NCBI Structures: Find Protein Structures with Specific Components

One way to explore structures is to start with a particular molecule or compound and link to structures containing that component. You can do this using PubChem.

Click Next to get started.

PubChem Search

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PubChem contains information about small molecules. Let's find structures with aspirin.

Search PubChem for aspirin.

PubChem Search

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The most relevant result is at the top.

Click to go to the record for aspirin (CID: 2244).

Using PubChem to Link from Molecules to Structures Containing Them

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Find the Contents section (you may have to scroll down).

Select 16 Interactions and Pathways.

Using PubChem to Link from Molecules to Structures Containing Them

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The Interactions and Pathways section shows a list of three-dimensional (3D) structures that contain the molecule.

Scan through these structures.

Using PubChem to Link from Molecules to Structures Containing Them

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At the bottom of this section, click View [X] proteins in NCBI Structure to pull up relevant records in the Structure Database (in this example, all the structures that contain aspirin).

Using PubChem to Link from Molecules to Structures Containing Them

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You are now viewing all of the structures in the Structure database that contain aspirin.

Conclusion

Congratulations! You now know how to use PubChem to find structures with specific components in the NCBI Structure database.

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