SDF to PDB Converter

How to convert SDF to PDB

To convert SDF to PDB, read the molecule with Open Babel or a structure viewer and write it out in PDB format: each atom becomes a HETATM line with its coordinates, and each bond becomes a CONECT record. You can do it online with this converter, with the obabel command, or by saving the file from PyMOL or ChimeraX. Check first that the SDF has 3D coordinates, because a 2D SDF gives a flat PDB.

Online with the SDF to PDB converter

The converter runs Open Babel in your browser, so the file is never uploaded to a server.

1. Upload an .sdf, .sd, or .mol file, or switch the input to text and paste its contents.
2. For a file with several molecules, choose a layout under Multiple molecules.
3. If the SDF is 2D, turn on Generate 3D coordinates, and turn on Add hydrogens if the file stores heavy atoms only.
4. Download the .pdb file for viewers, docking, or alignment.

On the command line with Open Babel

With Open Babel installed, one command converts the file, and the input and output formats come from the extensions:

obabel input.sdf -O output.pdb

A multi-molecule SDF goes into one PDB file by default. Add -m to write one numbered file per molecule (ligand1.pdb, ligand2.pdb, and so on), and add -h --gen3d to give a 2D SDF hydrogens and 3D coordinates:

obabel library.sdf -O ligand.pdb -m
obabel input.sdf -O output.pdb -h --gen3d

In PyMOL or ChimeraX

In PyMOL, open the SDF with File, then Open, and export it with File, then Export Molecule, choosing PDB as the format. The command line equivalent is load input.sdf followed by save output.pdb. PyMOL loads each molecule of a multi-molecule SDF as a separate state and saves only the current one unless you add state=0. In ChimeraX, run open input.sdf and then save output.pdb.

Sample input and output

A small molecule like formaldehyde converts as follows with this converter. Input:

Formaldehyde
  ProteinIQ

  4  3  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5000    0.9000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5000   -0.9000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
M  END
$$$$

Output with default settings:

HEADER    SMALL MOLECULE                          19-AUG-26   CONV
TITLE     CONVERTED FROM SDF FORMAT
COMPND    MOL_ID: 1; MOLECULE: Formaldehyde;
SOURCE    MOL_ID: 1; SYNTHETIC: YES;
KEYWDS    CHEMICAL COMPOUND
HETATM    1  C   UNL A   1       0.000   0.000   0.000  1.00  0.00           C
HETATM    2  O   UNL A   1       1.200   0.000   0.000  1.00  0.00           O
HETATM    3  H   UNL A   1      -0.500   0.900   0.000  1.00  0.00           H
HETATM    4  H   UNL A   1      -0.500  -0.900   0.000  1.00  0.00           H
CONECT    1    2    2    3    4
CONECT    2    1    1
CONECT    3    1
CONECT    4    1
END

Open Babel preserves the molecule's atom order, geometry, elements, connectivity, and formal charges that PDB can represent. It assigns PDB atom names and may repeat a bonded atom serial in CONECT to represent a multiple bond. ProteinIQ remaps those source records only when needed for the selected model, chain, residue, record-type, or centering settings.

A file holding several molecules keeps every entry. With the default Separate MODEL records mode, each compound lands in its own MODEL block while atom serials and CONECT records stay continuous:

MODEL        1
HETATM    1  C   UNL A   1       0.000   0.000   0.000  1.00  0.00           C
HETATM    2  O   UNL A   1       1.200   0.000   0.000  1.00  0.00           O
HETATM    3  H   UNL A   1      -0.500   0.900   0.000  1.00  0.00           H
HETATM    4  H   UNL A   1      -0.500  -0.900   0.000  1.00  0.00           H
ENDMDL
MODEL        2
HETATM    5  C   UNL A   1       0.000   0.000   0.000  1.00  0.00           C
HETATM    6  O   UNL A   1       1.200   0.000   0.000  1.00  0.00           O
HETATM    7  H   UNL A   1      -0.500   0.900   0.000  1.00  0.00           H
HETATM    8  H   UNL A   1      -0.500  -0.900   0.000  1.00  0.00           H
ENDMDL
CONECT    1    2    2    3    4
CONECT    2    1    1
CONECT    3    1
CONECT    4    1
CONECT    5    6    6    7    8
CONECT    6    5    5
CONECT    7    5
CONECT    8    5
END

Input

Paste content directly or upload a file up to 50 MB. Both V2000 (fixed-width columns) and V3000 (keyword based) molblocks are detected automatically, so no version flag is needed.

Settings

Add hydrogens and Generate 3D coordinates process each molecule in the browser and are capped at 200 molecules per file. Plain conversion has no such limit.

Results

Both files are named after the input file (an uploaded aspirin.sdf produces aspirin.pdb and aspirin-conversion-log.txt) and appear in the Files tab to copy or download. Warnings, for example a V3000 stereochemistry notice or the already-3D notice, also show above the output.

What are SDF and PDB

SDF (Structure-Data File), developed by MDL, stores small-molecule atoms, explicit bonds with bond orders, and tagged data fields. It is the standard exchange format for chemical libraries and the output of most cheminformatics toolkits.

PDB (Protein Data Bank) is a fixed-width coordinate format that most structure viewers and docking tools read. It records atom positions and connectivity through CONECT lines, but bond-order handling is not portable: Open Babel may repeat a target serial for a multiple bond, while many consumers treat every CONECT entry as plain connectivity. Converting SDF to PDB preserves geometry and connectivity but cannot reliably carry SDF bond-order and stereo semantics into every PDB consumer.

Which converter should I use

Once a ligand is in PDB, it can be docked into a receptor with AutoDock Vina.

FAQ

How do I convert SDF to PDB in Open Babel?

Run obabel input.sdf -O output.pdb. Open Babel reads the format from each file extension. Add -m to split a multi-molecule SDF into one PDB per molecule, or -h --gen3d for a 2D SDF that needs hydrogens and 3D coordinates.

Why is my converted PDB flat?

The SDF stored 2D drawing coordinates, so every z value is zero and the PDB copies them. Turn on Generate 3D coordinates, or add --gen3d to the obabel command, to build a 3D conformer.

Can I convert SDF to PDB in PyMOL?

Yes. Load the SDF, then use File, then Export Molecule, and choose PDB, or type save output.pdb. For a file with several molecules, save output.pdb, state=0 writes every one as a separate MODEL.

Does SDF to PDB keep bond orders?

Not reliably. Open Babel can encode a multiple bond by repeating a target atom in CONECT, but many PDB readers ignore that multiplicity. Keep the SDF if a downstream tool needs authoritative bond orders or stereochemistry.

Why are hydrogens missing from my PDB?

The converter writes exactly the atoms in the input. If the SDF stored only heavy atoms, the PDB has only heavy atoms. Turn on Add hydrogens to add explicit hydrogens with Open Babel before conversion.

Can it convert a 2D SDF into a 3D structure?

Yes. Enable Generate 3D coordinates to build coordinates with Open Babel. For a structure that is already 3D, leave it off, since regenerating discards the original conformation.

How are multiple molecules in one SDF handled?

All entries are kept. Separate MODEL records wraps each in a MODEL block, Different chain IDs assigns chains A, B, C, and Concatenate in same chain keeps one chain with incrementing residue numbers. CONECT numbering stays correct in every mode.

What residue name should I use for docking?

UNL is a safe default for an unknown ligand. Many docking and preparation pipelines expect a three-letter code, and LIG is a common choice when a tool keys on a specific residue name.