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All residues and small molecule components found in PDB entries, including standard and modified amino acids/nucleotides, small molecule ligands, ions, and solvent molecules, are described in the wwPDB's Chemical Component Dictionary.
The information stored in this dictionary can be easily searched using any of these query options:
- Simple top bar searching (with autocomplete suggestions)
Click on the Ligand icon (located above the top search box) to limit your search. Enter a ligand name or the 3-character chemical component ID. (More on top bar searching).
- Chemical Component Search
This powerful form can be accessed by selecting the top bar ligand icon and then [ additional ligand options ]. Launch the chemical structure editor to draw a structure, or paste in a SMILES or SMARTS string, and then perform a substructure, exact, similarity, or superstructure search. In addition, ligands can be searched by name, identifier, formula, and molecular weight. A tutorial and screencast demonstrating the chemical structure search is available.
- Advanced Search
Supports the searches mentioned above, plus additional searches by chemical component type, binding affinity, sub-component, and more. These types of searches can be combined and even amended with searches for the associated structures. Learn more about the advanced search with this tutorial with this list of available queries.
These searches will return a Ligand Summary page that contains an
overview of the chemical component, 2D and 3D images, links to other
resources, and links to related ligands and PDB entries.
