How to Extract the Co-crystallized Ligand from a PDB File

By BioDockify Computational Research Team · September 3, 2026 · Tutorials

Extract the co-crystallized ligand from any PDB: identify HETATM codes, grep or use viewers, fix bond orders, and prepare it for redocking validation.

Read the complete article with tables, code and references on BioDockify.

Key References

• Berman HM et al. The Protein Data Bank. Nucleic Acids Res. 2000;28:235-242. doi:10.1093/nar/28.1.235
• O\u2019Boyle NM et al. Open Babel: an open chemical toolbox. J Cheminform. 2011;3:33. doi:10.1186/1758-2946-3-33
• RCSB PDB ligand pages and chemical component dictionaries, rcsb.org.

Scope & Limitations

Extracted ligands reflect crystallographic resolution; unresolved atoms and bond orders require repair before reuse