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pdb-database

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Python API for RCSB PDB 3D structures (search, fetch coordinates, metadata). Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers — pass only the target protein name or PDB accession.

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Oct 30, 2026
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# PDB Database

## Overview

RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules. Search for structures, retrieve coordinates and metadata, perform sequence and structure similarity searches across 200,000+ experimentally determined structures and computed models.

## Query Limitations — Read Before Using

PDB stores **experimentally determined 3D structures of proteins and nucleic acids**. Queries must target a protein, gene, or known PDB ID. Drug/chemistry phrases return zero results.

| ❌ Fails (not a structure query) | ✅ Works |
|---|---|
| "KRAS covalent inhibitors" | "KRAS" → returns KRAS structures |
| "covalent warhead selectivity" | "6OIM" (direct PDB ID for KRAS-G12C/AMG-510) |