PDB to SMILES Converter
In short: Convert PDB structure text to SMILES using a best-effort public chemistry resolver workflow. It is free, works in your web browser and needs no download.
Paste PDB text and convert to SMILES with a best-effort resolver. For large proteins, use ligand-only PDB blocks.
Input and output formats
| Input: PDB | Output: SMILES | |
|---|---|---|
| Full name | PDB (Protein Data Bank format) | SMILES (Simplified Molecular Input Line Entry System) |
| What it holds | 3D atom coordinates in fixed columns. Used for proteins and small molecules. | Atoms, bonds, rings, charges and stereo as one line of text. No coordinates. |
| File or form | .pdb | .smi or plain text |
File Format Explained
PDB stores 3D atom coordinates, residue names, chains, occupancy, B-factor, and element data. It is common for proteins, ligands, crystal structures, and molecular visualization.
SMILES stores a molecule as a compact line of connectivity text. It is best for small molecules and ligands, not full protein macromolecules.
For best results, convert ligand-only PDB blocks. Protein PDB files often contain many residues and missing bond-order information, so a direct PDB to SMILES conversion can be ambiguous.
Converting PDB ligands to SMILES
PDB files store atom coordinates, mainly for proteins and nucleic acids from crystallography, NMR, or cryo-EM. Small-molecule ligands appear as HETATM records. The format often lacks explicit bond orders for ligands, so converting coordinates into a SMILES string involves inferring bonds from atom distances and residue templates. That is why results are best-effort.
Getting good results
- Extract only the ligand: copy its HETATM lines (and any CONECT lines for it) rather than the whole protein.
- Remove water molecules (residue name HOH) and unrelated ions.
- Convert and check the SMILES by drawing it with SMILES to Structure.
Common issues
- Missing hydrogens: most crystal structures omit hydrogens, so bond orders and charges may need checking.
- Wrong bond orders: aromatic rings and carbonyls can be misassigned when geometry is distorted; compare with the ligand's entry in the PDB Chemical Component Dictionary.
- Alternate conformations: keep only one (for example altLoc A) to avoid duplicated atoms.
To view the protein itself, use the Protein Viewer.
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