@pipeworx/pubchem

PubChem MCP — NIH chemistry compound database, no auth.

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

Tools

• search_by_name(name, max_results?) — name → CIDs.

• get_compound(cid) — formula, MW, SMILES, InChI, properties.

• get_synonyms(cid, max_results?) — all known names.

• get_classification(cid) — pharmacology classification tree.

Related MCP server: PubChem Chemical Safety MCP Server

Data source

https://pubchem.ncbi.nlm.nih.gov/rest/pug (PUG-REST + PUG-VIEW). No key. Be reasonable on RPS (5/sec recommended).

Quick Start

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

{
  "mcpServers": {
    "pubchem": {
      "url": "https://gateway.pipeworx.io/pubchem/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 Pubchem data" })

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

More

• Docs and guides

• pipeworx.io

License

MIT