PDB to SDF

How to convert a ligand PDB to SDF?

Upload a PDB containing a small-molecule ligand. RDKit reads its coordinates and connectivity, then writes an SDF and reports the perceived SMILES and atom count. Check the resulting chemistry before further use, because PDB does not reliably encode the original bond orders and formal charges.

1. Extract the intended small-molecule ligand into a .pdb.
2. Choose whether to infer bonds from proximity and remove hydrogens.
3. Run the converter and check the reported SMILES.
4. Download the SDF and verify its chemistry.

Worked example

Input .pdb:

COMPND    ethanol
HETATM    1  C1  UNL     1      -0.953   0.048   0.042  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.488  -0.322  -0.189  1.00  0.00           C  
HETATM    3  O1  UNL     1       1.277   0.325   0.738  1.00  0.00           O  
HETATM    4  H1  UNL     1      -1.357   0.734  -0.733  1.00  0.00           H  
HETATM    5  H2  UNL     1      -1.593  -0.863   0.022  1.00  0.00           H  
HETATM    6  H3  UNL     1      -1.071   0.596   1.011  1.00  0.00           H  
HETATM    7  H4  UNL     1       0.787  -0.141  -1.236  1.00  0.00           H  
HETATM    8  H5  UNL     1       0.590  -1.426  -0.044  1.00  0.00           H  
HETATM    9  H6  UNL     1       1.832   1.048   0.389  1.00  0.00           H  
CONECT    1    2    4    5    6
CONECT    2    3    7    8
CONECT    3    9
END

Actual .sdf output:

ethanol
     RDKit          3D

  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.9530    0.0480    0.0420 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4880   -0.3220   -0.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2770    0.3250    0.7380 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
M  END
$$$$

The blocks show the complete input and output for one ethanol molecule. Coordinates and chemistry shown here come from this conversion run.

Input

Settings

Results

Downloads are available from Files. Inspect both the structure preview and the chemical content of the downloaded file.

PDB coordinates do not fully define chemistry

PDB is primarily a coordinate format. CONECT records can provide connectivity; proximity bonding lets RDKit infer additional bonds from atom distances. Neither guarantees the intended bond orders, aromaticity or charges for an arbitrary ligand.

Prefer an original SDF or chemically complete SMILES when available. Successful conversion means a molecular file was written, not that perceived chemistry matches the intended ligand. Every result warns about this limitation. Compare the reported SMILES with a chemically complete reference.

By default, explicit hydrogens are removed during PDB reading. Turn Remove hydrogens off to retain input hydrogens. This does not add missing hydrogens, predict protonation or repair coordinates.

Extract a ligand before conversion

Supply the intended small molecule as its own PDB. Complete protein structures containing standard amino acid residues are rejected. Ensure an extracted file contains the intended atoms and connectivity; waters or unrelated molecules can otherwise enter the result.

For docking preparation from known chemistry, use SMILES to PDBQT. With a complete 3D SDF, SDF to PDBQT avoids interpreting chemistry from PDB.

FAQ

Can I convert a complete protein PDB to SDF?

This page handles small molecules. Standard protein residues are rejected rather than presented as a ligand.

Does PDB to SDF recover missing bond orders?

It writes RDKit's perceived chemistry. Missing bond-order or charge information cannot be guaranteed without a complete chemical reference.

Why are there fewer atoms in the SDF?

With Remove hydrogens on, explicit hydrogens are removed during reading. Heavy atoms remain in the parsed structure.