MCP For Claude Marketplace
PubChem

PubChem MCP Connector for Claude

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Search 116M+ chemical compounds with molecular properties, SMILES notation, formulas, and drug-like properties from the world's largest free chemistry database.

3 tools Official Updated Jun 28, 2026 Official Vinkius Partner
More Details Connect to Claude

Connect your AI agent to PubChem — the world's largest open chemistry database, maintained by the National Center for Biotechnology Information (NCBI/NIH).

What you can do

  • Compound Search — Find chemical compounds by common name (aspirin, caffeine, glucose), IUPAC name, or CAS number across 116M+ indexed compounds
  • CID Lookup — Get comprehensive molecular data for any compound by its PubChem Compound ID including formula, weight, SMILES, InChI, and physicochemical properties
  • Formula Search — Find all compounds matching a specific molecular formula (e.g., C9H8O4 for aspirin)

How it works

  1. Subscribe to this server
  2. Start searching compounds immediately — no API key required

Who is this for?

  • Medicinal Chemists — quickly retrieve molecular properties and drug-like characteristics for lead compounds
  • Pharmacy Students — look up drug structures, formulas, and physicochemical data during coursework
  • Biochemistry Researchers — identify compounds by formula and explore metabolite databases
chemistrymolecular-datadrug-discoveryscientific-database

3 tools expose this connector's capabilities to your AI agent.

get_pubchem_compound

Get full chemical data for a PubChem compound by CID

search_pubchem_formula

g. C9H8O4, C8H10N4O2, H2O) and find matching compounds. Find compounds by molecular formula

search_pubchem

Returns molecular formula, weight, SMILES, InChI, XLogP, hydrogen bond donors/acceptors, and complexity. Try: aspirin, caffeine, glucose, penicillin, dopamine. Search PubChem for chemical compounds by name

See how to talk to your AI agent using PubChem.

What are the molecular properties of aspirin?

Aspirin (CID 2244): Formula C9H8O4, MW 180.16, SMILES CC(=O)OC1=CC=CC=C1C(O)=O, XLogP 1.2, H-bond donors: 1, H-bond acceptors: 4. Passes Lipinski's Rule of Five — classified as drug-like.

Search for compounds with the molecular formula C8H10N4O2.

Found compounds matching C8H10N4O2: Primary result is Caffeine (CID 2519) — the alkaloid found in coffee, tea, and chocolate. MW: 194.19, SMILES: CN1C=NC2=C1C(=O)N(C(=O)N2C)C. Also found: Theophylline (CID 2153) — used as bronchodilator for asthma treatment.

Get the full chemical details for PubChem compound CID 5090.

CID 5090: Metformin — Formula C4H11N5, MW 129.16, SMILES CN(C)C(=N)NC(=N)N. XLogP: -1.4 (highly water-soluble). H-bond donors: 3, acceptors: 3. Widely used as first-line treatment for type 2 diabetes. Molecular complexity: 95.

No. PubChem PUG REST is completely free and open without any authentication. The only limitation is a rate limit of 5 requests per second and 400 requests per minute, which is more than sufficient for conversational AI usage.

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