Ligands

Why

The goal of a crystallographic study is often to visualize the interaction of a small molecule or ligand with a macromolecule. This is a core process in the development of new therapeutics. It is also common to discover density for an unanticipated small molecule in complex with a protein while solving a structure. In both cases, you need to fit the small molecule into the electron density to complete the atomic model. As part of this process, you frequently need to generate appropriate stereochemical restraints for new ligands for use in structure refinement.

How

In Phenix, the principal tool for fitting ligands into electron density is phenix.ligand_fit. This program identifies unfilled electron density in a map and attempts to place the user-defined ligand in the density by rotating around any torsional degrees of freedom. The process requires an electron density map, coordinates for the macromolecule, and information about the ligand (either as coordinates or as a chemical description that can be used to generate coordinates). The program outputs the coordinates of the ligand fitted into the density.

After ligand(s) are fit, subsequent refinement steps will require stereochemical restraints. In some cases, these may be present in the default restraint libraries. However, you often need to generate new restraints. The phenix.elbow (eLBOW) program automatically generates geometry restraints for novel ligands or improves restraints for standard ligands, starting from a variety of different formats.

How to use the ligand fitting GUI: Click here

Phenix reference manual for phenix.ligand_fit

How to use the phenix.elbow GUI: Click here

Phenix reference manual for phenix.elbow

Common issues

• Frequently asked questions about ligands

Related programs

• phenix.guided_ligand_replacement: This program uses prior knowledge from a previously fit ligand to expedite the fitting of a similar ligand into the same or similar protein. This is very useful when studying a series of compounds for the same or related macromolecular targets.
• phenix.ligand_identification: This program determines the identity of an unknown ligand by analyzing difference density peaks to reveal which ligand is likely to be present. Using a library of the 180 most frequently observed ligands in the PDB, the tool ranks each molecule by density fit and chemical interaction with the macromolecule.
• phenix.ready_set: This program prepares a model for refinement by generating all necessary ligand restraints with eLBOW and then updating the model file to reflect atom name changes from the new restraints.
• phenix.reel: This Restraints Editor Especially Ligands (REEL) tool includes a 3D view of the ligand and a tabular view of the restraints, allowing target values and standard deviations to be easily edited.