SDF to PDB Converter

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:

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                          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:

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

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, 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

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.