io.github.cyanheads/pubchem-mcp-server

up checked 2026-11-11T00:38:09.605Z

Unclaimed · Unverified

Agent searches it appeared in, last 30 days: 0. Run this server? Claim the listing: verified label, uptime alerts and analytics.

Publisher-provided description

Search PubChem compounds, properties, safety data, bioactivity, and cross-references.

Summary by lookupd

Agents can search PubChem for compounds, retrieve properties, GHS safety data, bioactivity, 3D structures, cross-references and summaries.

Install

Claude Code, remote (streamable-http)

claude mcp add --transport http pubchem-mcp-server https://pubchem.caseyjhand.com/mcp

Claude Code, npm package (stdio)

claude mcp add pubchem-mcp-server -- npx -y @cyanheads/pubchem-mcp-server

Claude Code, npm package (stdio)

claude mcp add pubchem-mcp-server -- npx -y @cyanheads/pubchem-mcp-server

Codex, remote (streamable-http)

codex mcp add pubchem-mcp-server --url https://pubchem.caseyjhand.com/mcp

Codex, npm package (stdio)

codex mcp add pubchem-mcp-server -- npx -y @cyanheads/pubchem-mcp-server

Codex, npm package (stdio)

codex mcp add pubchem-mcp-server -- npx -y @cyanheads/pubchem-mcp-server

Cursor, remote (streamable-http) → .cursor/mcp.json

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "url": "https://pubchem.caseyjhand.com/mcp"
    }
  }
}

Cursor, npm package (stdio) → .cursor/mcp.json

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server"
      ]
    }
  }
}

Cursor, npm package (stdio) → .cursor/mcp.json

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server"
      ]
    }
  }
}

Other clients: docs. Or tell your agent: Set up lookupd for me: read https://lookupd.com/agent.md and follow it.

Tools (10 tools)

Publisher-provided text

• pubchem_search_compounds Search PubChem for chemical compounds by identifier (name, SMILES, InChI, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or s
• pubchem_get_compound_details Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual
• pubchem_get_compound_image Fetch a 2D structure diagram (PNG image) for a compound by CID.
• pubchem_get_compound_3d_structure Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured field
• pubchem_get_compound_xrefs Get external database cross-references for a compound: PubMed citations, patent IDs, gene associations, CAS and EC numbers with the number of source records tha
• pubchem_get_compound_safety Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements
• pubchem_get_bioactivity Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBan
• pubchem_get_compound_interactions Get a compound's interaction data: drug-food interactions, and the molecular targets its bioassays name — one entry per target as kinds defines it, with its ass
• pubchem_search_assays Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a pag
• pubchem_get_summary Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per

Changes

Newest first, as lookupd saw them

• 2026-11-11: version 0.8.0 → 0.8.1

Details

• Version: 0.8.1
• Transports: streamable-http, stdio
• Uptime (7 days): 100%
• Median latency: 778 ms
• First indexed: 2026-11-01T09:26:32.438Z
• Last seen in registry: 2026-11-11T08:17:23.524Z
• Repository: https://github.com/cyanheads/pubchem-mcp-server

Badge for your README

Shows this live status and links here; updates hourly.

[![lookupd status](https://lookupd.com/badge/io.github.cyanheads/pubchem-mcp-server.svg)](https://lookupd.com/servers/io.github.cyanheads/pubchem-mcp-server)

• 62141 servers
• Last crawl: 2026-11-11T18:17:25.333Z
• API base: https://api.lookupd.com
• MCP URL: https://api.lookupd.com/mcp