Vinkius
PubChem PUG REST API

PubChem PUG REST API MCP for AI. Audit compounds and formulas by CID or name instantly.

Claude Claude
ChatGPT ChatGPT
Cursor Cursor
Gemini Gemini
Windsurf Windsurf
VS Code VS Code
JetBrains JetBrains
Vercel Vercel
See Vinkius in Action

Works with every AI agent you already use

…and any MCP-compatible client

PubChem PUG REST API MCP on Cursor AI Code EditorPubChem PUG REST API MCP on Claude Desktop AppPubChem PUG REST API MCP on OpenAI Agents SDKPubChem PUG REST API MCP on Visual Studio CodePubChem PUG REST API MCP on GitHub Copilot AI AgentPubChem PUG REST API MCP on Google Gemini AIPubChem PUG REST API MCP on Lovable AI DevelopmentPubChem PUG REST API MCP on Mistral AI AgentsPubChem PUG REST API MCP on Amazon AWS Bedrock

Connect to your AI in seconds.

The PubChem PUG REST API MCP Server lets your AI agent access authoritative molecular data from PubChem, a resource managed by the National Library of Medicine.

It allows you to audit chemical compounds, retrieve detailed metadata, and query specific formulas and Compound Identifiers (CIDs) without ever visiting a scientific portal.

You can search for CIDs using keywords or look up full compound details instantly just by providing a name or an ID.

What your AI can do

Check api status

Verifies if the PubChem PUG REST service is currently running and accessible.

Get compound by cid

Retrieves detailed information for a chemical compound using its specific CID number.

Get compound by name

Gets comprehensive details and formulas for a chemical compound when you provide its name.

+ 1 more capabilities included
Validate API Health

Checks the operational status of the PubChem PUG REST service to ensure data retrieval won't fail.

Lookup by Compound CID

Retrieves all technical metadata, formulas, and details for a chemical compound when provided with its unique Identifier (CID).

Lookup by Common Name

Finds detailed records, including molecular formulas and IUPAC names, using the known name of a chemical compound.

Search for CIDs via Keyword

Scans the database to find multiple Compound Identifiers (CIDs) that match a general keyword or search phrase.

Retrieve Technical Specifications

Access high-resolution properties and formulas needed for scientific auditing of any chemical record.

Included with Plan

Waiting for input…

AI Agent

PubChem PUG REST API: 4 Tools for Molecular Data Access

Use these tools to check service status, find compound details by name or ID, and search the PubChem database using keywords.

Make your AI actually useful.

Add this MCP to Claude, Cursor, or Windsurf and your AI stops guessing. It gets real tools to look things up, take action, and handle the stuff you keep doing by hand.

Start using PubChem PUG REST API on Vinkius

Check Api Status

Verifies if the PubChem PUG REST service is currently running and accessible.

Get Compound By Cid

Retrieves detailed information for a chemical compound using its specific CID number.

Get Compound By Name

Gets comprehensive details and formulas for a chemical compound when you provide its...

Search Compound Cids

Searches the database to find multiple CIDs that match a given keyword or search...

Security and governance baked right in.

Pick your AI client below to get set up. Just create a Vinkius account, subscribe, and you're instantly up and running. We handle the entire backend infrastructure, delivering out-of-the-box support for HTTPS Streamable, SSE, and OAuth2—zero messy routing required.

Claude AI

Claude AI

1

Open Claude Settings

Go to claude.ai, click your profile icon, then navigate to Customize → Connectors.

2

Add Custom Connector

Click the "+" button and select Add custom connector. Paste your Vinkius endpoint URL:

https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp

Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. For OAuth-protected servers, expand Advanced settings to add credentials.

3

Start a conversation

Open a new chat. The PubChem PUG REST API integration is available immediately — no restart needed.

Choose How to Get Started

Build a custom MCP for your own tools, or connect a ready-made integration from our catalog.

Build Your Own

Turn any API into an MCP. Import a spec, define Agent Skills, or deploy with MCPFusion.

  • Import from OpenAPI, Swagger, or YAML specs
  • Create Agent Skills with progressive disclosure
  • Deploy to edge with MCPFusion framework
  • Built in DLP, auth, and compliance on every call
  • Real time usage dashboard and cost metering
  • Publish to catalog or keep private
Start building

Make Your AI Do More

Start with PubChem PUG REST API, then connect any of our 5,100+ other servers whenever your AI needs more. One click, no limits.

  • Use this MCP plus 5,100+ others, all in one place
  • Add new capabilities to your AI anytime you want
  • Every connection is secured and compliant automatically
  • Track usage and costs across all your servers
  • Works with Claude, ChatGPT, Cursor, and more
  • New servers added to the catalog every week
PubChem PUG REST API MCP server cover

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by PubChem. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

VINKIUS INFRASTRUCTURE

Cloud Hosted

Managed infra

V8 Isolated

Sandboxed per request

Zero-Trust Proxy

No stored credentials

DLP Enforced

Policy on every call

GDPR Compliant

EU data residency

Token Compression

~60% cost reduction

Your data is protected. See how we built it.

Works with Claude, ChatGPT, Cursor, and more

The Model Context Protocol standardizes how applications expose capabilities to LLMs. Instead of operating in isolation, your AI gains direct access to external platforms, live data, and real-world actions through secure, standardized connections.

This connection provides 4 powerful capabilities that interface natively with Claude, ChatGPT, Cursor, and other compatible AI platforms. No middleware. No custom integration required.

Sifting through scientific portals for basic compound data takes forever.

Today, getting accurate chemical details means opening PubChem's website or a specialized database. You search by name, click through multiple pages to find the CID, then copy-paste that ID into another tool just to get the formula. It’s slow, it involves several tabs, and you risk copying an incorrect identifier.

With this MCP server, your agent handles the entire flow. You tell it the compound's name; it runs `get_compound_by_name` and delivers the CID, IUPAC name, *and* formula in a single chat response. It’s immediate verification.

PubChem PUG REST API MCP Server: Get confirmed molecular data.

You don't have to manually check if the service is down before starting your research. You simply ask the agent to run `check_api_status`. If it confirms the service is operational, you know every subsequent call—whether using `get_compound_by_cid` or another tool—will be reliable.

This guarantees that your entire chemical audit workflow stays online and predictable. It's about knowing your data source is rock solid before you commit to analysis.

What your AI can actually do with this

Listen up. This server hooks your AI agent right into PubChem, which is basically the gold standard for molecular data—it’s run by the National Library of Medicine. It lets your agent audit chemical compounds, pull deep metadata, and query specific formulas or Compound Identifiers (CIDs) without you ever having to visit a clunky scientific website yourself.

You're getting direct access to authoritative chemistry info.

When you use this tool set, your agent doesn’t just search; it performs structured chemical audits. It handles the complex stuff so you don't have to babysit databases manually. This speeds up your workflow big time.

Here’s how your AI client uses the tools:

First, before running anything else, your agent checks the service health using check_api_status. That confirms whether the PubChem PUG REST service is actually online and ready to spit out data. You don't want a failed retrieval because the endpoint was down.

To pull specific details on an already known compound, you’ve got two main options. If you know the exact Compound Identifier (CID), you use get_compound_by_cid. This tool retrieves all the technical metadata, molecular formulas, and detailed specs for that chemical record. On the other hand, if you only have a common or IUPAC name—say, 'Aspirin'—you use get_compound_by_name.

That gives your agent comprehensive records and formulas based purely on the name you feed it.

If you don’t know which CID to start with, you search first. You run search_compound_cids by giving it a general keyword or phrase. This scans the whole database and finds multiple CIDs that match your search term.

Knowing these tools lets your agent handle everything from basic lookups to deep technical auditing. It gathers high-resolution properties and formulas you need when you’re verifying any chemical record. You can find detailed records, including IUPAC names and molecular formulas, using the known name of a compound via get_compound_by_name. For full scientific verification, all available details for a compound are pulled through get_compound_by_cid once that unique ID is provided.

If you just need to know which CIDs exist for a term—like 'glucose' or something else—you use search_compound_cids to get that list of matching identifiers.

This setup makes sure your agent never gets stuck waiting on another person to run the search, giving it immediate access to core molecular data. You just hook up your preferred AI client and point it at this server. It handles all the necessary calls—status checks, name lookups, CID lookups, and keyword searches—so you're always working with verified chemical information.

Built · Hosted · Managed by Vinkius PubChem PUG REST API - Chemical Data Lookup Tool
Server ID 019d8471-f7a1-7202-b3cf-a9805e1fcfcf
Vinkius Inspector
Compliance Grade A+
Score 100/100
Vinkius Inspector Badge — Score 100/100

Questions you might have

How do I find the CID for a compound using PubChem PUG REST API? +

Use search_compound_cids and input the common name or keyword. This tool scans the database and returns multiple potential CIDs, which you can then use with get_compound_by_cid.

Is `get_compound_by_name` better than `get_compound_by_cid`? +

No. If you have the CID, always use get_compound_by_cid. It is faster and more precise because you are querying by a guaranteed unique identifier.

What should I run if I want to know if PubChem is working? +

Run the check_api_status tool. This confirms that the entire data service is up, which is critical before running any compound lookups or searches.

Can I find a formula using only my agent and PubChem PUG REST API? +

Yes. You can run get_compound_by_name (if you know the name) or get_compound_by_cid (if you have the ID). Both tools return the molecular formula as part of the comprehensive metadata.

How do I authenticate my agent when using PubChem PUG REST API? +

You don't need to worry about authentication. The service is free and open, so your AI client connects immediately without needing an API key or credentials.

What should I do if my call to `search_compound_cids` fails due to rate limiting? +

If the search request fails, your agent must implement retry logic with exponential backoff. Always check PubChem's published usage policy for specific rate limits and quotas.

Does `get_compound_by_name` return the full molecular formula or just basic details? +

It returns comprehensive metadata. You'll get structured data including IUPAC names, structural formulas, and technical properties necessary for deep auditing.

If a chemical name I pass to `get_compound_by_name` doesn't exist, how does PubChem PUG REST API handle the error? +

The tool will return an explicit error code or an empty dataset rather than crashing. Your agent must check the response structure for null values before attempting to process results.

Is an API Key required for PubChem API? +

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

What is a CID? +

CID stands for Compound Identifier. It is a unique numerical ID assigned to each chemical compound in the PubChem database.

Can the agent show molecular formulas? +

Yes. The compound details retrieved by your agent include the molecular formula and IUPAC name metadata where available.

Built & Managed by Vinkius 30s setup 4 tools

We've already built the connector for PubChem PUG REST API. Just plug in your AI agents and start using Vinkius.

No hosting. No infrastructure. No complex setup.
All 4 tools are live and waiting. You're up and running in seconds.

Vinkius runs on Claude Claude
Vinkius runs on ChatGPT ChatGPT
Vinkius runs on Cursor Cursor
Vinkius runs on Gemini Gemini
Vinkius runs on Windsurf Windsurf
Vinkius runs on VS Code VS Code
Vinkius runs on JetBrains JetBrains
Vinkius runs on Vercel Vercel
+ other MCP clients

Vinkius gives your AI agents access to the full catalog of app connectors, all fully managed, secure, and enterprise-ready. One subscription, every tool you need.

Zero hosting required Full MCP catalog included Enterprise-grade security Auto-updated by Vinkius

Built, hosted, and secured by Vinkius. You just connect and go.