PubChem MCP Server for OpenAI Agents SDK 3 tools — connect in under 2 minutes
The OpenAI Agents SDK enables production-grade agent workflows in Python. Connect PubChem through Vinkius and your agents gain typed, auto-discovered tools with built-in guardrails. no manual schema definitions required.
ASK AI ABOUT THIS MCP SERVER
Vinkius supports streamable HTTP and SSE.
import asyncio
from agents import Agent, Runner
from agents.mcp import MCPServerStreamableHttp
async def main():
# Your Vinkius token. get it at cloud.vinkius.com
async with MCPServerStreamableHttp(
url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
) as mcp_server:
agent = Agent(
name="PubChem Assistant",
instructions=(
"You help users interact with PubChem. "
"You have access to 3 tools."
),
mcp_servers=[mcp_server],
)
result = await Runner.run(
agent, "List all available tools from PubChem"
)
print(result.final_output)
asyncio.run(main())
* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure
About PubChem MCP Server
Connect your AI agent to PubChem — the world's largest open chemistry database, maintained by the National Center for Biotechnology Information (NCBI/NIH).
The OpenAI Agents SDK auto-discovers all 3 tools from PubChem through native MCP integration. Build agents with built-in guardrails, tracing, and handoff patterns. chain multiple agents where one queries PubChem, another analyzes results, and a third generates reports, all orchestrated through Vinkius.
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)
The PubChem MCP Server exposes 3 tools through the Vinkius. Connect it to OpenAI Agents SDK in under two minutes — no API keys to rotate, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.
How to Connect PubChem to OpenAI Agents SDK via MCP
Follow these steps to integrate the PubChem MCP Server with OpenAI Agents SDK.
Install the SDK
Run pip install openai-agents in your Python environment
Replace the token
Replace [YOUR_TOKEN_HERE] with your Vinkius token from cloud.vinkius.com
Run the script
Save the code above and run it: python agent.py
Explore tools
The agent will automatically discover 3 tools from PubChem
Why Use OpenAI Agents SDK with the PubChem MCP Server
OpenAI Agents SDK provides unique advantages when paired with PubChem through the Model Context Protocol.
Native MCP integration via `MCPServerSse`, pass the URL and the SDK auto-discovers all tools with full type safety
Built-in guardrails, tracing, and handoff patterns let you build production-grade agents without reinventing safety infrastructure
Lightweight and composable: chain multiple agents and MCP servers in a single pipeline with minimal boilerplate
First-party OpenAI support ensures optimal compatibility with GPT models for tool calling and structured output
PubChem + OpenAI Agents SDK Use Cases
Practical scenarios where OpenAI Agents SDK combined with the PubChem MCP Server delivers measurable value.
Automated workflows: build agents that query PubChem, process the data, and trigger follow-up actions autonomously
Multi-agent orchestration: create specialist agents. one queries PubChem, another analyzes results, a third generates reports
Data enrichment pipelines: stream data through PubChem tools and transform it with OpenAI models in a single async loop
Customer support bots: agents query PubChem to resolve tickets, look up records, and update statuses without human intervention
PubChem MCP Tools for OpenAI Agents SDK (3)
These 3 tools become available when you connect PubChem to OpenAI Agents SDK via MCP:
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
Example Prompts for PubChem in OpenAI Agents SDK
Ready-to-use prompts you can give your OpenAI Agents SDK agent to start working with PubChem immediately.
"What are the molecular properties of aspirin?"
"Search for compounds with the molecular formula C8H10N4O2."
"Get the full chemical details for PubChem compound CID 5090."
Troubleshooting PubChem MCP Server with OpenAI Agents SDK
Common issues when connecting PubChem to OpenAI Agents SDK through the Vinkius, and how to resolve them.
MCPServerStreamableHttp not found
pip install --upgrade openai-agentsAgent not calling tools
PubChem + OpenAI Agents SDK FAQ
Common questions about integrating PubChem MCP Server with OpenAI Agents SDK.
How does the OpenAI Agents SDK connect to MCP?
MCPServerSse(url=...) to create a server connection. The SDK auto-discovers all tools and makes them available to your agent with full type information.Can I use multiple MCP servers in one agent?
MCPServerSse instances to the agent constructor. The agent can use tools from all connected servers within a single run.Does the SDK support streaming responses?
Connect PubChem with your favorite client
Step-by-step setup guides for every MCP-compatible client and framework:
Anthropic's native desktop app for Claude with built-in MCP support.
AI-first code editor with integrated LLM-powered coding assistance.
GitHub Copilot in VS Code with Agent mode and MCP support.
Purpose-built IDE for agentic AI coding workflows.
Autonomous AI coding agent that runs inside VS Code.
Anthropic's agentic CLI for terminal-first development.
Python SDK for building production-grade OpenAI agent workflows.
Google's framework for building production AI agents.
Type-safe agent development for Python with first-class MCP support.
TypeScript toolkit for building AI-powered web applications.
TypeScript-native agent framework for modern web stacks.
Python framework for orchestrating collaborative AI agent crews.
Leading Python framework for composable LLM applications.
Data-aware AI agent framework for structured and unstructured sources.
Microsoft's framework for multi-agent collaborative conversations.
Connect PubChem to OpenAI Agents SDK
Get your token, paste the configuration, and start using 3 tools in under 2 minutes. No API key management needed.