MCP For Claude Marketplace
PubChem PUG REST API

PubChem PUG REST API MCP Connector for Claude

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Access chemical data — audit compounds, formulas, and CIDs via AI.

4 tools Official Updated Jun 28, 2026 Official Vinkius Partner
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Empower your AI agent to orchestrate your entire chemical research and compound auditing workflow with the PubChem PUG REST API, the authoritative source for molecular data from the National Library of Medicine. By connecting PubChem to your agent, you transform complex chemical searches into a natural conversation. Your agent can instantly retrieve compound details, audit molecular formulas, and query specific Compound Identifiers (CIDs) without you ever touching a scientific portal. Whether you are conducting pharmacological research or managing laboratory constraints, your agent acts as a real-time chemical consultant, ensuring your data is always verified and precise.

What you can do

  • Compound Auditing — Search for thousands of chemical compounds by name or keyword and retrieve detailed metadata, including IUPAC names and formulas.
  • CID Oversight — Audit specific Compound Identifiers (CIDs) to understand the technical reach of your chemical data instantly.
  • Formula Discovery — Query molecular formulas for specific compounds to assist in deep-dive archival classification.
  • Metadata Intelligence — Retrieve high-resolution technical properties for any chemical record to assist in scientific auditing.
  • Operational Monitoring — Check API status to ensure your chemical research workflow is always operational.

How it works

  1. Subscribe to this server
  2. No API Key required (PubChem is a free and open service)
  3. Start managing your chemical intelligence through Claude, Cursor, or any MCP-compatible client

Who is this for?

  • Scientists & Researchers — monitor chemical data and retrieve official metadata straight from your workflow.
  • Pharmacologists — verify compound details and audit molecular patterns without manual searching.
  • Students & Educators — perform rapid audits of chemical properties and identify relevant stylistic markers through natural language.
  • Operations Leads — automate scientific data querying to orchestrate cross-functional research teams smoothly.
chemistrymolecular-datacompound-searchbiomedical-dataresearch-toolsapi-integration

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

check_api_status

Check if the PubChem PUG REST service is operational

get_compound_by_cid

Get comprehensive details for a chemical compound by CID

get_compound_by_name

Get comprehensive details for a chemical compound by name

search_compound_cids

Search for compound CIDs matching a name or keyword

See how to talk to your AI agent using PubChem PUG REST API.

Get details for compound 'Aspirin' using PubChem.

I've retrieved the details for Aspirin! It has a CID of 2244 and its molecular formula is identified as C9H8O4. Would you like the full IUPAC name or other technical metadata for this compound?

What is the molecular formula for CID '2519'?

I've identified the compound for CID 2519! It is Caffeine, and its molecular formula is identified as C8H10N4O2. I can assist you with more technical properties for this record if you'd like.

Search for compound CIDs matching 'glucose'.

I've scanned the PubChem database for glucose! I've identified several matching CIDs, including 5793 and 107526. I can provide the full metadata for any of these identifiers to help you in your research.

No. PubChem is a free and open service provided by the NIH. This server works out of the box without any static credentials required.

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