PubChem MCP Server

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Tools

Ten tools for querying PubChem's chemical information database:

Tool Name	Description
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.

pubchem_search_compounds

Search PubChem for chemical compounds across five search modes.

• Identifier lookup — resolve compound names, SMILES, or InChIKeys to CIDs (batch up to 25)
• Formula search — find compounds by molecular formula in Hill notation
• Substructure/superstructure — find compounds containing or contained within a query structure
• 2D similarity — find structurally similar compounds by Tanimoto similarity (configurable threshold)
• Optionally hydrate results with properties to avoid a follow-up details call

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pubchem_get_compound_details

Get detailed compound information by CID.

• Batches up to 100 CIDs in a single request
• 27 available properties: molecular weight, SMILES, InChIKey, XLogP, TPSA, complexity, stereo counts, and more
• Optionally includes textual descriptions (pharmacology, mechanism, therapeutic use) from PUG View
• Optionally includes all known synonyms (trade names, systematic names, registry numbers)
• Optionally computes drug-likeness assessment (Lipinski Rule of Five + Veber rules) from fetched properties
• Optionally fetches pharmacological classification (FDA classes, mechanisms of action, MeSH classes, ATC codes)

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pubchem_get_bioactivity

Get a compound's bioactivity profile from PubChem BioAssay.

• Returns assay outcomes (Active/Inactive/Inconclusive), target info (protein accessions, NCBI Gene IDs), and quantitative values (IC50, EC50, Ki)
• Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession)
• Caps at 100 results per request (well-studied compounds may have thousands)

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pubchem_get_summary

Get descriptive summaries for four PubChem entity types.

• Assays (AID), genes (Gene ID), proteins (UniProt accession), taxonomy (Tax ID)
• Up to 10 entities per call
• Type-specific field extraction for clean, structured output

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pubchem_get_compound_interactions

Get a compound's interaction data by CID.

• Drug-drug interactions (DrugBank), drug-food interactions, and chemical-target binding/activity (BindingDB, ChEMBL, and others)
• Select which interaction kinds to fetch and cap entries per kind
• Each entry carries its originating source — coverage is richest for approved drugs

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pubchem_get_compound_3d_structure

Get a compound's default 3D conformer by CID.

• format="json" returns parsed atoms (element + x/y/z) and bonds for direct reasoning; format="sdf" returns raw V2000 SDF for passthrough to docking or rendering
• Optionally lists alternate conformer IDs
• Returns a typed not-found when PubChem has no computed 3D coordinates (large molecules, mixtures, some salts)

Resources

Compound and assay records are also exposed as URI-templated MCP resources, backed by the same client methods as the tools:

URI Template	Returns
pubchem://compound/{cid}	Core physicochemical properties (JSON).
pubchem://compound/{cid}/safety	GHS hazard classification (JSON).
pubchem://compound/{cid}/image	2D structure diagram (PNG).
pubchem://compound/{cid}/xrefs	External cross-references (JSON).
pubchem://compound/{cid}/bioactivity	Bioassay activity profile (JSON).
pubchem://assay/{aid}	BioAssay summary (JSON).

Features

Built on @cyanheads/mcp-ts-core:

• Declarative tool definitions — single file per tool, framework handles registration and validation
• Unified error handling across all tools
• Pluggable auth (none, jwt, oauth)
• Swappable storage backends: in-memory, filesystem, Supabase, Cloudflare KV/R2/D1
• Structured logging with optional OpenTelemetry tracing
• Runs locally (stdio/HTTP) or containerized via Docker

PubChem-specific:

• Rate-limited client for PUG REST and PUG View APIs (5 req/s with automatic queuing)
• Retry with exponential backoff on 5xx errors and network failures
• All tools are read-only and idempotent — no API keys required

Getting Started

Public Hosted Instance

A public instance is available at https://pubchem.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "type": "streamable-http",
      "url": "https://pubchem.caseyjhand.com/mcp"
    }
  }
}

Self-Hosted / Local

Add to your MCP client config (e.g., claude_desktop_config.json):

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["@cyanheads/pubchem-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio"
      }
    }
  }
}

Prerequisites

• Bun v1.3.0 or higher (or Node.js v24+)

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/pubchem-mcp-server.git

1. Navigate into the directory:

cd pubchem-mcp-server

1. Install dependencies:

bun install

Configuration

No API keys are required — PubChem's API is freely accessible.

Variable	Description	Default
MCP_TRANSPORT_TYPE	Transport: stdio or http.	stdio
MCP_HTTP_PORT	Port for HTTP server.	3010
MCP_HTTP_HOST	Host for HTTP server.	localhost
MCP_AUTH_MODE	Auth mode: none, jwt, or oauth.	none
MCP_LOG_LEVEL	Log level (RFC 5424).	info
STORAGE_PROVIDER_TYPE	Storage backend.	in-memory
OTEL_ENABLED	Enable OpenTelemetry.	false

Running the Server

Local Development

• Build and run:

  bun run rebuild
  bun run start:stdio   # or start:http
  

• Run checks and tests:

  bun run devcheck     # Lints, formats, type-checks
  bun run test         # Runs test suite
  

Docker

docker build -t pubchem-mcp-server .
docker run -p 3010:3010 pubchem-mcp-server

Project Structure

Directory	Purpose
src/mcp-server/tools/definitions/	Tool definitions (*.tool.ts).
src/services/pubchem/	PubChem API client with rate limiting and response parsing.
scripts/	Build, clean, devcheck, and tree generation scripts.

Development Guide

See CLAUDE.md for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for domain-specific logging
• Register new tools in the index.ts barrel file

Contributing

Issues and pull requests are welcome. Run checks before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.