Method 3: Search the PubChem Compound database to retrieve a chemical of interest and similar compounds, then retrieve the protein structures bound to those compounds:

• Open the PubChem Compound database.



• In the query box, enter the term aspirin or it's PubChem Compound identifer (CID) 2244 and press GO. (The former will retrieve compounds that contain the term aspirin anywhere in their records; the latter will only retrieve the specific record for aspirin. See the PubChem help document for search tips.)



• On the search results page, select the Related Structures/Similar Compounds for the compound of interest, in this case for CID 2244.



• The next page shows the broader set of compounds. Click on a compound of interest to view its PubChem record, then follow the Other Links/Protein Structures link that appears in the right margin of the display.



• A list of protein structure records from MMDB that contain the compound(s) will appear



• Click on the accession number of any record of interest to view its summary information.



• On the structure summary page, press the Structure View in Cn3D button to open an interactive view of the 3D protein structure and its bound chemical. (The Cn3D program must first be installed on your computer in order for that button to work. The program is free and installation only takes a minute or two.)

Additional notes:

• Method 3 will retrieve protein structures bound to your query compound or similar compounds. However, the cutoff score for "Related Structures/Similar Compounds" is very stringent (similarity score [Tanimoto] >90%) so you might not get as many additional records as you'd like. It does not find salicylic acid (CID 338), for example, if we start with aspirin (CID 2244). See the PubChem CrossLinks section of the PubChem help document for more information on score cutoffs that were used for Related Structures links and additional details about identical structures and similar compounds.



• Method 4, which uses the PubChem Structure Search tool, offers greater flexibility by allowing you to select a desired similarity score cutoff.

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