PubChem Connector for AI agents.
3 live capabilities
Research chemical properties and drug-like data for your next project.
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Why people use PubChem
PubChem for Drug Discovery and Chemical Data
This Connector lets your agent do the heavy lifting. Just tell it what you're looking for and it pulls the formula, weight, and SMILES directly to you. You get to stay in your flow while the agent handles the database digging.
What Vinkius changes
You get instant access to 116 million chemical records without ever leaving your chat window.
Use it from Claude, ChatGPT, Cursor or another AI client you already have.
One account · 5,900+ Connectors
- Real-world use case 01
Quickly checking drug-like properties
A chemist needs to know if a compound is viable for a drug.
- Real-world use case 02
Matching formulas to chemical names
A student has a molecular formula and needs the name.
- Real-world use case 03
Retrieving SMILES for modeling
A researcher needs the SMILES string for a specific CID.
Complete set · 3capabilities
The complete PubChem capability set.
These are the exact actions your AI can choose when you ask it to work with PubChem.
01—03
3 capabilities in this set.
Part of 3 available through PubChem.
- 01 Capability
Get pubchem compound
Get the full chemical profile for a specific compound using its PubChem CID. This is useful for deep dives into specific molecular data.
- 02 Capability
Search pubchem formula
Find all compounds that match a specific molecular formula. This helps you identify chemicals when you only have the formula.
- 03 Capability
Search pubchem
Search for chemical compounds by common name. This lets you quickly get basic properties like molecular weight and SMILES strings.
Set up in minutes
One URL. Then ask PubChem to work.
Claude and ChatGPT only need the Connector URL. Copy it once, add it in settings, and use PubChem from the conversation.
Choose your client
Live previewAdvanced clients IDE · CLI
Claude · Web + desktop
Connector URL · ready to paste
Streamable HTTPhttps://edge.vinkius.com/vk_preview_bfnYDABzlJ07TJu7Do9K5lCyve4Fg9F5YGb6KetY/mcp - Step 01
Open Connectors
In Claude Web or Claude Desktop, open Settings and choose Connectors.
- Step 02
Add the URL
Choose Add custom connector, name it PubChem, and paste the URL above.
- Step 03
Turn it on in chat
Select +, open Connectors, and enable PubChem for the conversation.
ChatGPT · Web + desktop
Connector URL · ready to paste
Streamable HTTPhttps://edge.vinkius.com/vk_preview_bfnYDABzlJ07TJu7Do9K5lCyve4Fg9F5YGb6KetY/mcp - Step 01
Open MCP settings
On desktop, open Settings and MCP servers. On web, open your workspace app or connector settings.
- Step 02
Add the URL
Choose Add server with Streamable HTTP, or create a custom MCP app, then paste the PubChem URL.
- Step 03
Save and start
Save the connection and enable PubChem in your conversation. Desktop may ask you to restart once.
Cursor · IDE configuration
Advanced setup
{
"mcpServers": {
"pubchem": {
"url": "https://edge.vinkius.com/vk_preview_bfnYDABzlJ07TJu7Do9K5lCyve4Fg9F5YGb6KetY/mcp"
}
}
}- Step 01
Open MCP Settings
Press Cmd+Shift+P (macOS) or Ctrl+Shift+P (Windows/Linux) → search "MCP Settings"
- Step 02
Add the server config
Paste the JSON configuration above into the mcp.json file that opens
- Step 03
Save the file
Cursor will automatically detect the new Connector
- Step 04
Start using PubChem
Open Agent mode in chat and ask: "Using PubChem, help me...". 3 tools available
VS Code Copilot · IDE configuration
Advanced setup
{
"mcpServers": {
"pubchem": {
"url": "https://edge.vinkius.com/vk_preview_bfnYDABzlJ07TJu7Do9K5lCyve4Fg9F5YGb6KetY/mcp"
}
}
}- Step 01
Create MCP config
Create a .vscode/mcp.json file in your project root
- Step 02
Add the server config
Paste the JSON configuration above
- Step 03
Enable Agent mode
Open GitHub Copilot Chat and switch to Agent mode using the dropdown
- Step 04
Start using PubChem
Ask Copilot: "Using PubChem, help me...". 3 tools available
Windsurf · IDE configuration
Advanced setup
{
"mcpServers": {
"pubchem": {
"url": "https://edge.vinkius.com/vk_preview_bfnYDABzlJ07TJu7Do9K5lCyve4Fg9F5YGb6KetY/mcp"
}
}
}- Step 01
Open MCP Settings
Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"
- Step 02
Add the server
Paste the JSON configuration above into mcp_config.json
- Step 03
Save and reload
Windsurf will detect the new server automatically
- Step 04
Start using PubChem
Open Cascade and ask: "Using PubChem, help me...". 3 tools available
Cline · IDE configuration
Advanced setup
{
"mcpServers": {
"pubchem": {
"url": "https://edge.vinkius.com/vk_preview_bfnYDABzlJ07TJu7Do9K5lCyve4Fg9F5YGb6KetY/mcp"
}
}
}- Step 01
Open Cline MCP Settings
Click the Connectors icon in the Cline sidebar panel
- Step 02
Add remote server
Click "Add Connector" and paste the configuration above
- Step 03
Enable the server
Toggle the server switch to ON
- Step 04
Start using PubChem
Ask Cline: "Using PubChem, help me...". 3 tools available
Claude Code · Terminal command
Advanced setup
claude mcp add pubchem --transport http "https://edge.vinkius.com/vk_preview_bfnYDABzlJ07TJu7Do9K5lCyve4Fg9F5YGb6KetY/mcp"- Step 01
Install Claude Code
Run npm install -g @anthropic-ai/claude-code if not already installed
- Step 02
Add the Connector
Run the command above in your terminal
- Step 03
Verify the connection
Run claude mcp to list connected servers, or type /mcp inside a session
- Step 04
Start using PubChem
Ask Claude: "Using PubChem, show me...". 3 tools are ready
Where the request belongs
Work PubChem can move forward.
This is for the researchers and students who are tired of manual data entry and want to move faster from hypothesis to data.
Medicinal Chemist
You use this to quickly pull drug-like properties and SMILES strings for lead compounds during discovery.
Pharmacy Student
You use this to look up drug structures and molecular formulas for coursework and study guides.
Biochemistry Researcher
You use this to identify metabolites and match chemical formulas to known records in the NCBI database.
Build the capability set
Add more capabilities.
Each Connector adds new actions and data without changing how you work.
Browse ConnectorsPubChem PUG REST API
Access chemical data. audit compounds, formulas, and CIDs via AI.
RCSB PDB
Explore 220K+ 3D molecular structures. search proteins, DNA, and RNA by name, experimental method, resolution, and bound ligands from the Protein Data Bank.
EBI Proteins API
Query the UniProt knowledge base for protein sequences, annotations, and functional data across millions of characterized entries.
UniProt
Search 250M+ protein sequences with functional annotations, gene names, subcellular locations, and amino acid data from the world's most comprehensive protein knowledge base.
EPA Computational Toxicology
Access the US EPA's CompTox Chemicals Dashboard data. search for chemicals, properties, hazard summaries, and exposure data.
KEGG
Access the Kyoto Encyclopedia of Genes and Genomes (KEGG) to query genomic, chemical, and systemic functional information directly from your AI agent.
Bring your own AI
Change the model, client or framework. Keep PubChem connected.
-
Claude -
ChatGPT -
Gemini -
Cursor -
VS Code -
Windsurf -
ZCode -
Cline -
Zed -
Continue -
Kiro -
Roo Code -
Zencoder -
Goose -
Void -
Augment Code -
Amp -
Qodo -
Tabnine -
Pieces -
Sourcegraph Cody -
JetBrains -
Warp -
Amazon Q -
Antigravity -
BoltAI -
Raycast -
Jan -
LM Studio -
AnythingLLM -
Open WebUI -
Msty -
Cherry Studio -
LibreChat -
TypingMind -
Chorus -
5ire -
n8n -
LangChain -
LlamaIndex -
CrewAI -
Vercel AI SDK
Before you connect
Questions about PubChem.
The practical details behind the request, access and result.
Can I use PubChem MCP to find drug-like properties?
Yes, the Connector lets your agent pull data like XLogP, hydrogen bond counts, and molecular complexity to help you evaluate drug-likeness.
How do I find a compound if I only know the formula?
You can ask your agent to search by molecular formula. It will find all matching chemicals in the database and list them for you.
Can this help with my biochemistry homework?
Absolutely. You can use it to look up drug structures, molecular weights, and chemical formulas quickly during your studies.
Does the PubChem MCP require an API key?
No, this Connector provides a direct connection to the database without requiring you to manage your own API keys.
What kind of chemical data can my agent pull?
Your agent can retrieve formulas, weights, SMILES strings, InChI codes, and various physicochemical properties for millions of compounds.
Is the data in PubChem MCP up to date?
It connects to the world's largest open chemistry database, which is maintained by the National Center for Biotechnology Information.
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 capability 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.
One connection away
Give your agent a direct line to PubChem.
Connect PubChem once. Keep it beside 5,900+ managed Connectors when the next task needs more.
Explore every Connector No credit card required · Free tier available