10.2210/pdb1OWZ/pdb

Classification: HYDROLASE
Organism(s): Escherichia virus T4
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-03-31 Released: 2004-04-13
Deposition Author(s): Wei, B.Q., Baase, W.A., Weaver, L.H., Matthews, B.W., Shoichet, B.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Observed: 0.187

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Testing a Flexible-receptor Docking Algorithm in a Model Binding Site

Wei, B.Q., Weaver, L.H., Ferrari, A.M., Matthews, B.W., Shoichet, B.K.

(2004) J Mol Biol 337: 1161-1182

PubMed: 15046985 Search on PubMed
DOI: 10.1016/j.jmb.2004.02.015
Primary Citation of Related Structures:
1OV7, 1OV5, 1OVK, 1OVJ, 1OVH, 1OWZ, 1OWY

PubMed Abstract:

Sampling receptor flexibility is challenging for database docking. We consider a method that treats multiple flexible regions of the binding site independently, recombining them to generate different discrete conformations. This algorithm scales linearly rather than exponentially with the receptor's degrees of freedom. The method was first evaluated for its ability to identify known ligands of a hydrophobic cavity mutant of T4 lysozyme (L99A). Some 200000 molecules of the Available Chemical Directory (ACD) were docked against an ensemble of cavity conformations. Surprisingly, the enrichment of known ligands from among a much larger number of decoys in the ACD was worse than simply docking to the apo conformation alone. Large decoys, accommodated in the larger cavity conformations sampled in the ensemble, were ranked better than known small ligands. The calculation was redone with an energy correction term that considered the cost of forming the larger cavity conformations. Enrichment improved, as did the balance between high-ranking large and small ligands. In a second retrospective test, the ACD was docked against a conformational ensemble of thymidylate synthase. Compared to docking against individual enzyme conformations, the flexible receptor docking approach improved enrichment of known ligands. Including a receptor conformational energy weighting term improved enrichment further. To test the method prospectively, the ACD database was docked against another cavity mutant of lysozyme (L99A/M102Q). A total of 18 new compounds predicted to bind this polar cavity and to change its conformation were tested experimentally; 14 were found to bind. The bound structures for seven ligands were determined by X-ray crystallography. The predicted geometries of these ligands all corresponded to the observed geometries to within 0.7A RMSD or better. Significant conformational changes of the cavity were observed in all seven complexes. In five structures, part of the observed accommodations were correctly predicted; in two structures, the receptor conformational changes were unanticipated and thus never sampled. These results suggest that although sampling receptor flexibility can lead to novel ligands that would have been missed when docking a rigid structure, it is also important to consider receptor conformational energy.

Related Citations:

A Model Binding Site for Testing Scoring Functions in Molecular Docking
Wei, B.Q., Baase, W.A., Weaver, L.H., Matthews, B.W., Shoichet, B.K.
(2002) J Mol Biol 322: 339

Organizational Affiliation:

Department of Pharmaceutical Chemistry, University of California, 600 16th St, San Francisco, CA 94143-2240, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A	164	Escherichia virus T4	Mutation(s): 2 Gene Names: E EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Protein Feature View Expand
( Mouse scroll to zoom / Hold left click to move ) Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4FA Query on 4FA Download CCD File	A	4-FLUOROPHENETHYL ALCOHOL C₈ H₉ F O MWUVGXCUHWKQJE-UHFFFAOYSA-N		Ligand Interaction
BME Query on BME Download CCD File	A	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download CCD File	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction