PubChem MCP Server

Read-only MCP wrapper over PubChem’s public chemical-compound database. Complements bioactivity-focused ChEMBL by adding broad compound lookup.

   
Type MCP server
Supplier JackKuo666 (community OSS, hosted on Smithery)
Availability GA
Pricing Free / OSS (MIT); PubChem API is public, no key required
Capabilities Read-only

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/structural-biology-drug-discovery/pubchem-compound-search into ~/.claude/skills/).
  • Claude Desktop / Code — Smithery one-liner (handles install + Claude config in one step): 
    npx -y @smithery/cli@latest install @JackKuo666/pubchem-mcp-server --client claude --config "{}"
  • Manual install — pip-install the package first, then register: 
    pip install pubchem-mcp-server

    Claude Code:

    claude mcp add --transport stdio pubchem -- python -m pubchem-mcp-server

    Claude Desktop — add to claude_desktop_config.json:

    {
  "mcpServers": {
    "pubchem": { "command": "python", "args": ["-m", "pubchem-mcp-server"] }
  }
}
  • Hosted HTTP alternative (cyanheads, no local install) — a public Streamable HTTP instance of the TypeScript @cyanheads/pubchem-mcp-server is published at https://pubchem.caseyjhand.com/mcp. Claude Code: 
    claude mcp add --transport http pubchem https://pubchem.caseyjhand.com/mcp

    Claude Desktop has no native HTTP transport — proxy it via mcp-remote in claude_desktop_config.json:

    {
  "mcpServers": {
    "pubchem": { "command": "npx", "args": ["-y", "mcp-remote", "https://pubchem.caseyjhand.com/mcp"] }
  }
}

    To run the cyanheads server locally instead (requires Bun ≥ 1.3 or Node ≥ 24), register the stdio package — Claude Code launches it itself, no separate terminal needed:

    claude mcp add --transport stdio pubchem -- bunx @cyanheads/pubchem-mcp-server@latest

What it does

  • search_pubchem_by_name
  • search_pubchem_by_smiles
  • get_pubchem_compound_by_cid
  • search_pubchem_advanced (formula / property filters)

Primary use cases: Look up compounds by name / SMILES / CID / formula, retrieve PubChem property records, generate structure files for downstream cheminformatics.

Notes

stdio transport. Backed by FastMCP. No authentication required. PubChem’s broad compound coverage makes this a natural pair with the ChEMBL bioactivity connector bundled in bio-research.

The cyanheads alternative (HTTP/stdio paths above) exposes a wider, read-only surface — 8 tools following a pubchem_verb_noun naming pattern, including substructure / superstructure / 2D-similarity search and GHS hazard classification (pubchem_get_compound_safety: signal word, pictograms, H-/P-codes) — and rate-limits PUG REST/View calls to 5 req/s with retry. Prefer it when you need safety data or structure-search modes; prefer the JackKuo666 server for a pure-Python stdio install.

Sources

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