MCP server

Bindingdb

io.github.pipeworx-io/bindingdb

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

BindingDB — measured protein/small-molecule binding affinities.

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 27,012 tokens per request once connected45 tools

https://gateway.pipeworx.io/bindingdb/mcp

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 45
Token cost: About 27,012 tokens per request
Sets up in: Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok
Last checked: 26 Oct 2026, 08:29 UTC

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http bindingdb https://gateway.pipeworx.io/bindingdb/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.bindingdb]
url = "https://gateway.pipeworx.io/bindingdb/mcp"

Gemini CLI

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

Cursor

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

VS Code

{"servers":{"bindingdb":{"type":"http","url":"https://gateway.pipeworx.io/bindingdb/mcp"}}}

Antigravity

agy mcp add bindingdb https://gateway.pipeworx.io/bindingdb/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"bindingdb","server_url":"https://gateway.pipeworx.io/bindingdb/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"bindingdb","server_url":"https://gateway.pipeworx.io/bindingdb/mcp"}

bindingdb_by_pdb ~174 tokens
Measured binding affinities for the ligands associated with a PDB structure entry, linking a solved co-crystal to the potency numbers published for that target. AUTHORITATIVE for "what is the measured affinity of the ligand in this PDB structure". Takes a single 4-character PDB ID (e.g. 3EML).
bindingdb_ligands_by_uniprot ~296 tokens
Measured binding affinities (Ki, Kd, IC50, EC50 in nM) for every ligand BindingDB has curated against a UniProt target, each with the PubMed ID of the paper it was measured in. AUTHORITATIVE for "what compounds bind this protein and how tightly" — this is experimental medicinal-chemistry data, not a
bindingdb_targets_by_smiles ~239 tokens
Given a compound SMILES, the protein targets BindingDB has measured it (or a structurally similar compound) against, with species and affinity. AUTHORITATIVE for compound-to-target and off-target lookups grounded in published measurements. Use a similarity cutoff below 1.0 to pull analogues as well

Nesso-1 Binding Affinity
Protein-ligand binding affinity with Nesso-1
Nullary
Negative results intelligence for drug discovery — query measured failures via MCP.
Guidetopharmacology
IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) MCP — BYO key. Expert-curated pharmacology database of…
Pdbe
PDBe (Protein Data Bank in Europe, EBI) MCP.
Jean — Molecular Biology & Genomics
Validated molecular biology tools: cloning, primers, CRISPR, Sanger, alignment, qPCR, phylogenetics
Rcsb Pdb
RCSB PDB MCP — experimentally determined macromolecular structures.
LULA-1.1 Protein-Ligand Binding Scorer
Sequence-only protein-ligand binding scorer (LULA-1.1)
LULA-1.1 Protein-Ligand Binding Scorer
Sequence-only protein-ligand binding scorer (LULA-1.1)

[![AptLynx](https://aptlynx.net/badge/io.github.pipeworx-io/bindingdb.svg)](https://aptlynx.net/servers/io.github.pipeworx-io/bindingdb)

Listing text is written by the maker; AptLynx lists tools and does not vouch for them. Find another tool · Browse by topic · For agents