Announcement: Ligand Expo To Be Retired in 2025

05/19

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 in 2025.

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

wwPDB File Downloads

Chemical Component Dictionary (CCD) Definitions (Overview)

Individual CCDs: mmCIF, SDF/MOL> with ideal coordinates
Concatenated CCDs: mmCIF (plain text) | mmCIF (gz) | SDF/MOL (gz with ideal coordinates)
Protonation Variants Companion Dictionary: mmCIF (plain text) | mmCIF (gz)

Chemical descriptors (concatenated files)

SMILES, InChI, and InChIKey

RCSB PDB Search Tools

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 }

Search for similar ligands based on formula, SMILES, InChI or 2D chemical drawing

In Advanced Search -> Chemical Similarity, select query type “Formula” for formula search or “Descriptor” for SMILES or InChI search, then set return type as "Molecular Definitions" and click on “Search”
In Advanced Search -> Chemical Similarity, select the “Open Chemical Sketch Tool” button to launch a 2D chemical drawing tool for substructure search, with an option to preload a molecule using CCD ID, SMILES, or InChI for modification

Search for Chemical name, synonyms, molecular weight, chemical component type, or InChIKey

Type the ID, Chemical name, or Chemical synonym into the top search bar and select from the list of suggestions
In Advanced Search -> Chemical Attributes From Chemical Components, select a search item (e.g., Chemical ID), then choose the return type as “Molecular Definitions” and click on the “Search” button