PubChem Download
v1.0.0Fetch downloadable PubChem compound files and identifiers from a CID, compound name, or InChIKey.
Fetch downloadable PubChem compound files and identifiers from a CID, compound name, or InChIKey.
PubChem Download fetches downloadable compound files from PubChem using a compound name, CID, or InChIKey. It returns the file links and inline text files in the results panel so you can download them individually or as a bundle.
Use this tool when you need PubChem compound records for docking, cheminformatics cleanup, database registration, or downstream conversion. The downloaded files come from the identifiers returned by PubChem; ProteinIQ does not rewrite structures or identifiers.
| Input | Description |
|---|---|
Entry ID | PubChem CID, compound name, or InChIKey. Examples: 2244, aspirin, BSYNRYMUTXBXSQ-UHFFFAOYSA-N. |
| Setting | Description |
|---|---|
Database | PubChem by default. Opens the selected database download tool. |
Output format | All formats by default, or JSON, SDF, or SMILES. Selecting SDF lists both the 2D and 3D file links. |
| File | Format | Use |
|---|---|---|
| JSON | .json | Complete PubChem compound record for programmatic use. |
| 2D SDF | .sdf | Two-dimensional structure file for cheminformatics tools. |
| 3D SDF | .sdf | Three-dimensional structure file when PubChem provides one. |
| SMILES | .smiles | Canonical SMILES text when available. |
The results panel lists every downloadable file returned for the compound. Remote files include a URL and download action. Inline sequence or text values, when present, are stored directly in the result file record.
The example aspirin resolves to CID 2244. With Output format set to All formats, the returned filenames are:
pubchem-2244-json.json
pubchem-2244-2d-sdf.sdf
pubchem-2244-3d-sdf.sdf
pubchem-2244-smiles.smilesThe output lists the selected compound files. Check the resolved CID in their filenames when looking up a compound by name.
Use a PubChem CID for the most direct lookup. Compound names and InChIKeys are also supported. A name can map to multiple records; this tool uses the first returned match. Confirm the CID before using the result, or use database search to compare matches.
Some PubChem compounds do not have a 3D conformer available. The tool lists the 3D download link, but that request can fail. Use the 2D SDF or SMILES output and generate coordinates with a structure preparation tool. A downloaded conformer is not automatically prepared for docking.
Yes. Download an SDF or SMILES file, then prepare the ligand with a tool such as Open Babel before docking.
Enter one identifier or compound name on a single line, up to 200 characters. Surrounding spaces are ignored. These lookups need an internet connection: ProteinIQ retrieves the record from the selected database, and file downloads contact its file service.
If a text file cannot be loaded in the browser, a warning appears and its download link stays available. A listed link does not guarantee that the database currently serves that file. Retry the download or check the original database record; a connection failure is different from an unknown entry.
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