Chemical Component Search Tools

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Use the forms below to search for chemical components within the PDB Component Dictionary.

• Search for chemical components by 3-letter component identifier code, molecular name, molecular formula, SMILES description, or InChi/InChiKey chemical description.
You can also check to see if a 3-letter code is being held by a deposition in progress.
• Either start with a SMILES description or chemical data file (see drop-menu for acceptable formats), or draw a 2D chemical structure from scratch (Launch without input). It can also generate chemical component definitions from your 2D structure.
• Search for instances of a chemical component throughout the PDB. The Display option allows you to simply see a list of PDB codes, or to download these coordinates in PDB, MOL/SDF and mmCIF formats.
• You can also search for analogs to the standard amino acids, nucleotides, popular drugs, and common aromatic ring systems by using the Browse feature in the top menu bar.

Your query results are also searchable! Each hit from your initial query will contain links to continue searching by similar name, chemical formula, or structure (SMILES).

Molecular name, formula, and descriptor search options

Search term    Search type Component identifier (3-letter code) Similar to component (3-letter code) Formula (all atom exact) Formula (heavy atom exact) Formula (exact subset) Formula (subset) Formula (close) Molecular name (exact) Molecular name (exact sub-string) Molecular name (similar) SMILES Chemically similar to SMILES InChI InChIKey

Alternately, use RCSB.org advanced search https://www.rcsb.org/search/advanced to search by Component ID, name, or synonym under "Chemical Attributes" category; Use RCSB.org chemical similarity search https://www.rcsb.org/search/advanced/chemical to search by Formula, SMILES or InChI; Use RCSB.org chemical sketch tool https://www.rcsb.org/chemical-sketch to search SMIELS and InChI as well as to convert the descriptors to their chemical drawing for modification on the chemical search.

Search for instances of chemical components by 3-letter ID code

Component ID code   Display PDB entry codes + coordinate files

Alternately, you can use PDB Search API to perform similar queries on specific ligands in PDB entries. To learn how to use PDB Search API, go to: https://search.rcsb.org/#search-api; An example to find all PDB entries with ligand ATP can be accessed here

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