alterlab-bindingdb

BindingDB Database

Overview

BindingDB (https://www.bindingdb.org/) is the primary public database of measured drug-protein binding affinities. It contains roughly 3.2 million binding data records for ~1.4 million compounds tested against ~11,400 protein targets, curated from scientific literature and patent literature. BindingDB stores quantitative binding measurements (Ki, Kd, IC50, EC50) essential for drug discovery, pharmacology, and computational chemistry research.

Key resources:

• BindingDB website: https://www.bindingdb.org/
• REST API base: https://bindingdb.org/rest/ (no key; default response is XML, append response=application/json)
• Downloads page: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/Download.jsp (the full TSV is the dated BindingDB_All_<YYYYMM>_tsv.zip, ~560 MB zipped, refreshed monthly)

When to Use This Skill

Use BindingDB when:

• Target-based drug discovery: What known compounds bind to a target protein? What are their affinities?
• SAR analysis: How do structural modifications affect binding affinity for a series of analogs?
• Lead compound profiling: What targets does a compound bind (selectivity/polypharmacology)?
• Benchmark datasets: Obtain curated protein-ligand affinity data for ML model training
• Repurposing analysis: Does an approved drug bind to an unintended target?
• Competitive analysis: What is the best reported affinity for a target class?
• Fragment screening: Find validated binding data for fragments against a target

Core Capabilities

1. BindingDB REST API

Base URL: https://bindingdb.org/rest

import requests

BASE_URL = "https://bindingdb.org/rest"

def bindingdb_query(method, params):
    """Query the BindingDB REST API."""
    url = f"{BASE_URL}/{method}"
    response = requests.get(url, params=params, headers={"Accept": "application/json"})
    response.raise_for_status()
    return response.json()

2. Query by Target (UniProt ID)

The getLigandsByUniprot endpoint takes a single uniprot parameter formatted as <UniProt accession>;<cutoff in nM>, e.g. P00519;10000.