Labsco
MCP SERVER

PubChem MCP Server

by JackKuo666

Ask about a compound by name or by SMILES string and get PubChem's structure and property data back in the chat.

Physical Sciences & Scientific Computing
Summary
Chemical facts from the source, not from the model.

Molecular weights and identifiers are exactly the kind of number a language model will produce confidently and get slightly wrong. Routing the question to PubChem means the property in the answer is the one on record, and a SMILES string works as the query when the name is ambiguous.

What it is

A lookup against PubChem, the public chemical database. A compound can be named in words or given as a SMILES string, and what comes back is its identifiers, structure and recorded properties.

What you get
  • Compound search by common or systematic name
  • Compound search by SMILES, for a structure you already have in hand
  • Molecular structures and the identifiers that go with them
  • The chemical and physical properties PubChem records for a compound
  • A cap on how many results come back, so a broad name does not flood the answer
Requirements

Python on your PATH. No account and no key — PubChem is open.

Setup effort

One command — uv tool install pubchem-mcp-server