Search and Download Tools for Small Molecule Data in the PDB archive

The Ligand Expo resource was retired on February 13, 2026 (announcement)

Current and regularly updated resources are available to access chemical and structural information about small molecules within the structure entries of the Protein Data Bank.

• Visit the wwPDB Chemical Component Dictionary (CCD) resource for file downloads, including the CCD, CCD model data, and SMILES/InChI/InChIKey data files
• 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)
• Access SMILES/InChI descriptors using the RCSB PDB Data API and given list of CCD IDs by using this example and adding the following to the return value, in parallel to chem_comp and rcsb_chem_comp_info groups:
  pdbx_chem_comp_descriptor{
  type
  descriptor
  }

Scripts are also available 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

Please contact RCSB PDB with any questions.