SDF to PDB Converter

Molecular File Converter

Convert between chemical file formats with our web-based tool powered by Open Babel

Convert Molecular Files

Input Format

Output Format

Drag & Drop Your File

Supports PDB, SDF, MOL2 and many more

Browse Files

Conversion Progress 0%

Was this tool helpful?

Thanks for your feedback 😍

Used this tool in your research?

Cite it instantly and export to BibTeX, EndNote, RIS, and more.

Generate Citation

Our SDF to PDB Converter is a reliable web-based utility designed to streamline your computational chemistry workflow. It efficiently converts Structure-Data Files (SDFs), which can contain multiple molecules and extensive data, to the widely used Protein Data Bank (PDB) format. This conversion isolates a single molecular structure and formats its atomic coordinates, making it perfectly suited for tasks like molecular visualization and structural analysis or as an input for further simulation setup.

How to use (step-by-step)

Follow these simple steps to convert your file in seconds.

Choose Your Formats: Use the “Input Format” and “Output Format” dropdown menus to select the conversion you need. Ensure SDF (Structure-Data File) is selected as the input and PDB (Protein Data Bank format) as the output.
Upload Your File: Click Upload File or drag and drop your file directly into the designated area. You can also paste the file’s content using the Paste Content option.
Start the Conversion: Press the Convert File button to begin the process. The tool will process your file instantly.
Download Your File: Once the conversion is complete, a download link for your new PDB file will appear. Click it to save the file to your device.

Tip: If you see an error during conversion, check the Troubleshooting Guide section below—common causes and fixes are listed.

Input, Output, and Key Changes

Understanding the transformation from SDF to PDB is essential for preparing your structures for analysis. Here’s a breakdown of the formats and the changes that occur during conversion.

Sample Input (SDF Format)

The SDF format is a versatile file type used in cheminformatics to store information for one or more molecules. Each molecule’s data is contained in a “molfile” block, which includes atomic coordinates, bond information, and can be followed by associated data fields. It is ideal for storing chemical libraries or conformer ensembles.

Example of an SDF file:

Molecule_Name
  SciCodons 09142514053D

 10 10  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2887    0.7887    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
$$$$

Sample Output (PDB Format)

The PDB format is the standard for representing the 3D structures of biological macromolecules like proteins and nucleic acids. It has a rigid, column-based structure that primarily stores atomic coordinate data for a single molecular model. It is widely supported by visualization and simulation software.

Example of the corresponding PDB output:

ATOM      1  C   MOL A   1       0.000   0.000   0.000  1.00  0.00           C

Key Changes in the Conversion Process

The conversion from SDF to PDB involves simplifying the input file to meet the PDB format’s structural requirements:

Structure Selection: An SDF file can contain multiple molecules. This converter will only process the first molecule found in the file and ignore all subsequent entries. This is crucial for creating a single-structure file required by most modeling software.
Removal of Associated Data: SDF files often contain extra data fields (e.g., calculated properties, database IDs) stored after the connection table. The PDB format does not support this data, so it is stripped during the conversion, leaving only the essential structural information.
Reformatting of Atomic Information: The tool reads the atomic coordinates and element types from the SDF and rewrites them into the strict, fixed-column format of a PDB file. This includes assigning generic residue names (MOL) and chain identifiers (A) if they are not specified.

Compatible Software

The generated PDB files are ready to be used with the following leading molecular modeling and visualization software:

PyMOL
UCSF Chimera/ChimeraX
VMD (Visual Molecular Dynamics)
GROMACS
AMBER

Troubleshooting Guide

Encountering an error can be frustrating, but most issues are easy to fix. Here are the most common problems you might face and how to resolve them.

General Tool Errors

Error: “File size exceeds the limit”
- Why it happens: Your uploaded file is larger than the maximum allowed size. Our server has this limit to ensure quick processing for all users.
- How to fix: If your SDF file contains many molecules, use a tool to split it into smaller files and upload them individually. For processing larger files, please contact us for custom solutions.
Error: “Processing timed out”
- Why it happens: The conversion for your molecule is taking too long, which can happen with extremely large or complex structures.
- How to fix: Ensure your file is not excessively large. If the issue persists because your structure is inherently complex, please contact us to discuss options for handling larger computations.
Error: “CAPTCHA validation failed”
- Why it happens: Our system uses a CAPTCHA to prevent automated bots. This error occurs if the CAPTCHA was not solved correctly or timed out.
- How to fix: Simply reload the page and try the CAPTCHA again.

Conversion-Specific Errors

These errors typically relate to the structural data within your SDF file.

Error: “Invalid SDF format or parsing error”
- Why it happens: The input file does not adhere to the standard SDF structure. This could be due to missing $$$$ delimiters between molecules, an incorrect atom/bond count line, or other formatting mistakes.
- How to fix: Carefully inspect your SDF file in a text editor to ensure it follows the correct format specifications. Validate that each molecular entry ends with the $$$$ delimiter on its own line.
Error: “3D coordinates not found”
- Why it happens: The source SDF file contains only 2D coordinates for the molecule. The PDB format is inherently 3D, and the conversion requires 3D structural information.
- How to fix: Before uploading, you must convert your 2D structure to a 3D structure using a chemistry software package that can generate 3D coordinates from 2D representations.
Warning: “Multiple molecules detected”
- Why it happens: Your SDF file contains more than one molecule. This tool is designed to convert only the first molecule in the file to the PDB format.
- How to fix: This is not a critical error, but a notification. If you intended to convert a different molecule from the file, you must first split your multi-molecule SDF file and then upload the specific SDF containing only the molecule of interest.

If your problem isn’t listed here, we want to know about it! Please help us improve the tool by reporting the issue.

Support Our Work

We are committed to keeping our scientific tools free and accessible for everyone. If this tool has been helpful in your work, please consider supporting our mission with a donation. Your support directly helps us cover server costs and fund the development of new, powerful tools for the scientific community.

FAQ

How does this converter work?

The tool parses the input SDF file, reads the atom and bond information for the first molecule, extracts the 3D atomic coordinates, and reformats this data into the standard, column-based PDB file format.

Can I perform batch conversions?

No, the free online version of this tool only processes one file at a time and converts only the first molecule within that file. For bulk processing needs, please contact our team to inquire about custom solutions.

What is the maximum file size?

The maximum allowed file size is 25 MB. If you need to process larger files, please get in touch with our support team.

Are my uploaded files stored on the server?

No. Your privacy and data security are our top priorities. Files are uploaded for the sole purpose of conversion and are permanently deleted from our servers immediately after the process is complete.

What’s the next step after converting my file?

After downloading your PDB file, you can use it directly in molecular visualization programs like PyMOL or UCSF Chimera, or use it as an input for molecular dynamics simulations or docking studies.

How should I cite or mention this tool?

Thank you for asking! If this tool helps your research or you feature it on your website, the best way to give credit is to link back to this page. This support helps us keep our tools free and available to the scientific community. For those who wish to support us further, donations are also greatly appreciated.

References & Suggested Reading

This tool was developed in line with established principles in computational chemistry for accurate, reliable results. The resources listed below are the foundational research and key papers that define these standards, and we highly recommend them for a deeper understanding of the scientific principles.

Dalby, A., Nourse, J. G., Hounshell, W. D., Gushurst, A. K., Grier, D. L., Leland, B. A., & Laufer, J. (1992). Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited. Journal of Chemical Information and Computer Sciences, 32(3), 244–255. https://doi.org/10.1021/ci00007a012
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
Schrödinger, LLC. (2015). The PyMOL Molecular Graphics System, Version 1.8.

Meet the Authors

Mahdi Morshedi Yekta

Founder & Bioinformatics Developer

Mahdi is the founder of ScienceCodons and a Medical Biotechnologist with a deep passion for computational biology. Holding an M.Sc. in Medical Biotechnology, he specializes in transforming complex biological algorithms into accessible, high-performance web tools, bridging the gap between laboratory sciences and software engineering.

Fatemeh Faryadras

Medical Biotechnologist & Researcher

Fatemeh is a Medical Biotechnologist and researcher. With extensive expertise in genetic engineering, molecular cloning, and cancer biology, she combines her rigorous laboratory background with intuitive design principles to create reliable, user-centered scientific calculators and tools.

5/5 (4 Reviews)