3D Macromolecular Structures
How to find 3D protein structures bound to a specific small biopolymer (e.g., a peptide)

Method 1: Search the PubChem Compound database to retrieve a small biopolymer of interest, then retrieve the protein structures bound to it:

  • Open the PubChem Compound database.

  • In the query box, enter the PubChem Compound identifer (CID) for the small biopolymer of interest, for example 5496545 and press GO. (See the PubChem help document for tips on additional ways to search the database.)

  • On the search results page, select the Other Links/Protein Structures link for the compound of interest, in this case for CID 5496545. (Alternatively, on the search results page you can first click on CID 5496545 to open the complete PubChem record for that compound and then select "Links: Protein Structure" from the right hand margin of the PubChem record.)

  • A list of protein structure records from MMDB that contain your compound(s) of interest 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.)

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Revised 05 February 2015