Bindingdb MCP Server

@pipeworx/bindingdb

Measured protein/small-molecule binding affinities from BindingDB — Ki, Kd, IC50 and EC50 values in nM, each curated out of a published paper and carrying the PubMed ID it came from.

Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources.

Tools

• bindingdb_ligands_by_uniprot(uniprot, cutoff?, limit?) — every ligand BindingDB has measured against a UniProt target, sorted by potency. Answers "what compounds bind this protein and how tightly".
• bindingdb_targets_by_smiles(smiles, similarity?, limit?) — the protein targets a compound (or a structurally similar one) has been measured against, with species. Answers compound-to-target and off-target questions.
• bindingdb_by_pdb(pdb, limit?) — affinities for the ligands associated with a PDB structure entry, linking a solved co-crystal to published potency.

Auth

Keyless. No registration, no header.

Data sources

• https://bindingdb.org/rest/getLigandsByUniprots — uniprot= (comma-separated accessions), cutoff= (affinity in nM), response=application/json.
• https://bindingdb.org/rest/getTargetByCompound — smiles=, cutoff= (Tanimoto similarity 0-1, NOT nM).
• https://bindingdb.org/rest/getLigandsByPDBs — pdb= (one 4-character ID).

Things that will otherwise cost you an afternoon:

• The base path is /rest/, not /rwd/bind/rest/. The latter is in older docs and 404s from Tomcat with an HTML body. /axis2/services/BDBService/... is also dead.
• The JSON envelope key does not match the endpoint name. All three respond under getLindsByUniprotsResponse / getLindsByUniprotResponse / getLindsByPDBsResponse — note "Linds", a typo that is part of the contract. The compound endpoint additionally prefixes every field with bdb..
• getLigandsByPDBs answers HTTP 500 with a SQL error in the body when it holds no data for that PDB ID — 2RH1 and 1ZZ1 both do this, 3EML works. That is an absent-data signal wearing a server-error costume; the pack says so rather than letting it read as an outage.
• Response size scales hard with cutoff. P24941 at cutoff 1 is 387 KB, at 10 is 1.1 MB, at 100 is 2.2 MB; P00533 at 100 is 5 MB. The default here is 10.
• An affinity of "0.000" means unreported, not infinitely potent. Values arrive as strings and may carry a qualifier (<1, >10000, " 348000"), so the pack splits them into affinity_nm + qualifier and nulls the zeros rather than ranking them first.
• getLigandsByUniprots returns rows for related targets as well as the exact accession you asked for — the query field on each row says which target the measurement is actually against.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "bindingdb": {
      "url": "https://gateway.pipeworx.io/bindingdb/mcp"
    }
  }
}

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/bindingdb/mcp returns the tools in the table above plus the shared Pipeworx meta-tools — ask_pipeworx, discover_tools, search_within, remember/recall and the rest of the gateway-wide set. So the tool count you see is larger than this table: a single-pack endpoint currently lists roughly 30 shared tools alongside the pack's own. The connection's initialize response states its exact scope, and is the authoritative answer for a given day.

This is deliberate, not multiplexing by accident. The meta-tools are what let a scoped connection answer a question this pack does not cover — via ask_pipeworx, which routes across the whole catalog — without you adding a second MCP server. There is currently no way to mount a pack endpoint without them; if the extra schemas cost you more context than the routing is worth, connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Both URLs reach the same gateway and the same 1683+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/bindingdb_ligands_by_uniprot \
  -H 'Content-Type: application/json' \
  -d '{"uniprot":"P24941","cutoff":1,"limit":3}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/bindingdb_ligands_by_uniprot. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Standalone (no gateway account)

This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:

{
  "mcpServers": {
    "bindingdb": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-bindingdb"]
    }
  }
}

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-bindingdb

It speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call for only this pack's tools — none of the shared meta-tools the gateway connection above adds. Same source, same tools, no ask_pipeworx routing.

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:

ask_pipeworx({ question: "your question about Bindingdb data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT