PubChem Download

Fetch downloadable PubChem compound files and identifiers from a CID, compound name, or InChIKey.

Input

Entry ID

Database

Output format

Output

Configure inputs to begin

Set options on the left, then click “Fetch downloads” — or start from an example.

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:

Text

pubchem-2244-json.json
pubchem-2244-2d-sdf.sdf
pubchem-2244-3d-sdf.sdf
pubchem-2244-smiles.smiles

The 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.

Related tools

ChEMBL Download

Download ChEMBL molecule records as JSON and SDF by ChEMBL compound ID.

BindingDB Download

Download BindingDB binding record files by BindingDB monomer ID.

ChEBI Download

Download ChEBI chemical entity records as JSON by ChEBI ID.

Open Babel

Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.

SDF to SMILES

Convert SDF ligand files, including multi-record batches, into SMILES strings.

SMILES to SDF

Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.

InChI to SMILES

Convert InChI strings into SMILES with batch support and downloadable outputs.

MOL to SMILES

Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.

MOL2 to SMILES

Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.

SMILES to InChI

Convert SMILES strings into InChI strings with batch support and downloadable outputs.