Ligand Expo

Ligand Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components. The data in Ligand Expo are updated weekly.

LigandExpo is no longer maintained.

Accessing Ligand Expo features
Users are strongly encouraged to use RCSB.org Search APIs and Data APIs to obtain ligand information.

Accessing Chemical Component Dictionary definitions from wwPDB.org
Some file downloads are available at https://www.wwpdb.org/data/ccd for all CCD definitions in a concatenated file or the variances of the standard residues.

To access SDF/MOL formatted CCD files with ideal coordinates:

  1. Download individual CCD files in SDF/MOL format from the PDB archive at https://files.wwpdb.org/pub/pdb/refdata/chem_comp/
  2. Download a concatenated CCD file in SDF/MOL format at https://files.wwpdb.org/pub/pdb/data/monomers/components-pub.sdf.gz which is accessible from the wwPDB website at https://www.wwpdb.org/data/ccd


Searching Chemical Components at RCSB.org

  1. Use Data API to obtain SMILES/InChI descriptors
    1. Use the example at https://data.rcsb.org/#gql-example-8 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
      }
  2. Search for similar ligands based on formula, SMILES, InChI or 2D chemical drawing
    1. Go to Advanced Search -> Chemical Similarity -> select query type “Formula” for formula search or “Descriptor” for SMILES or InChI search, then choose the return type as "Molecular Definitions" and click on the “Search” button.
    2. Go to Advanced Search -> Chemical Similarity -> Click on “Open Chemical Sketch Tool” button to launch 2D chemical drawing tool for substructure search. You can also preload a molecule using CCD ID, SMILES, or InChI for further modification.
  3. Search for CCD ID, chemical name, synonyms, molecular weight, chemical component type, or InCheyKey
    1. Go to Advanced Search -> Chemical Attributes -> Chemical Components -> then select a search item (e.g., Chemical ID), then choose the return type as “Molecular Definitions” and click on the “Search” button.
  4. If searching by CCD ID alone, type the ID at the RCSB.org top simple search bar, then choose “in Chemical ID” from the drop down list.

 

Getting Started:



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