SDF to PDB converter

Convert your SDF molecular structure files to PDB format. Upload an SDF file or paste the structure data below.

Input (SDF format)

SDF

Click to upload or drag and drop

SDF file (.sdf, .mol, .sd)

Max size: 50MB

Advanced conversion options

3-letter code for the residue (e.g., UNL for unknown ligand, LIG for ligand)

Output (PDB format)

PDB

What's the difference between SDF and PDB formats?

SDF (Structure Data Format) files contain molecular structure data including atoms, bonds, connectivity, and 3D coordinates primarily for small molecules and ligands.

Key features of the SDF format:

  • Molecule title and comment lines at the top
  • Counts line specifying number of atoms and bonds
  • Atom block with Cartesian coordinates and element symbols
  • Bond block defining connectivity between atoms
  • Property block (after M END) for additional molecular data
  • Designed for small molecule databases and chemical informatics
Methanol
  Generated by Example
Example molecule for documentation
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.7480    0.0150    0.0240 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6670    0.0150    0.0240 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1420   -0.5050   -0.8610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1420   -0.5050    0.9090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1420    1.0350    0.0240 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9620    0.5350    0.7890 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  2  6  1  0  0  0  0
M  END
> <MOLECULAR_WEIGHT>
32.04

> <FORMULA>
CH4O

$$$$

PDB (Protein Data Bank) files store atomic coordinates for proteins, nucleic acids, and other macromolecules, often including experimental metadata and biological context.

Key features of the PDB format:

  • Fixed-width columns with specific positioning
  • ATOM records contain chain ID, residue name, and atom serial numbers
  • CONECT records explicitly define atomic bonds
  • Header information includes experimental metadata
  • Primarily designed for macromolecular structures
HEADER    SMALL MOLECULE                          15-JUN-25   DEMO
TITLE     EXAMPLE MOLECULE - METHANOL
ATOM      1  C   UNL A   1      -0.748   0.015   0.024  1.00 20.00           C
ATOM      2  O   UNL A   1       0.667   0.015   0.024  1.00 20.00           O
ATOM      3  H   UNL A   1      -1.142  -0.505  -0.861  1.00 20.00           H
ATOM      4  H   UNL A   1      -1.142  -0.505   0.909  1.00 20.00           H
ATOM      5  H   UNL A   1      -1.142   1.035   0.024  1.00 20.00           H
ATOM      6  H   UNL A   1       0.962   0.535   0.789  1.00 20.00           H
CONECT    1    2    3    4    5
CONECT    2    1    6
END

The conversion from SDF to PDB essentially reformats the coordinate and connectivity data while adding PDB-specific metadata like chain identifiers and residue names.

Common use cases for converting SDF to PDB include:

  • Preparing ligands for molecular docking simulations
  • Visualizing small molecules in protein structure viewers
  • Integrating compound libraries with protein analysis workflows
  • Converting drug databases for structure-based drug design

Other SDF to PDB conversion methods

The ProteinIQ SDF to PDB converter is ideal for quick conversions without installing additional software, especially useful for researchers who need occasional format conversion with customizable output options.

Using OpenBabel (Command Line)

OpenBabel is a popular open-source chemical toolbox for format conversion:

# Basic SDF to PDB conversion
obabel input.sdf -O output.pdb

# Convert with 3D coordinate generation
obabel input.sdf -O output.pdb --gen3d

# Batch convert multiple SDF files
obabel *.sdf -O combined.pdb

Using PyMOL

PyMOL provides both GUI and command-line options for conversion:

# PyMOL command line
load input.sdf
save output.pdb

# Or using PyMOL Python API
import pymol
pymol.cmd.load("input.sdf")
pymol.cmd.save("output.pdb")

Using RDKit (Python)

For programmatic conversion with additional processing options:

from rdkit import Chem
from rdkit.Chem import AllChem

# Read SDF file
supplier = Chem.SDMolSupplier('input.sdf')
writer = Chem.PDBWriter('output.pdb')

for mol in supplier:
    if mol is not None:
        # Add hydrogens and generate 3D coordinates if needed
        mol = Chem.AddHs(mol)
        AllChem.EmbedMolecule(mol)
        writer.write(mol)

writer.close()

Using Discovery Studio

Discovery Studio offers a GUI-based approach:

1. File → Import → Import Molecules
2. Select your SDF file
3. Right-click on the loaded molecule
4. Export → Export Molecule
5. Choose PDB format and save