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 1679+ live data sources.

Tools

BindingDB has measured against a UniProt target, sorted by potency. Answers "what compounds bind this protein and how tightly".

• bindingdbligandsby_uniprot(uniprot, cutoff?, limit?) — every ligand

targets a compound (or a structurally similar one) has been measured against, with species. Answers compound-to-target and off-target questions.

• bindingdbtargetsby_smiles(smiles, similarity?, limit?) — the protein

a PDB structure entry, linking a solved co-crystal to published potency.

• bindingdbbypdb(pdb, limit?) — affinities for the ligands associated with

Auth

Keyless. No registration, no header.

Data sources

accessions), cutoff= (affinity in nM), response=application/json.

• — uniprot= (comma-separated

(Tanimoto similarity 0-1, NOT nM).

• — smiles=, cutoff=

• — pdb= (one 4-character ID).

Things that will otherwise cost you an afternoon:

docs and 404s from Tomcat with an HTML body. /axis2/services/BDBService/... is also dead.

• The base path is /rest/, not /rwd/bind/rest/. The latter is in older

under getLindsByUniprotsResponse / getLindsByUniprotResponse / getLindsByPDBsResponse — note "Linds", a typo that is part of the contract. The compound endpoint additionally prefixes every field with bdb..

• The JSON envelope key does not match the endpoint name. All three respond

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.

• **getLigandsByPDBs answers HTTP 500 with a SQL error in the body when it

10 is 1.1 MB, at 100 is 2.2 MB; P00533 at 100 is 5 MB. The default here is 10.

• Response size scales hard with cutoff. P24941 at cutoff 1 is 387 KB, at

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.

• An affinity of "0.000" means unreported, not infinitely potent. Values

accession you asked for — the query field on each row says which target the measurement is actually against.

• getLigandsByUniprots returns rows for related targets as well as the exact

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 — askpipeworx, discovertools, 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.

Shortened. The full README is on GitHub.