PubChem

liveChemistryScienceHealth

NIH chemistry compound database — 100M+ molecules with structures, properties, pharmacology. No auth.

4tools
0msauth
free tier50 calls/day

Tools

search_by_namerequired: 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

Parameters
NameTypeDescription
namereqstringCommon, IUPAC, or brand name
max_resultsoptnumberCap (default 5)
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get_compoundrequired: cid

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,

Parameters
NameTypeDescription
cidreqnumberPubChem Compound ID
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get_synonymsrequired: cid

List all names (synonyms) for a CID — common names, IUPAC, trade names, CAS numbers, etc.

Parameters
NameTypeDescription
cidreqnumberPubChem Compound ID
max_resultsoptnumberCap (default 50)
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get_classificationrequired: cid

Pharmacological classification tree for a CID — drug class, mechanism of action, biological role tags. Useful for "what kind of drug is X" questions.

Parameters
NameTypeDescription
cidreqnumberPubChem Compound ID
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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/pubchem/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/pubchem/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"search_by_name","arguments":{"name": "test"}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("search_by_name", {"name":"example"});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("nih chemistry compound database — 100m+ molecules with structures, properties, pharmacology");