SDF to PDB Converter

Convert SDF or MOL structures to PDB with connectivity records, headers, and chain assignments.

Input

SDF file

Include PDB header

Include CONECT records

Chain ID

Residue name

Atom record type

Multiple molecules

Center coordinates

Add hydrogens

Generate 3D coordinates

Output

Configure inputs to begin

Set options on the left, then click “Convert”.

How to convert SDF to PDB

Paste or upload an SDF or MOL file and the converter rewrites every atom and bond into PDB records in the browser. Each atom becomes a HETATM line with its coordinates and element, bonds become CONECT records, and the result downloads as a .pdb file ready for viewers, docking, or alignment. Nothing is uploaded to a server.

A small molecule like formaldehyde converts as follows. Input:

Text

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:

Text

HEADER    SMALL MOLECULE                          20260607   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 20.00           C
HETATM    2  O   UNL A   1       1.200   0.000   0.000  1.00 20.00           O
HETATM    3  H1  UNL A   1      -0.500   0.900   0.000  1.00 20.00           H
HETATM    4  H2  UNL A   1      -0.500  -0.900   0.000  1.00 20.00           H
CONECT    1    2    3    4
CONECT    2    1
CONECT    3    1
CONECT    4    1
END

Atoms keep their input order and serial numbers. Atoms that share an element get a numbered name (H1, H2), and the bond block becomes reciprocal CONECT records so viewers draw the right bonds. Formal charges from the SDF, including modern M CHG lines, are written into the PDB charge columns.

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:

Text

MODEL        1
HETATM    1  C   UNL A   1       0.000   0.000   0.000  1.00 20.00           C
HETATM    2  O   UNL A   1       1.200   0.000   0.000  1.00 20.00           O
HETATM    3  H1  UNL A   1      -0.500   0.900   0.000  1.00 20.00           H
HETATM    4  H2  UNL A   1      -0.500  -0.900   0.000  1.00 20.00           H
ENDMDL
MODEL        2
HETATM    5  C   UNL A   1       0.000   0.000   0.000  1.00 20.00           C
HETATM    6  O   UNL A   1       1.200   0.000   0.000  1.00 20.00           O
HETATM    7  H1  UNL A   1      -0.500   0.900   0.000  1.00 20.00           H
HETATM    8  H2  UNL A   1      -0.500  -0.900   0.000  1.00 20.00           H
ENDMDL
CONECT    1    2    3    4
CONECT    2    1
CONECT    3    1
CONECT    4    1
CONECT    5    6    7    8
CONECT    6    5
CONECT    7    5
CONECT    8    5
END

Input

Format	Description
`.sdf`, `.sd`	Structure-Data File holding one or more molecules.
`.mol`	MDL Molfile, a single molecule in the same atom and bond block as SDF.

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

Setting	Description
`Include PDB header`	Write HEADER, TITLE, COMPND, SOURCE, and KEYWDS lines with the molecule name and conversion date. Default: on.
`Include CONECT records`	Emit CONECT connectivity from the SDF bond block. Most viewers need it to draw bonds for a ligand. Default: on.
`Chain ID`	Single letter (`A` to `Z`) for the chain column. Anything else falls back to `A`. Default: `A`.
`Residue name`	Up to three characters for the residue name column. `UNL` (unknown ligand), `LIG`, and `MOL` are common. Default: `UNL`.
`Atom record type`	`Auto (HETATM for small molecules)` and `HETATM` both write HETATM lines; `ATOM` forces ATOM records instead. Default: `Auto`.
`Multiple molecules`	How a multi-molecule file is laid out. `Separate MODEL records` puts each molecule in its own MODEL/ENDMDL block. `Different chain IDs` gives molecules sequential chains `A`, `B`, `C`, each starting at residue 1. `Concatenate in same chain` keeps one chain and increments the residue number per molecule. Default: `Separate MODEL records`.
`Center coordinates`	Shift each molecule so its centroid sits at the origin (0, 0, 0). Default: off.
`Add hydrogens`	Add missing explicit hydrogens with Open Babel before conversion. Requires a free account, and the Open Babel runtime loads only when this is on, so plain conversions stay instant. Default: off.
`Generate 3D coordinates`	Build 3D coordinates with Open Babel, useful for a 2D-only SDF. It runs after hydrogen addition so new atoms are placed correctly. If the input already has 3D coordinates, the tool warns that regenerating rebuilds the geometry and can change the conformation. Requires a free account, loads on first use only. Default: off.

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

File	Contents
`name.pdb`	The converted structure: optional header lines, HETATM or ATOM coordinate records with occupancy, B-factor, element, and charge columns, CONECT records, and a final END.
`name-conversion-log.txt`	Settings used, molecule, atom, and bond counts, any warnings, and Open Babel output when hydrogen or 3D generation ran.

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, through CONECT lines, connectivity, but it has no concept of bond order: a single and a double bond both appear as a plain CONECT pair. Converting SDF to PDB therefore preserves geometry and connectivity while dropping bond-order and stereo flags, which is why the conversion is common for visualization, for placing a ligand next to a receptor, or for preparing input to tools that only accept PDB.

Which converter should I use

Goal	Tool
Turn a PDB structure back into SDF	PDB to SDF
Read a SMILES string from an SDF	SDF to SMILES
Build a 3D PDB from a SMILES string	SMILES to PDB
Convert among mol2, pdbqt, cif, or inchi with hydrogen and pH control	Open Babel Format Converter

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

FAQ

Does SDF to PDB keep bond orders?

No. PDB has no bond-order field. Single, double, and aromatic bonds all become plain CONECT connectivity. The geometry and which atoms are bonded are preserved; the order is not. Keep the SDF if a downstream tool needs bond orders.

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.

Related tools

Open Babel

Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.

PDB to SDF Converter

Convert Protein Data Bank files to Structure Data Format

SDF to SMILES

Convert SDF ligand files, including multi-record batches, into SMILES strings.

SMILES to PDB

Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.

SMILES to SDF

Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.

InChI to SMILES

Convert InChI strings into SMILES with batch support and downloadable outputs.

MOL to SMILES

Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.

MOL2 to SMILES

Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.

SMILES to InChI

Convert SMILES strings into InChI strings with batch support and downloadable outputs.

SMILES to MOL2

Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.

How to convert SDF to PDB

A small molecule like formaldehyde converts as follows. Input:

Text

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:

Text

HEADER    SMALL MOLECULE                          20260607   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 20.00           C
HETATM    2  O   UNL A   1       1.200   0.000   0.000  1.00 20.00           O
HETATM    3  H1  UNL A   1      -0.500   0.900   0.000  1.00 20.00           H
HETATM    4  H2  UNL A   1      -0.500  -0.900   0.000  1.00 20.00           H
CONECT    1    2    3    4
CONECT    2    1
CONECT    3    1
CONECT    4    1
END

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:

Text

MODEL        1
HETATM    1  C   UNL A   1       0.000   0.000   0.000  1.00 20.00           C
HETATM    2  O   UNL A   1       1.200   0.000   0.000  1.00 20.00           O
HETATM    3  H1  UNL A   1      -0.500   0.900   0.000  1.00 20.00           H
HETATM    4  H2  UNL A   1      -0.500  -0.900   0.000  1.00 20.00           H
ENDMDL
MODEL        2
HETATM    5  C   UNL A   1       0.000   0.000   0.000  1.00 20.00           C
HETATM    6  O   UNL A   1       1.200   0.000   0.000  1.00 20.00           O
HETATM    7  H1  UNL A   1      -0.500   0.900   0.000  1.00 20.00           H
HETATM    8  H2  UNL A   1      -0.500  -0.900   0.000  1.00 20.00           H
ENDMDL
CONECT    1    2    3    4
CONECT    2    1
CONECT    3    1
CONECT    4    1
CONECT    5    6    7    8
CONECT    6    5
CONECT    7    5
CONECT    8    5
END

Input

Format	Description
`.sdf`, `.sd`	Structure-Data File holding one or more molecules.
`.mol`	MDL Molfile, a single molecule in the same atom and bond block as SDF.

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

Setting	Description
`Include PDB header`	Write HEADER, TITLE, COMPND, SOURCE, and KEYWDS lines with the molecule name and conversion date. Default: on.
`Include CONECT records`	Emit CONECT connectivity from the SDF bond block. Most viewers need it to draw bonds for a ligand. Default: on.
`Chain ID`	Single letter (`A` to `Z`) for the chain column. Anything else falls back to `A`. Default: `A`.
`Residue name`	Up to three characters for the residue name column. `UNL` (unknown ligand), `LIG`, and `MOL` are common. Default: `UNL`.
`Atom record type`	`Auto (HETATM for small molecules)` and `HETATM` both write HETATM lines; `ATOM` forces ATOM records instead. Default: `Auto`.
`Multiple molecules`	How a multi-molecule file is laid out. `Separate MODEL records` puts each molecule in its own MODEL/ENDMDL block. `Different chain IDs` gives molecules sequential chains `A`, `B`, `C`, each starting at residue 1. `Concatenate in same chain` keeps one chain and increments the residue number per molecule. Default: `Separate MODEL records`.
`Center coordinates`	Shift each molecule so its centroid sits at the origin (0, 0, 0). Default: off.
`Add hydrogens`	Add missing explicit hydrogens with Open Babel before conversion. Requires a free account, and the Open Babel runtime loads only when this is on, so plain conversions stay instant. Default: off.
`Generate 3D coordinates`	Build 3D coordinates with Open Babel, useful for a 2D-only SDF. It runs after hydrogen addition so new atoms are placed correctly. If the input already has 3D coordinates, the tool warns that regenerating rebuilds the geometry and can change the conformation. Requires a free account, loads on first use only. Default: off.

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

File	Contents
`name.pdb`	The converted structure: optional header lines, HETATM or ATOM coordinate records with occupancy, B-factor, element, and charge columns, CONECT records, and a final END.
`name-conversion-log.txt`	Settings used, molecule, atom, and bond counts, any warnings, and Open Babel output when hydrogen or 3D generation ran.

What are SDF and PDB

Which converter should I use

Goal	Tool
Turn a PDB structure back into SDF	PDB to SDF
Read a SMILES string from an SDF	SDF to SMILES
Build a 3D PDB from a SMILES string	SMILES to PDB
Convert among mol2, pdbqt, cif, or inchi with hydrogen and pH control	Open Babel Format Converter

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

FAQ

Does SDF to PDB keep bond orders?

Why are hydrogens missing from my PDB?

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?

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.