Pubchem MCP Server - install, status & alternatives [2026]

01 · Install Pubchem MCP Server

before you install - you'll need

Set MCP_TRANSPORT_TYPE before connecting.

Claude Code

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

Claude Desktop / Cursor / VS Code - add to config

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

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

https://pubchem.caseyjhand.com/mcp

transport: streamable-http

endpoint alive - responded to MCP initialize · probed 2026-09-17

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions · remote - your agent's requests go to pubchem.caseyjhand.com

endpoint auth accepted our unauthenticated MCP initialize - no credentials needed to connect

license Apache-2.0 - declared in the repository

npm package @cyanheads/pubchem-mcp-server - published under the repo owner's npm scope (@cyanheads)

registry namespace io.github.cyanheads is GitHub-verified and matches the repo owner

03 · What Pubchem MCP Server can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity, get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID, fetch a 2D structure diagram (PNG) for a compound by CID, and fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.

The 10 tools it gives your agent

Extracted from the project's README - what pubchem-mcp-server lets an agent do.

pubchem_search_compounds: - Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity.
pubchem_get_compound_details: - Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID.
pubchem_get_compound_image: - Fetch a 2D structure diagram (PNG) for a compound by CID.
pubchem_get_compound_3d_structure: - Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.
pubchem_get_compound_xrefs: - Get external database cross-references (PubMed, patents, genes, proteins, etc.).
pubchem_get_compound_safety: - Get GHS hazard classification and safety data for one or more compounds by CID (batch).
pubchem_get_bioactivity: - Get a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target.
pubchem_get_compound_interactions: - Get drug-drug, drug-food, and chemical-target interactions for a compound by CID.
pubchem_search_assays: - Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).
pubchem_get_summary: - Get summaries for PubChem entities: assays, genes, proteins, taxonomy.

Latest releases

v0.6.2 · 2026-09-13

Framework adoption and HTTP retry handling · PubChem HTTP retries transient 500 responses once and fails a non-retryable 501 immediately. · Published HTTP metadata defaults to stateless sessions. · Framework skills…

v0.6.1 · 2026-08-21

mcp-ts-core ^0.12.3 - MCP SDK v2, and top-level truncation disclosure · Tool arguments are strict: an undeclared argument key is rejected by name instead of stripped, and the advertised inputSchema carries…

v0.6.0 · 2026-07-28

Constrain per-page cap inputs to integers · Four tool inputs that advertised an unconstrained number where a · count was meant now advertise integer: pubchem_get_compound_xrefs.maxPerType…

04 · Who maintains Pubchem MCP Server

pubchem-mcp-server is maintained by cyanheads. We track 125 MCP servers from cyanheads - 119 actively maintained, 1,816 combined GitHub stars, oldest repo from Dec 2024. Full record: all servers from cyanheads.

05 · Facts

repository: github.com/cyanheads/pubchem-mcp-server
category: science & health - ranked #14 of 71 actively-maintained science & health servers as of 2026-09-18.
release cadence: 10+ releases in the last 90 days (latest 2026-09-13)
registry: io.github.cyanheads/pubchem-mcp-server (active, first published 2026-03-21 · 35 versions)
packages: npm:@cyanheads/pubchem-mcp-server · npm:@cyanheads/pubchem-mcp-server

06 · Pubchem MCP Server FAQ

Is Pubchem MCP Server still maintained?

Yes - as of 2026-09-18, its last commit was 2026-09-13 and it shipped 10+ releases in the last 90 days. We re-verify nightly.

What can Pubchem MCP Server do?

With this server connected, an agent can search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity, get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID, fetch a 2D structure diagram (PNG) for a compound by CID, and fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.

How do I install Pubchem MCP Server?

Run `npx -y @cyanheads/pubchem-mcp-server`. The README documents one environment variable (MCP_TRANSPORT_TYPE) to set first. Set MCP_TRANSPORT_TYPE before connecting. You can also paste the ready-made client config above.

Does Pubchem MCP Server require authentication?

No - the endpoint accepted our unauthenticated MCP initialize when probed on 2026-09-17; you can connect without credentials.

07 · Alternatives to Pubchem MCP Server

Alternatives to Pubchem MCP Server

Maintained science & health servers if Pubchem MCP Server isn't the fit.

More science & health MCP servers · Who Gho MCP Server · Cytoscape Desktop MCP · Apple Health MCP · Eight Sleep MCP

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