ChEMBL Download

Fetch ChEMBL compound structure and metadata files by ChEMBL molecule ID.

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.

CHEMBL25

CHEMBL941

CHEMBL1201585

How to download ChEMBL records?

ChEMBL Download fetches downloadable molecule files from ChEMBL using a ChEMBL molecule ID. It returns JSON and SDF files in the results panel with metadata such as molecule type, molecular formula, molecular weight, AlogP, and SMILES when available.

Use this tool when you need ChEMBL compound files for cheminformatics, ligand preparation, screening, or reproducible molecule metadata.

Input	Description
`Entry ID`	ChEMBL molecule ID. Examples: `CHEMBL25`, `CHEMBL941`, `CHEMBL1201585`.

Setting	Description
`Database`	Opens the selected database download tool.
`Output format`	Return all files, JSON, or SDF.

Supported ChEMBL downloads

File	Format	Use
JSON	`.json`	ChEMBL molecule record for programmatic use.
SDF	`.sdf`	Structure file for cheminformatics and ligand workflows.

Understanding the results

The results panel lists each downloadable ChEMBL file. The Details tab includes the database, ChEMBL ID, record title, file label, format, source type, filename, and URL.

Filenames follow the pattern:

Text

chembl-CHEMBL25-json.json
chembl-CHEMBL25-sdf.sdf

If you need to convert ChEMBL SDF files into another ligand format, use Open Babel, SDF to PDB, or SDF to SMILES.

Common use cases

Download ChEMBL SDF files before ligand preparation.
Store JSON molecule metadata with screening results.
Retrieve structures for known drug-like compounds.
Convert ChEMBL structures into docking-ready formats.

FAQ

Can I enter a compound name?

This download tool is intended for direct ChEMBL IDs. Use database search first if you only know a compound name.

Why does the filename use the ChEMBL ID?

The ID is the stable database identifier and prevents ambiguity when compound names have synonyms or multiple spelling variants.

Can I use the SDF output for docking?

Yes, but docking tools often require preparation steps such as protonation, charge assignment, 3D coordinate cleanup, and format conversion.

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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.

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

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

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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.