PDB to SDF converter

Convert PDB protein structure files to SDF format for cheminformatics and molecular analysis. Upload a PDB file or paste the structure data below.

Input (PDB format)

PDB

Or fetch by PDB ID

Enter a 4-character PDB ID to fetch the structure from RCSB database

Click to upload or drag and drop

PDB file (.pdb, .ent)

Max size: 50MB

Advanced conversion options

Chain selection

All chainsSpecific chains

Atom inclusion options

Include hydrogen atomsInclude heteroatoms (ligands, water, etc.)

Structure options

Separate models into individual SDF entriesAdd basic bond order information

Output (SDF format)

SDF