bindingdb-database

BindingDB Database

Overview

BindingDB (https://www.bindingdb.org/) is the primary public database of measured drug-protein binding affinities. It contains over 3 million binding data records for ~1.4 million compounds tested against ~9,200 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: https://www.bindingdb.org/axis2/services/BDBService
• Downloads: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp
• GitHub: https://github.com/drugilsberg/bindingdb

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://www.bindingdb.org/axis2/services/BDBService

import requests

BASE_URL = "https://www.bindingdb.org/axis2/services/BDBService"

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)

def get_ligands_for_target(uniprot_id, affinity_type="Ki", cutoff=10000, unit="nM"):
    """
    Get all ligands with measured affinity for a UniProt target.

    Args:
        uniprot_id: UniProt accession (e.g., "P00519" for ABL1)
        affinity_type: "Ki", "Kd", "IC50", "EC50"
        cutoff: Maximum affinity value to return (in nM)
        unit: "nM" or "uM"
    """
    params = {
        "uniprot_id": uniprot_id,
        "affinity_type": affinity_type,
        "affinity_cutoff": cutoff,
        "response": "json"
    }
    return bindingdb_query("getLigandsByUniprotID", params)

# Example: Get all compounds binding ABL1 (imatinib target)
ligands = get_ligands_for_target("P00519", affinity_type="Ki", cutoff=100)