PubChem MCP Server

Ten tools for querying PubChem's chemical information database:

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)
- Caps at 200 CIDs per page;offsetpages further, to a ceiling of 10,000. Identifier lookups page over the set already resolved; formula and structure searches widen their bounded upstream request to reach a page, so deep pages cost more upstream
- Optionally hydrate results with properties to avoid a follow-up details call

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 — fetched for the first 10 CIDs of a batch, with the skipped CIDs named in the response
- Optionally includes known synonyms (trade names, systematic names, registry numbers)
- Synonyms and descriptions are paged:synonymOffsetanddescriptionOffsetwindow every compound in the batch at the same position, reaching the entries past a page
- 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)

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 page;offsetreaches the rest (well-studied compounds may have thousands)

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

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
- Paged per kind: each reports its source-record total and its ownnextOffset, andoffsetreaches the records past a page
- Each entry carries its originating source — coverage is richest for approved drugs

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
- maxAtoms/maxBondsbound the atom/bond preview andincludeRawSdfopts into a large raw SDF past the safe line cap;atomCount/bondCountalways report the totals and any capping is disclosed
- Optionally lists alternate conformer IDs
- Returns a typed not-found when PubChem has no computed 3D coordinates (large molecules, mixtures, some salts)

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

- 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

- 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

A public instance is available athttps://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" } } }

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

- Handlers throw, framework catches — notry/catchin tool logic
- Usectx.logfor domain-specific logging
- Register new tools in theindex.tsbarrel file

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

Access and interact with Allen Institute for Neural Dynamics (AIND) metadata directly within your IDE.

A high-performance JavaScript server for the Alliance of Genome Resources (AGR) MCP.

Access the AlphaFold Protein Structure Database for protein structure prediction and analysis.

Interface with Biomart, a biological data query tool, using the pybiomart Python package.

Agent-first rewrite of genomeoncology's BioMCP in TypeScript to provide next-gen biomedical data access for agents.

Perform complex queries on the DANDI Archive, a platform for neurophysiology data.

Interact with DROMA drug-omics association analysis databases using natural language.

A bridge to the Drug Gene Interaction Database (DGIdb) API, enabling AI clients to query drug-gene interaction data.

Query the Materials Project database using the mp_api client. Requires an MP_API_KEY environment variable.