Ligand and Environments

The Ligands and Environments tab provides detailed information about all chemically distinct ligands present in the Preferred Assembly of a PDB entry, along with their interactions with binding site residues. These interactions are calculated using  PDBe Arpeggio. 

Ligand summary

In this section, ligands are displayed with a 2D diagram and an annotation of their likely function in the macromolecule. (e.g. Cofactor-like)

• Click on a ligand to reveal additional details, including a short summary with Ligand name, Formula, and Molecular weight. 
• Navigate to Ligand Pages* to know more about the ligand using the provided links
  • bound structures – List of PDB entries containing the ligand, with details of associated proteins 
  • interaction statistics – Aggregated percentages of interactions between ligand atoms and amino acid residues across the PDB archive  
  • related ligands – List of all structurally similar ligands 

Interaction data

This section provides the details of interactions between the ligand and macromolecule. To explore the interaction data in detail:

• Select an instance of the ligand bound to a specific macromolecule chain using the drop-down menu. This will update the table, 3D viewer and 2D viewer with interactions of the selected instance of the ligand.
• The table lists the details of the interatomic interaction between the ligand and the macromolecule. 
• Hover over a row of the table to highlight interacting binding site residues in the 3D viewer. 
• Use the search bar to filter interactions by type, binding site residue, or ligand atom. Both the 3D and 2D viewers will update to display only the filtered interactions, making it easier to focus on specific details.

If you want to know even more about a specific ligand follow the “View more about this ligand” links to visit the Ligand Pages. 

Ligand pages bring together all the key information about ligands found in the Protein Data Bank (PDB). Each page gives you an overview of ligands, including:

• What the ligand is – with a short description and its basic physicochemical properties
• Where it’s found – proteins the ligand binds to and the role it plays in those complexes
• How it interacts – statistics about its binding interactions with macromolecules
• Similar molecules – a list of structurally similar ligands you can explore further
• Connections – links to other scientific databases for more details

These pages are designed to help you quickly understand what a ligand does, how it behaves, and why it matters in biology or medicine.

Example: Check out the ligand page for Imatinib (CCD ID: STI) at pdbe.org/chem/sti