The Protein Data Bank (PDB) is a global archive containing over 200,000 experimentally-determined 3D structures of biomolecules like proteins, DNA, and RNA. Interestingly, about 75% of these structures also include small molecules (ligands), which play vital roles, such as cofactors, reactants, or inhibitors (drugs). 

Each structure deposited in the PDB is assigned a unique PDB ID, and provides valuable details, such as  3D coordinates, structure data quality, and information about small molecules bound to the structure. However, understanding how the same small molecule interacts across different structures can be challenging, as ligand-related data is scattered across various PDB entries. Aggregating and comparing this data is often necessary to gain meaningful insights and address various biological questions.

To bridge this gap, PDBe presents novel PDBe-KB Ligand Pages that aggregate and summarise all structure data for each ligand in PDB. These pages offer a comprehensive view of each ligand, covering chemical, structural, interaction and functional details. They aggregate key data, including bound structures and proteins, PDB-wide ligand-protein interaction statistics, and related ligands. Additionally, the pages provide details such as molecular descriptors, 2D/3D structural view, cross-links to external databases like ChEMBL, PubChem, and DrugBank for further exploration. This unified resource enables users to easily explore and analyse ligand data across the PDB.

In this webinar, we will showcase the features of PDBe-KB Ligand Pages and guide you on how to use them to uncover scientific insights about small molecules in the PDB.

Who is this course for?

This webinar is suitable for individuals working on protein biology. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

Outcomes

By the end of the webinar you will be able to:

• Navigate and utilise tools on PDBe-KB ligand pages to explore and analyse aggregated ligand data across the PDB
• Visualise small molecules and their interactions with macromolecular structures in the PDB
• Interpret PDB-wide ligand-protein interaction statistics to gain insights into common binding residues and ligand-interacting atoms
• Download the relevant data for your ligand of interest

DOI: 10.6019/TOL.PDBeLigand-w.2025.00001.1

This webinar took place on 5th February 2025. Please click the 'Watch video' button to view the recording.