MCP server

Pubchem

io.github.pipeworx-io/pubchem

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

PubChem MCP — NIH chemistry compound database (no auth)

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

46

Token cost

About 26,793 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http pubchem https://gateway.pipeworx.io/pubchem/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.pubchem]
url = "https://gateway.pipeworx.io/pubchem/mcp"

Gemini CLI

{"mcpServers":{"pubchem":{"httpUrl":"https://gateway.pipeworx.io/pubchem/mcp"}}}

Cursor

{"mcpServers":{"pubchem":{"url":"https://gateway.pipeworx.io/pubchem/mcp"}}}

VS Code

{"servers":{"pubchem":{"type":"http","url":"https://gateway.pipeworx.io/pubchem/mcp"}}}

Antigravity

agy mcp add pubchem https://gateway.pipeworx.io/pubchem/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"pubchem","server_url":"https://gateway.pipeworx.io/pubchem/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"pubchem","server_url":"https://gateway.pipeworx.io/pubchem/mcp"}

Tools

• get_classification ~100 tokens
  Pharmacological classification tree for a CID — drug class, mechanism of action, biological role tags. Useful for "what kind of drug is X" questions.
• get_compound ~126 tokens
  Get standard properties for a PubChem CID: molecular formula, molecular weight, IUPAC name, canonical SMILES, isomeric SMILES, InChI, InChIKey, exact mass, charge, complexity, H-bond donors/acceptors, rotatable bonds, TPSA, XLogP, heavy atom count.
• get_synonyms ~100 tokens
  List all names (synonyms) for a CID — common names, IUPAC, trade names, CAS numbers, etc.
• search_by_name ~164 tokens
  Resolve a common chemical or drug name to PubChem CIDs. Use for "what's the CID of ibuprofen?" or to disambiguate. Returns CIDs (Compound IDs) matched to the name. Then use get_compound with the CID for properties.

Browse

• GitHub tools
• Atom tools
• GitHub and code hosting
• Databases
• Health and medicine

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