Downloading Ligand Structures

Downloading Your Ligand Library 

Once you have identified the desired set of molecules, you can download their structural information in various file formats suitable for molecular modeling software. Common formats include:

SDF (Structure Data File): Contains information about the 3D structure of molecules. 

SMILES (Simplified Molecular Input Line Entry System): A linear notation for describing molecular structures. 

CSV (Comma Separated Values): Can contain molecule identifiers and associated properties.

Once you’ve selected a compound:

1. On the Compound Summary page, scroll to the "3D Conformer" section

2. Click “Download”

3. Choose the format:

   • .sdf for structure data file (best for libraries)

   • .mol2 or .pdb for docking

   • .smiles for text-based input

Figure 1: Download options showing formats

Preparing a Ligand Library (Batch Download) To collect multiple ligands at once:

1. Go to the PubChem website. 

2. Click on "Upload ID list" (Figure 2). 

3. Click on "STEP 2. Provide a List of Identifiers".

4. Enter identifiers separated by comma or space. "Paste a list of CIDs (e.g., 2244, 3672, 5281), click on the search lens.

5. Click “Download” in the navigation bar.

6.  Use the "Download by List" tool 

7. Select format: .sdf, .smiles, or .csv 

8. Click Download.

Figure 2: Download options to collect multiple ligands at once