Chembl

ChEMBL MCP — drug-discovery database from EBI: bioactive molecules, drug targets, mechanism of action, clinical phases. Keyless.

Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.

Tools

• search(query, type?, limit?) — search molecules / targets / assays / docs
• molecule(chembl_id) — full molecule record
• target(chembl_id) — target (protein) record
• mechanism(chembl_id) — raw mechanism rows for one exact molecule ID
• chembl_mechanism(drug | molecule_chembl_id, candidates?, limit?) — mechanism of action from a drug name. Searches every molecule form the name matched (base + salts) in one mechanism query, so drugs whose pharmacology is curated on the salt still resolve — e.g. metformin's two mechanisms live on CHEMBL1703 (METFORMIN HYDROCHLORIDE), while the best name match CHEMBL1431 (METFORMIN) has none. Returns action_type, mechanism text, named target + organism, the form each mechanism was recorded on, and PubMed refs.
• activities(molecule_chembl_id?, target_chembl_id?, limit?) — activity records
• drug_indications(molecule_chembl_id?, mesh_id?, limit?) — disease indications

Data source

https://www.ebi.ac.uk/chembl/api/data/

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "chembl": {
      "url": "https://gateway.pipeworx.io/chembl/mcp"
    }
  }
}

Or connect to the full Pipeworx gateway for access to all 1394+ data sources:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

ask_pipeworx({ question: "your question about Chembl data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT