Introduction

What are Ligands?

Small molecules such as ions, cofactors, inhibitors, drugs, etc. are called ligands in the PDB. They are often found interacting with biological polymers (like proteins and nucleic acids) and may have structurally stabilizing or functional roles in their interactions with macromolecules.

Why learn about ligands?

Ligands often bind to pockets, cavities, and surfaces to facilitate their structural or functional roles. Thus, exploring the location of ligand binding and understanding a ligand’s interactions can help you understand the mechanism of biomolecular functions. It can also help you design or customize these interactions for specific purposes - e.g., to regulate the protein or nucleic acid function to treat or prevent a disease.

What are ligands of interest?

While there may be many different ligands interacting with the biological macromolecules in a structure, only those having an impact on the function(s) of the molecules in the structure are examined closely and validated. Note that at this time only X-ray structures that have experimental data and complete validation information are validated to assess goodness of fit for ligands. Learn more about Ligand Validation.

Documentation

The Interface

The Ligands tab displays the following plots and table for all validated non-polymer ligands, and indicate whether they are the ligands of interest (LOI). LOI is a functional ligand in macromolecular complexes designated as focus of research in the experiment by structure authors or by RCSB PDB under the criteria of: (1) Formula Weight > 150 Da, and (2) Not in an exclusion list of likely non-functional ligands, as described in Ligand Validation.

Figure 1: A 2D plot of the quality of the ligand HEM’s goodness of fit for the best instance in the structure (green diamond) for the PDB entry 7lad (as of December 2023)

In the Figure 1 (for the PDB ID 7lad) the

• Top half of the page has 2D plots showing
• quality of all instances of the ligand (HEM) in the entry (left plot).
• a comparison of the ligand quality in structures where the same ligand is bound to the same target (middle plot, yellow circles) or other targets (right plot, blue circles).
• Bottom half presents measures of ligand quality in instances of the ligand displayed in the 2D plots.
• Note for this structure there is no validation data available for the ligand XRD.

Learning about the Structure

The experimental data fitting vs geometry 2D plot in the left presents ligand quality for all instances of the ligand in the structure. The best instance is shown as a green diamond, while all other instances are shown as green circles. All other data on the ligands tab compares the quality of the ligand in the entry of interest in other structures.

Exploring other structures

The experimental data fitting vs geometry 2D plot in the left presents ligand quality for all instances of the ligand in the structure. The best instance is shown as a green diamond, while all other instances are shown as green circles. All other data on the ligands tab compares the quality of the ligand in the entry of interest in other structures.

Various measures of fit to electron density and geometry of the ligand in other entries are presented in 2D plots and tabular format. This analysis allows you to compare the ligand of interest in these structures to the same ligand in other structures (either bound to the same or different targets) and select the best instance(s) for visualization, analysis, and hypothesis development. Learn more about the ligand validation process and measures.

All instances of the ligand of interest in the archive can be found from the Ligand Definition and Summary page by clicking on the button on the top right corner of the page.