LadleAgent PubChem MCP (Chemical Database)
v0.4.1PubChem MCP based on @cyanheads/pubchem-mcp-server. Read-only tools for compound search, details, 2D/3D structures, GHS safety, bioactivity, interactions, and entity summaries. No API key required — use the public hosted endpoint or run locally via npx/bunx (stdio).
§ Connection Config
§ Quickstart
Add the following to your MCP client configuration (Cursor, Claude Desktop, etc.):
Use the public Streamable HTTP endpoint with no install. Works with remote-MCP clients such as Cursor.
MCP Client Configuration
{
"mcpServers": {
"pubchem-mcp-server": {
"type": "streamableHttp",
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}Config file locations
- Hosted by a third party; for production or sensitive use, prefer the local option below.
§ Tools Reference
10 tools
pubchem_search_compounds
Search compounds by name, SMILES, InChIKey, formula, substructure, or 2D similarity
| Parameter | Type | Required | Description |
|---|---|---|---|
| query | string | ✓ | Search term or structure identifier |
pubchem_get_compound_details
Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification by CID
| Parameter | Type | Required | Description |
|---|---|---|---|
| cids | number[] | ✓ | Compound CID list |
pubchem_get_compound_image
Fetch a 2D structure diagram (PNG) by CID
| Parameter | Type | Required | Description |
|---|---|---|---|
| cid | number | ✓ | Compound CID |
pubchem_get_compound_3d_structure
Fetch a 3D conformer (JSON or SDF) by CID
| Parameter | Type | Required | Description |
|---|---|---|---|
| cid | number | ✓ | Compound CID |
pubchem_get_compound_xrefs
Get external database cross-references
| Parameter | Type | Required | Description |
|---|---|---|---|
| cid | number | ✓ | Compound CID |
pubchem_get_compound_safety
Get GHS hazard classification and safety data by CID (batch)
| Parameter | Type | Required | Description |
|---|---|---|---|
| cids | number[] | ✓ | Compound CID list |
pubchem_get_bioactivity
Get bioactivity profile: assays, targets, and activity values
| Parameter | Type | Required | Description |
|---|---|---|---|
| cid | number | ✓ | Compound CID |
pubchem_get_compound_interactions
Get drug-drug, drug-food, and chemical-target interactions
| Parameter | Type | Required | Description |
|---|---|---|---|
| cid | number | ✓ | Compound CID |
pubchem_search_assays
Find bioassays by biological target (gene, protein, Gene ID, UniProt)
| Parameter | Type | Required | Description |
|---|---|---|---|
| target | string | ✓ | Target identifier |
pubchem_get_summary
Get summaries for assay, gene, protein, or taxonomy entities
| Parameter | Type | Required | Description |
|---|---|---|---|
| entityType | string | ✓ | Entity type |
§ Examples
Once configured, you can ask the AI directly:
Compound lookup
Look up aspirin in PubChem for its CID, molecular weight, and a GHS safety summary
search → details + safety
Target assays
Find PubChem bioassays related to EGFR and summarize the top results
search_assays → get_summary
Similar structures
Find 2D-similar compounds to caffeine and list key physicochemical properties
similarity search + details