pubchem-mcp

A production-ready Model Context Protocol server for PubChem chemical data. Built in TypeScript, designed to be embedded in MCP clients like Claude Desktop, Claude Code, Cursor, and Cline.

It uses PubChem's documented APIs — PUG-REST as primary backend and PUG-View for curated annotations — and respects PubChem's published rate-limit and dynamic throttling policy.

What this server does

Resolves compound identifiers (name, CID, SMILES, InChI, InChIKey, formula) to PubChem CIDs.
Retrieves normalized compound summaries and computed properties.
Returns synonyms, structures (SMILES / InChI / InChIKey / SDF / full JSON).
Runs identity, similarity, substructure, and superstructure searches.
Fetches bioassay summaries and the assays associated with a compound.
Pulls curated annotation sections from PUG-View with source citations.
Exposes server diagnostics including the most recent PubChem throttle state.

What this server does not do

It does not scrape PubChem HTML pages.
It does not predict ADMET, toxicity, regulatory status, environmental fate, or pharmacophore features.
It does not provide medical, legal, regulatory, or laboratory-safety advice.
It does not write to PubChem; this server is read-only.

Annotation text returned from PUG-View is source data drawn from PubChem's references. It is not the server's analysis or recommendation.

Install

Requires Node.js ≥ 18.17.

# Run without installing
npx pubchem-mcp

# or install globally
npm install -g pubchem-mcp
pubchem-mcp

MCP client configuration

Claude Desktop

Add this to your claude_desktop_config.json (~/Library/Application Support/Claude/ on macOS, %APPDATA%\Claude\ on Windows):

{
  "mcpServers": {
    "pubchem": {
      "command": "npx",
      "args": ["-y", "pubchem-mcp"]
    }
  }
}

See examples/mcp-configs/claude-desktop.json.

Claude Code

Add this to your project's .mcp.json:

{
  "mcpServers": {
    "pubchem": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "pubchem-mcp"]
    }
  }
}

See examples/mcp-configs/claude-code.mcp.json.

Local development

git clone <repo-url>
cd pubchem-mcp
npm install
npm run build
npm run typecheck
npm run lint
npm test
npm start          # runs dist/index.js (stdio)

Live integration tests (which call the real PubChem API) are skipped by default. They require outbound DNS+HTTPS access to pubchem.ncbi.nlm.nih.gov; sandboxed environments without network access should leave the flag unset. Run them with:

PUBCHEM_MCP_LIVE_TESTS=1 npm test

If a live test fails, the assertion message includes the full structured tool-error payload (error, category, retryable, endpoint) — diagnose from that rather than re-running blindly.

Tools

| Name | Purpose | Backend | |---|---|---| | resolve_compound | Resolve a free-form identifier (name / CID / SMILES / InChI / InChIKey / formula) to CIDs. | PUG-REST | | get_compound | Fetch a normalized compound summary by CID. | PUG-REST | | get_compound_properties | Batch computed properties for up to 100 CIDs from an allowlisted set. | PUG-REST | | get_compound_synonyms | Synonyms for a CID (up to 500). | PUG-REST | | get_compound_structure | Get a compound structure as SMILES, InChI, InChIKey, SDF, or full JSON. | PUG-REST | | search_structure | Identity / similarity / substructure / superstructure search by SMILES or InChI. | PUG-REST | | get_assay | Normalized assay summary by AID. | PUG-REST | | get_compound_assays | List AIDs of bioassays associated with a CID. | PUG-REST | | get_compound_annotations | Curated annotation sections (pharmacology, hazards, literature, etc.) with source citations. | PUG-View | | get_server_status | Diagnostics: version, configured limits, cache stats, throttle state, uptime. | — |

Full tool reference with example inputs and outputs lives in docs/tools.md.

Resources

| URI template | Returns | |---|---| | pubchem://compound/{cid} | Normalized compound summary | | pubchem://compound/{cid}/properties | Default computed property set | | pubchem://compound/{cid}/synonyms | Up to 50 synonyms | | pubchem://compound/{cid}/structure | Full PUG-REST JSON structure record | | pubchem://compound/{cid}/annotations | PUG-View annotation sections | | pubchem://assay/{aid} | Normalized bioassay summary |

See docs/resources.md.

Prompts

compound-research-brief — sourced research brief for one compound.
compare-compounds — markdown comparison table across multiple compounds.
safety-annotation-review — review of PubChem-sourced safety annotations with strict no-extrapolation rules.

Environment variables

All optional. See .env.example for the full list.

| Var | Default | Purpose | |---|---|---| | PUBCHEM_RPS | 4 | Per-second cap (hard max 5; PubChem documents 5 req/sec) | | PUBCHEM_RPM | 240 | Per-minute cap (hard max 400) | | PUBCHEM_TIMEOUT_MS | 30000 | Per-request timeout | | PUBCHEM_MAX_RETRIES | 4 | Retry attempts for transient failures | | PUBCHEM_CACHE_TTL_MS | 86400000 | 24h cache TTL | | PUBCHEM_CACHE_DISABLE | unset | Set to 1 to disable cache | | PUBCHEM_CACHE_MAX_ENTRIES | 1000 | Cache LRU bound | | PUBCHEM_BASE_URL | PubChem PUG-REST | Override for testing/proxying | | PUBCHEM_VIEW_BASE_URL | PubChem PUG-View | Override for testing/proxying | | PUBCHEM_CONTACT_URL | unset | Appended to User-Agent (recommended for production) | | PUBCHEM_LOG_LEVEL | info | pino level (trace/debug/info/warn/error/fatal/silent) | | PUBCHEM_MCP_LIVE_TESTS | unset | Set to 1 to run live PubChem tests |

PubChem rate-limit policy

The server defends both directions of the rate limit:

Outbound throttling: a token bucket caps requests at 4 req/sec (configurable, hard max 5) and a sliding 60-second window caps at 240 req/min (configurable, hard max 400). Requests queue rather than burst.
Dynamic throttling: every response's X-Throttling-Control header is parsed. Yellow / Red / Black states cause the next request to wait 200 ms / 1 s / 5 s respectively. The most recent state is reported by get_server_status.
Retries: 429 / 500 / 502 / 503 / 504 and network errors are retried with exponential backoff (500 ms → 16 s) plus jitter, capped at PUBCHEM_MAX_RETRIES attempts. 400 / 404 / 405 / 501 are not retried.
Caching: identical GET requests are cached in memory for 24h by default. Disable with PUBCHEM_CACHE_DISABLE=1.
User-Agent: pubchem-mcp/<version> plus the optional PUBCHEM_CONTACT_URL.

Full discussion in docs/pubchem-access.md.

Safety and limitations

This server retrieves data from PubChem. It does not provide medical, toxicological, regulatory, legal, or laboratory-safety advice. Users must verify critical chemistry and safety decisions with authoritative primary sources and qualified professionals.

See docs/safety-and-limitations.md.

Troubleshooting

503 Service Unavailable — PubChem is throttling. The client retries automatically with exponential backoff; if it persists, reduce PUBCHEM_RPS (default 4, hard cap 5) and PUBCHEM_RPM. Watch get_server_status for the parsed X-Throttling-Control color.
Persistent yellow/red throttle status — your traffic is steadily near PubChem's window. Lower PUBCHEM_RPS to 2–3 and add a longer delay between bursts. Set PUBCHEM_CONTACT_URL to a project URL so PubChem operators can identify your traffic.
List key polling timed out — a large async structure search exceeded the 60s polling budget. Reduce the result set or use a fast* (synchronous) search.
Unsupported property name(s) — get_compound_properties rejects values outside the allowlist; the error returns category: "validation", retryable: false, and lists every supported name.
InChI lookup returns 400 Bad Request — InChI lookups are sent as POST /compound/inchi/cids/JSON with a form-urlencoded body. If you see a 400, the InChI string itself is malformed; path-encoded InChI is no longer used. Validate the InChI with an external InChI parser before resubmitting.
MCP server appears to "hang" on startup — stdio servers wait silently for an initialize frame; this is normal behavior for stdio MCP servers. Pair it with a client.
No data returned for a compound annotation heading — PubChem may not have that section for that compound. The server will not fabricate one.
Live test failures when network is unavailable — transport failures (DNS, TLS, refused, reset, timeout) are mapped to a typed PubChemTransientError and surface in MCP tool payloads as { "category": "transient", "retryable": true, "endpoint": "...", "error": "Network error while contacting PubChem (ENOTFOUND)" | "PubChem request timed out after Nms" }. The live test suite uses a short timeout (10 s) and a low retry cap (2) so the suite completes within ~60 s on hosts without HTTPS to pubchem.ncbi.nlm.nih.gov, and every test closes its MCP client+server transports in finally. Leave PUBCHEM_MCP_LIVE_TESTS unset on offline hosts.

CI/CD and releases

This repository uses GitHub Actions for CI, release validation, and npm publishing via Trusted Publishing (OIDC). Future versions (0.1.1 onwards) publish through .github/workflows/publish.yml; no long-lived NPM_TOKEN is used. Version 0.1.0 was published manually before this pipeline existed and the workflow refuses to republish it.

Pipeline overview, Trusted Publisher setup, npm-publish environment configuration: docs/ci-cd.md
Per-release runbook (bump → tag → approve → verify): docs/release-checklist.md
Publish gates, metadata requirements, rollback policy: PUBLISHING.md
Changelog: CHANGELOG.md

License

MIT

MCP Servers