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 Oct 1, 2026 Official Vinkius Partner
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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

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

search_pubchem_formula

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

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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