PubChem MCP Server

Community

Search the PubChem chemical database for compounds, properties, safety data, bioactivity, and cross-references via MCP. STDIO or Streamable HTTP.

How to install ↓ Compare GitHub source repository ↗

Category: Database #20 of 58
Stars: ★ 10 Popular
Transport: stdio (local process) · Streamable HTTP
Runtime: Bun 1.3.0+ · Node.js 24+ · Docker · Hosted (no local runtime)
Credentials: No credential needed
License: Apache-2.0
Last commit: 6 days ago
Tools: 10

59FMRS · C

This is a feature-rich and well-documented server for users wanting to integrate PubChem data into AI workflows. It offers a comprehensive set of tools and resources with easy setup. Note that it is not an official PubChem project, and the public endpoint is community-hosted.

Strongest · Documentation 14/20 Weakest · Reliability 10/20

Reliability

10/20

Security and permissions

12/20

Maintenance

10/20

Documentation

14/20

Setup experience

13/20

Why each score

Reliability 10/20: README outlines a coherent feature set with rate limiting, retries, and typed error handling, but no real CI workflows or committed tests are visible in the supplied files as verifiable execution evidence, capping the static score at 12; the handshake and tool behavior are unverified, and documented test commands carry no proof of passing.
Security and permissions 12/20: Read-only tools, no API keys, default bind to 127.0.0.1, and optional JWT/OAuth keep the risk surface small; however MCP_AUTH_MODE defaults to 'none', the public hosted endpoint's auth posture and operator identity are undisclosed in the files, and external network calls, while disclosed, lack confirmation/least-privilege hardening. No red-line violations.
Maintenance 10/20: Version 0.6.1 aligns with the npm package, license is Apache-2.0, not archived, only 3 open issues; but with 9 stars, no evidence of release cadence, security-response channel, or dependency-update policy, governance signals are weak.
Documentation 14/20: Well-layered docs: all 10 tools documented with parameters, pagination caps, batch limits, and disclosed capping behavior for 3D structures; complete configuration table with Docker instructions. Deductions for a version mismatch (README badge 0.6.0 vs manifest 0.6.1), thin troubleshooting content, and limited discussion of upstream rate/cost limits beyond the 5 req/s note.
Setup experience 13/20: One-click install links for Claude Desktop, Cursor, and VS Code, an .mcpb package, Docker, and simple bunx examples make the path short; deductions for the relatively new runtime requirement (Bun 1.3+/Node 24+), a minor inconsistency between the manifest runtimeHint 'bun' and generic npx examples, and no post-install verification step. No execution evidence allows up to 15, awarded 13.

Static review · not runListed 2026-09-08

Read the FMRS scoring method →

Fit and risk

What it can accessUses the network

Best for

Researchers and developers integrating chemical database queries into LLM-driven tools.
Those preferring a public hosted endpoint or self-hosting their own MCP server.

Not for

Clinical applications requiring rich drug interaction coverage (the report covers mostly approved drugs).
Use cases needing write access or data ingestion (the server is read-only).

Required permissions

Reads PubChem public APIs; no authentication required.
Optional environment variables for logging/HTTP configuration.

Risks and side effects

The public hosted instance's availability may vary (not officially affiliated).
Deep pagination may incur additional upstream requests and potential rate limits.
Error handling depends on remote service reliability.

Setup

Before you start

Runtime：Bun 1.3.0+ · Node.js 24+ · Docker · Hosted (no local runtime)

Other optional settings (8)

MCP_TRANSPORT_TYPE optional Chooses stdio or http transport; defaults to stdio; no setup needed.

MCP_HTTP_HOST optional Hostname for the HTTP server; defaults to 127.0.0.1; optional.

MCP_HTTP_PORT optional Port for the HTTP server; defaults to 3010; optional.

MCP_HTTP_ENDPOINT_PATH optional Endpoint path for MCP; defaults to /mcp; optional.

MCP_AUTH_MODE optional Auth mode: none, jwt, or oauth; defaults to none; optional.

MCP_LOG_LEVEL optional Minimum log level (RFC 5424); defaults to info; optional.

STORAGE_PROVIDER_TYPE optional Storage backend; defaults to in-memory; optional.

OTEL_ENABLED optional Enable OpenTelemetry tracing; defaults to false; optional.

Install Bun v1.3.0 or higher (or Node.js v24+). Then add a configuration to your MCP client (e.g., claude_desktop_config.json) with type 'stdio', command 'bunx', and args ['@cyanheads/pubchem-mcp-server@latest']. No API keys are required.

claude_desktop_config.json

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

Shown for Claude Desktop. Other clients may use a different file or key (VS Code uses "servers") — the configurator below converts it.

.vscode/mcp.json

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

Goes in your project's .vscode/mcp.json (VS Code uses a "servers" key).

Terminal

claude mcp add pubchem-mcp-server -e MCP_TRANSPORT_TYPE=stdio -- bunx @cyanheads/pubchem-mcp-server@latest

Run it in a terminal; replace any <…> placeholders with your own values first.

Generate and validate client config

Check that it works

After connecting, the client should list the 10 tools such as pubchem_search_compounds; asking 'What is the molecular weight of aspirin?' and getting PubChem data back confirms the install works.

Troubleshooting

Ensure you have a compatible version of Bun or Node.js installed.
Check network connectivity and firewall settings if using a remote endpoint.
Avoid excessive concurrent requests to prevent rate-limiting.

Things to try

Once connected, you can ask your AI assistant things like:

Search PubChem for aspirin and give me its CID
Show GHS hazard classification and safety data for CID 2244
Fetch the 2D structure image and 3D conformer of caffeine
Get the bioactivity profile of CID 2244 filtered to active outcomes

Tools 10

pubchem_search_compounds read-only

Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity.

pubchem_get_compound_details read-only

Get detailed information for compounds by CID: properties, descriptions, synonyms, drug-likeness, and classification.

pubchem_get_compound_image read-only

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

pubchem_get_compound_3d_structure read-only

Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID.

pubchem_get_compound_xrefs read-only

Get external database cross-references (PubMed, patents, genes, proteins, etc.).

pubchem_get_compound_safety read-only

Get GHS hazard classification and safety data for one or more compounds by CID (batch).

pubchem_get_bioactivity read-only

Get a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target.

pubchem_get_compound_interactions read-only

Get drug-drug, drug-food, and chemical-target interactions for a compound by CID.

Show 2 more tools

pubchem_search_assays read-only

Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).

pubchem_get_summary read-only

Get summaries for PubChem entities: assays, genes, proteins, taxonomy.

Use cases

Drug discovery and chemical research: search analogues, examine structure-activity relationships.

Safety assessment: obtain GHS hazard classifications and safety data.

Bioinformatics: connect compounds to assays, genes, and proteins.

Supported clients

Claude Desktop

Cursor

VS Code

Listed from the project's documentation, not tested by this site.

Overview

PubChem MCP Server is a community-maintained server that enables AI assistants to query the PubChem chemical database. It provides tools for searching compounds by name, structure, etc., fetching detailed information, images, 3D structures, external cross-references, safety data, bioactivity, interactions, and entity summaries. It also exposes resources for direct access to compound and assay data. It supports Streamable HTTP and can be used via a public hosted instance or self-hosted locally over stdio or HTTP. No API keys are required, and all tools are read-only.

Similar servers

MCP ClickHouse 79 · B

Connect ClickHouse to your AI assistants

★ 889 · Tools 4 Compare with this →

ChEMBL MCP Server 75 · B

Unofficial MCP server providing advanced access to the ChEMBL chemical database

★ 89 · Tools 27 Compare with this →

MCP Toolbox for Databases 74 · B

Google's official database MCP toolbox — define AI-accessible database tools via config

★ 16.7k Compare with this →

DBHub 74 · B

Bytebase's official, minimalist two-tool database MCP server

★ 3.7k · Tools 2 Compare with this →

Compare with other MCP servers

Source revision 4d00a1eebf14 Data synced 2026-10-19 Read the FMRS scoring method