Method 2: Use the PubChem Structure Search tool to retrieve a compounds that are identical or 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 5496545 for the biopolymer featured in this example



• 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 expand your search to retrieve similar structures, change the option to a less stringent setting. For this example, select: Similar Compounds, score>=95%. (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.



• Select Other Links: Protein Structures from the grey area at the top of the page. That will retrieve protein structures that are bound to any of the compounds listed on the page (default) or those you have selected with checkboxes.



• 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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