Fetch downloadable PubChem compound files and identifiers from a CID, compound name, or InChIKey. Learn more
Fetch downloadable PubChem compound files and identifiers from a CID, compound name, or InChIKey. Learn more
Fetch downloadable PubChem compound files and identifiers from a CID, compound name, or InChIKey. Learn more
Download ChEMBL molecule records as JSON and SDF by ChEMBL compound ID.
Download BindingDB binding record files by BindingDB monomer ID.
Download ChEBI chemical entity records as JSON by ChEBI ID.
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
Convert SDF ligand files, including multi-record batches, into SMILES strings.
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
Convert InChI strings into SMILES with batch support and downloadable outputs.
Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.
Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
Download ChEMBL molecule records as JSON and SDF by ChEMBL compound ID.
Download BindingDB binding record files by BindingDB monomer ID.
Download ChEBI chemical entity records as JSON by ChEBI ID.
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
Convert SDF ligand files, including multi-record batches, into SMILES strings.
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
Convert InChI strings into SMILES with batch support and downloadable outputs.
Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.
Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
Configure inputs to begin
Set options on the left, then click “Fetch downloads” — or start from an example.
2244
aspirin
BSYNRYMUTXBXSQ-UHFFFAOYSA-N
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. |
| 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.
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.
Use a PubChem CID for the most direct lookup. Compound names and InChIKeys are also supported, but names can map to multiple records.
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.
Yes. Download an SDF or SMILES file, then prepare the ligand with a tool such as Open Babel before docking.