3D Macromolecular Structures
How to find 3D protein structures bound to a query compound or to similar compounds (e.g., aspirin or chemicals like it)

Method 4: Use the PubChem Structure Search tool to retrieve a compounds that are similar to a query compound, then retrieve the protein structures bound to those compounds:

  • Open the PubChem Structure Search page, which can be used to search for PubChem compounds by identity/similarity, substructure/superstructure, or molecular formula

  • For this example, select Search by: Identity/Similarity

  • Select the option for searching by CID, SMILES, InChI

  • Enter the CID 2244 for aspirin

  • Under Options, select the desired level of similarity for the structures you want to retrieve. Identical structures are shown as the default selection, but if you want to retrieve similar structures such as salicylic acid, change the option to a less stringent setting, in this case: Similar Compounds, score>=80%. (The PubChem help document provides details about identical structures and similar compounds.)

  • Under Filters: Data Source, select From: MMDB
    This will limit retrieval to PubChem compounds that originated from the Molecular Modeling Database (MMDB), ensuring that all compounds retrieved also appear in corresponding 3D protein structure records, where they can be viewed in 3D bound to a protein structure.

  • Scroll to the top of the search page and press the Search button

  • A drawing of your query compound will appear. Press the Continue button to view the search results.

  • The Search results page will show the query compound and similar compounds, including, for example, CID 338: salicylic acid. 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.

  • Once you are viewing the list of protein structure records in the Entrez Structure (MMDB) database, 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.)

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Revised 23 September 2016