Pubchem MCP Server

io.github.cyanheads/pubchem-mcp-server

answering

Pubchem MCP Server is answering right now. Last checked 13 min ago. 1 179 installs a week from npm. It exposes 10 tools. Last commit 30 Jul 2026.

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

Installs per day peak 811 · avg 62 · +495% w/w

a month agotoday

Uptime history 41 hours of history · worst hour 75%

41 hours agonow

100.0%

Uptime 24h

91 of 91 checks

Tools

read from the server

359 ms

Response time

average over 24h

1 179

Installs / week

npm and PyPI

Connect this server

Endpoint below is the one we actually reach during checks — not the one copied from a README. Last verified 13 min ago.

Claude Code Claude Desktop Codex Cursor VS Code

run in your terminal

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

~/Library/Application Support/Claude/claude_desktop_config.json

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

~/.codex/config.toml

[mcp_servers.pubchem-mcp-server]
url = "https://pubchem.caseyjhand.com/mcp"

.cursor/mcp.json

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

.vscode/mcp.json

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

Available tools 10

Read directly from the server with tools/list, grouped by what they act on. If a tool disappears, we record the date.

pubchem

pubchem_get_bioactivity

Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession) to focus the profile — e.g. "is this compound active against target T?".

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 fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).

pubchem_get_compound_details

Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Accepts up to 100 CIDs per call.

pubchem_get_compound_image

Fetch a 2D structure diagram (PNG image) for a compound by CID.

pubchem_get_compound_interactions

Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records.

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 (H-codes), and precautionary statements (P-codes) per compound. Data sourced from PubChem depositors — source attribution included.

pubchem_get_compound_xrefs

Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset.

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 call.

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 page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.

pubchem_search_compounds

Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.

Endpoints

URL	Transport	State	Latency	Checked
https://pubchem.caseyjhand.com/mcp	streamable-http	answering	167 ms	13 min ago

Pubchem MCP Server — questions

Answers built from our own checks of this server.

What can Pubchem MCP Server do?

It exposes 10 tools, read directly from the server on our last check. Among them: pubchem_get_bioactivity, pubchem_get_compound_3d_structure, pubchem_get_compound_details, pubchem_get_compound_image, pubchem_get_compound_interactions, pubchem_get_compound_safety and 4 more. The full list with descriptions is on this page — we take it from the server itself via tools/list, not from a README. How MCP servers expose tools in the first place →

Is Pubchem MCP Server working right now?

We send a real MCP handshake every 15 minutes. Over the last 24 hours 91 of 91 checks got a reply (100.0%), average response time 359 ms. The bar chart above shows every period we have measured.

How do I connect Pubchem MCP Server?

Copy the ready config from this page — we generate it for Claude Code, Claude Desktop, Codex, Cursor and VS Code, each with the file path that client actually reads. It is a remote server, so there is nothing to install — the client connects to the address.

Does Pubchem MCP Server need an API key?

No. Pubchem MCP Server completed a full MCP handshake with us as an anonymous client and listed its tools without asking for anything. All 10 of them are readable on this page. This is what we observed, not what the docs claim.

How fast is Pubchem MCP Server?

It answers our handshake in 359 ms on average, which is faster than 39% of all working MCP servers we measure. The comparison comes from our own checks across the whole registry, every 15 minutes.

How many people use Pubchem MCP Server?

The npm package @cyanheads/pubchem-mcp-server was installed 1 179 times in the last week. Week over week that is +495%. We show installs rather than GitHub stars on purpose: a star is a bookmark, an install is someone actually running it.

Is Pubchem MCP Server open source?

Yes — it is published under the Apache-2.0 licence, written in TypeScript, 9 stars on GitHub and 3 open issues. The source link is on this page, so you can read exactly what it does with your data before you connect it.