Downloading Small Molecules from PubChem

Downloading Small Molecules from PubChem for Docking with PyRx.

We have already talked about PubChem and how to obtain small molecules from PubChem; check the tutorial here.

For molecular docking in PyRx, you’ll usually need the 3D structure of your small molecule in a format like SDF or .mol2.

You can create a Table (Table 1) in the following forms. If you are working on a few compounds, this will help to track the molecules you are working with and also to make use of the SMILES if you want to predict some parameters, such as the Druglikeness screening or ADMET prediction.

We are going to work on the following compounds (small molecules/Ligand): Nicotinamide, Pyridoxine, Luteolin, Vernomygdin, Vernomenin.

1. Open PubChem (Figure 1).

2. In the search bar, type: Nicotinamide (Figure 2).

3. Click Search (Figure 3).

4. Select the compound from the results list (Figure 4).

5. Copy the PubChem CID and the SMILES (Figure 5), and paste them into Table 2.

 6. Downloading the Molecule.

Once on the compound’s page:

Look for the “Download” button (Figure 6 ). 

7. Select the format:

1. • SDF (3D) – most commonly used in PyRx (Figure 7).

   • Choose 3D coordinates (very important; don’t select 2D).

   • Click Download/Save.

   • This will save a file like compound.sdf to your computer.

Figure 2: Download options to get the SDF format for Nicotinamide.  

Follow the same procedure for the remaining compounds and fill the table with the PubChem CID and the SMILES. 

Table 1: Information about Nicotinamide, Pyridoxine, Luteolin, Vernomygdin, Vernomenin. from PubChem.