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PubChem MCP Server

Name: PubChem
Availability: InStock
Author: Vinkius

pubchem.ncbi.nlm.nih.gov

Built by Vinkius GDPR ToolsFree for Subscribers

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

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What is the PubChem MCP Server?

The PubChem MCP Server gives AI agents like Claude, ChatGPT, and Cursor direct access to PubChem via 3 tools. Search 116M+ chemical compounds with molecular properties, SMILES notation, formulas, and drug-like properties from the world's largest free chemistry database. Powered by the Vinkius - no API keys, no infrastructure, connect in under 2 minutes.

Built-in capabilities (3)

get_pubchem_compoundsearch_pubchemsearch_pubchem_formula

Tools for your AI Agents to operate PubChem

Ask your AI agent "What are the molecular properties of aspirin?" and get the answer without opening a single dashboard. With 3 tools connected to real PubChem data, your agents reason over live information, cross-reference it with other MCP servers, and deliver insights you would spend hours assembling manually.

Works with Claude, ChatGPT, Cursor, and any MCP-compatible client. Powered by the Vinkius - your credentials never touch the AI model, every request is auditable. Connect in under two minutes.

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One subscription gives you access to thousands of MCP servers - and you can deploy your own to the Vinkius Edge. Your AI agents only access the data you authorize, with DLP that blocks sensitive information from ever reaching the model, kill switch for instant shutdown, and up to 60% token savings. Enterprise-grade infrastructure and security, zero maintenance.

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PubChem MCP Server capabilities

3 tools

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

What the PubChem MCP Server unlocks

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

Frequently asked questions about the PubChem MCP Server

Do I need an API key to use PubChem?

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.

What molecular properties are returned for each compound?

Each compound includes: CID, IUPAC name, molecular formula, molecular weight, canonical SMILES, InChI identifier, XLogP (lipophilicity), hydrogen bond donor count, hydrogen bond acceptor count, and molecular complexity score. These cover Lipinski's Rule of Five for drug-likeness assessment.

Can I search by molecular formula instead of name?

Yes! Use the formula search tool with standard notation (e.g., C8H10N4O2 for caffeine, C9H8O4 for aspirin, H2O for water). PubChem will return all compounds matching that exact formula with their names and properties.

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