@pipeworx/pubchem

Connect: https://gateway.pipeworx.io/pubchem/mcp · Install: one-click buttons

Tools: 4

PubChem MCP — NIH chemistry compound database, no auth.

Tools

• search_by_name(name, max_results?) — name → CIDs.
• get_compound(cid) — formula, MW, SMILES, InChI, properties.
• get_synonyms(cid, max_results?) — all known names.
• get_classification(cid) — pharmacology classification tree.

Data source

https://pubchem.ncbi.nlm.nih.gov/rest/pug (PUG-REST + PUG-VIEW). No key. Be reasonable on RPS (5/sec recommended).

Tools

• search_by_name — 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 f
• get_compound — 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,
• get_synonyms — List all names (synonyms) for a CID — common names, IUPAC, trade names, CAS numbers, etc.
• get_classification — Pharmacological classification tree for a CID — drug class, mechanism of action, biological role tags. Useful for “what kind of drug is X” questions.