News

Announcement: Ligand Expo To Be Retired February 13, 2026

01/20

RCSB PDB and wwPDB offer robust resources to access chemical and structural information about small molecules within PDB entries.

As such, the legacy Ligand Expo website (ligand-expo.rcsb.org), established nearly 20 years ago as an auxiliary service for small molecules, will be retired on February 13, 2026 (announced previously).

Most of the data previously available on the Ligand Expo download pages have been migrated to the wwPDB Chemical Component Dictionary (CCD) resource or integrated into RCSB.org chemical search tools.

Users should transition to RCSB PDB and wwPDB services as soon as possible, including:

wwPDB File Downloads

Chemical Component Dictionary (CCD) Definitions (Overview)

Chemical Descriptors (concatenated files)

RCSB PDB Search Tools

Chemical Search

Use the RCSB PDB Chemical Search to screen residues and small molecule components for structural similarity to a query chemical molecule and to search by attribute (e.g., Chemical Name, Synonyms, InChiKey)

SMILES/InChI Descriptors via Data API

  • To query for specific items in the chemical component dictionary based on a given list of CCD IDs, use this example and add the following to the return value, in parallel to chem_comp and rcsb_chem_comp_info groups:

pdbx_chem_comp_descriptor{
type
descriptor
}

Scripts to Generate Specific Data Content/Files

#generate_pdb_ligand_mappings.py (GitHub)

  • A mapping between all PDB structures and the ligands present in each structure, as a tabulation of PDB IDs and chemical component IDs (pdb-to-cc.tsv)
  • A mapping between all ligands in the PDB and the corresponding list of PDB structures in which they are present, as a tabulation of chemical component IDs and PDB IDs (cc-to-pdb.tsv)
  • A statistics file with the occurrence count of chemical components in PDB entries along with the corresponding chemical name and formula (cc-counts-extra.tsv)

#extract_ligand_coordinates.py (GitHub)

  • Chemical component coordinate data files on an user-specified CCD ID basis, including finding all PDB entries with this specific ligand, and then extracting the atomic coordinates of the ligand in all these PDB entries

These scripts were created in part by Krish Parmar (Rutgers ‘28) during his 2025 summer internship with RCSB PDB and the Rutgers RAD Collaboratory.

<I>Use the Chemical Search: Chemical Similarity feature to create a 2D chemical drawing tool for substructure searching</I>Use the Chemical Search: Chemical Similarity feature to create a 2D chemical drawing tool for substructure searching
<I>Register for the February 26 Webinar on Searching and Downloading Small Molecules in the PDB for an overview of these resources</I>Register for the February 26 Webinar on Searching and Downloading Small Molecules in the PDB for an overview of these resources