PDB to SDF Converter
SDF keeps 3D coordinates and per-record metadata, which makes it a better container than SMILES when the geometry matters.
PDB to SDF vs PDB to SMILES
Both start from the same file, but SDF preserves the three-dimensional coordinates in the original frame. That matters when the ligand's pose inside the binding site is the point — for example when preparing a reference ligand for docking or comparing binding modes.
Practical workflow
- Extract the
HETATMrecords for the ligand of interest. - Convert that fragment to SDF.
- Add hydrogens and assign charges in your modelling tool.
Caveat
Crystal structures rarely include hydrogens and may have alternate conformations. Treat the converted SDF as a starting point, not a finished ligand.