PubChem Download
Fetch downloadable PubChem compound files and identifiers from a CID, compound name, or InChIKey.
Input
Output
2244
aspirin
BSYNRYMUTXBXSQ-UHFFFAOYSA-N
Input
Output
2244
aspirin
BSYNRYMUTXBXSQ-UHFFFAOYSA-N
How to download PubChem records?
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 | Opens the selected database download tool. |
Output format | Return all files, JSON, SDF, or SMILES. |
Supported PubChem downloads
| 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. |
Understanding the results
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.
Filenames follow the pattern:
pubchem-2244-json.json
pubchem-2244-2d-sdf.sdf
pubchem-2244-3d-sdf.sdf
pubchem-2244-smiles.smilesThe Details tab summarizes the database, entry ID, record title, file label, format, source type, filename, and URL.
Common use cases
- Download SDF structures before format conversion with Open Babel.
- Fetch canonical SMILES before ligand cleanup or screening.
- Collect PubChem JSON records for reproducible compound metadata.
- Retrieve aspirin or other reference compounds by CID instead of copying structures manually.
FAQ
What identifier should I enter?
Use a PubChem CID for the most direct lookup. Compound names and InChIKeys are also supported, but names can map to multiple records.
Why is there no 3D SDF for my compound?
Some PubChem compounds do not have a 3D conformer available. In that case, use the 2D SDF or SMILES output and generate 3D coordinates with a structure preparation tool.
Can I use this for docking?
Yes. Download an SDF or SMILES file, then prepare the ligand with a tool such as Open Babel before docking.
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