SDF to PDB Converter
Convert SDF or MOL structures to PDB with connectivity records, headers, and chain assignments.
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What is SDF to PDB conversion?
SDF (Structure-Data File) and PDB (Protein Data Bank) are two widely used molecular file formats in computational chemistry and structural biology. SDF files, developed by MDL (now Biovia), store 2D or 3D coordinates of small molecules along with atom connectivity and associated data properties. PDB files, the legacy format of the Protein Data Bank, describe atomic coordinates of macromolecules and ligands in a fixed-width text format readable by most molecular visualization software.
Converting SDF to PDB is commonly needed when preparing ligands for molecular docking, visualizing compounds in protein structure viewers, or integrating small molecule data into structural biology workflows.
How to convert SDF to PDB
The conversion process transforms the SDF connection table into PDB-compliant records:
- Parse the SDF structure block: The converter reads the molecule header (name, source, comments), counts line (atom and bond counts), atom block (3D coordinates and element symbols), and bond block (connectivity information). Both V2000 (fixed-width columns) and V3000 (keyword-based) formats are supported.
- Generate HETATM records: Each atom from the SDF becomes a HETATM line in PDB format. HETATM (heteroatom) records are standard for small molecules and ligands, distinguishing them from protein backbone atoms (ATOM records). The converter assigns atom serial numbers, formats coordinates to 8.3 decimal precision, and maps element symbols to the correct PDB columns.
- Assign chain and residue identifiers: Unlike proteins with natural chain divisions, small molecules need artificial identifiers. The converter assigns a chain ID (typically A) and residue name (commonly UNL for "unknown ligand" or LIG) to group atoms as a single residue.
- Build CONECT records: SDF files explicitly store bond information, which PDB represents through CONECT records listing which atoms connect to which. Each atom's bonded neighbors are listed, with multiple CONECT lines for atoms with more than four connections.
- Add header information: Optional HEADER, TITLE, COMPND, and other records provide metadata about the structure's origin and contents.
For multi-molecule SDF files, each compound can become a separate MODEL (like NMR ensembles), receive distinct chain IDs, or be concatenated into one chain with incrementing residue numbers.
How to use SDF to PDB Converter online
ProteinIQ converts SDF files to PDB format instantly in the browser with no software installation.
Input
| Format | Description |
|---|---|
.sdf, .sd | Structure-Data File containing one or more molecules |
.mol | MDL Molfile (single molecule, same internal format as SDF) |
Paste molecular data directly or upload files up to 50 MB. Both V2000 and V3000 format versions are automatically detected.
Settings
| Setting | Description |
|---|---|
Include PDB header | Add HEADER, TITLE, COMPND records with molecule name and conversion date. Default: on. |
Include CONECT records | Generate connectivity records from SDF bond information. Required for correct bond display in most viewers. Default: on. |
Chain ID | Single letter (A-Z) identifying the chain. Default: A. |
Residue name | Three-letter code for the ligand residue. Common choices: UNL (unknown ligand), LIG, MOL. Default: UNL. |
Atom record type | Auto uses HETATM for small molecules (recommended). HETATM or ATOM forces a specific record type. |
Multiple molecules | How to handle multi-molecule SDF files. Separate MODEL records: each molecule in its own MODEL/ENDMDL block. Different chain IDs: molecules get sequential chains A, B, C... Concatenate in same chain: all molecules share one chain. |
Center coordinates | Translate the molecule so its centroid sits at the origin (0, 0, 0). Useful for visualization or combining with other structures. |
Output
The converter produces a PDB-formatted text file containing:
- Header records (if enabled): HEADER, TITLE, COMPND, SOURCE, KEYWDS
- Coordinate records: HETATM lines with atom serial, name, residue, chain, coordinates, occupancy, temperature factor, and element
- Connectivity: CONECT records mapping bonded atom pairs
- Termination: END record
The output can be copied to clipboard or downloaded as a .pdb file.
Limitations
- Stereochemistry in V3000: Bond stereo information from V3000 format SDF files is not preserved in the PDB output. V2000 stereo flags are also not explicitly converted, though 3D coordinates implicitly encode chirality.
- Hydrogen atoms: The converter does not add missing hydrogens. If the input SDF lacks explicit hydrogens, the output PDB will too.
- Properties lost: SDF data items (key-value pairs after the molecule block) are not converted to PDB REMARK records.
- Chain ID limit: When using different chain IDs for multiple molecules, only 26 molecules (A-Z) can be distinguished before chain IDs wrap.