.SD file extension

To open .SD files on Windows, install a tool that supports MDL SD/SDF, such as Open Babel (the command-line tool is often named "obabel").

To open a .sd file, use a chemistry/cheminformatics program that supports MDL SD/SDF (for example, Open Babel). If you don’t have a compatible app, the file is plain text, so you can also inspect it with a text editor, but that won’t render the chemical structure visually.

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Last updated: June 11, 2026 · Reviewed by Julian Stricker

What “reviewed” means on this page

Format fit: whether the “what is this file?” description matches common real-world use of the extension, including category, typical MIME types, and aliases.
Opening paths: whether Windows / macOS / Linux steps read plausibly for current OS dialogs and default apps; we remove fantasy menus and unsafe shortcuts.
Security framing: whether risk notes match the extension class (for example executables vs plain data) and whether affiliate wording does not contradict the security section.
Sources and further reading: whether external links point to vendors, standards bodies, or other primary references where possible; we avoid inventing details we cannot ground.
Limits: this is clarity and safety-messaging QA, not a guarantee that every statement is exhaustive or that every binary you download is harmless.

Full methodology in the Imprint — The Imprint also states where AI is used and what that does—and does not—replace.

Open on your device

Choose your operating system for a dedicated step-by-step opening guide.

How to open .SD files

Use these platform-specific instructions to open .SD files safely.

Windows

Install a tool that supports MDL SD/SDF, such as Open Babel (the command-line tool is often named "obabel").
Open/convert the file: use Open Babel to read .sd and (optionally) convert it to another format (e.g., SDF, MOL, SMILES) if needed.
If you only need to inspect content, open the .sd file in a plain text editor to view records and property tags.

Full Windows guide

Mac

Install a tool that supports MDL SD/SDF, such as Open Babel (command-line "obabel").
Use Open Babel to open/convert the .sd file into another format your workflow expects (e.g., .sdf, .mol, .smi).
For quick troubleshooting, open it in a text editor to confirm it looks like an SDfile (structure block plus tagged data fields).

Full Mac guide

Linux

Install a tool that supports MDL SD/SDF, such as Open Babel (command-line "obabel").
Open or convert the file with Open Babel; Linux desktops may also identify it via the shared MIME database depending on your environment.
If you just need to validate the contents, view it as text to check record delimiters and property fields.

Full Linux guide

iOS

iOS typically won’t provide a native preview for SDfile chemistry data; transfer the .sd file to a desktop cheminformatics tool (for example, Open Babel) to view/convert it.

Full iOS guide

Android

Android typically won’t provide a native viewer for SDfile chemistry data; transfer the .sd file to a desktop cheminformatics tool (for example, Open Babel) to view/convert it.

Full Android guide

Security notes

An SDfile is data (text) and normally not executable, but it can still be risky if opened in vulnerable chemistry parsers; only open SDfiles from trusted sources in up-to-date tools.
Be cautious with very large SDfiles (many records or huge property blocks): they can cause high memory/CPU usage or application crashes when imported.
If you receive an .sd file that doesn’t look like chemistry data when opened as text, treat it as suspicious or misnamed and verify the source before proceeding.

If you did not expect this file

This extension is usually plain data, text, or structured content—not a program by itself. The practical risk is social engineering (a scam attachment or misleading filename). For trusted senders you rarely need heavy-handed antivirus wording; use these tools when you want an extra check on unexpected downloads.

Avast

Avast offers free and premium antivirus software that protects against viruses, malware, ransomware, and phishing. Scan files before opening them to ensure safety.

Norton

Norton 360 delivers comprehensive antivirus protection, VPN, and identity theft monitoring. Scan files for threats before opening to keep your device secure.

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Can't open this file?

These are the most common causes and fixes when .SD files fail to open.

Common reasons

The .SD file opens as unreadable text or in the wrong app
Import fails or only some molecules load
File type identification (MIME) is inconsistent across systems

Fix steps

Open it with a cheminformatics tool that supports MDL SD/SDF (for example, Open Babel).
If your workflow expects .sdf, convert the file to .sdf using a proper converter rather than renaming the extension.

OS-specific troubleshooting

What is a .SD file?

.sd (SDfile) is a Structure-Data Format (SDF) chemical table file used to represent one or more molecules along with key–value property data. It is a text format originally associated with MDL formats (MOL/SD/SDF) and is commonly used for exchanging compound libraries and annotations. Many tools treat .sd and .sdf as the same underlying format.

Background

An SDfile (often seen as .sdf, but sometimes .sd) is a standard way to bundle molecular structures with metadata such as identifiers, measured properties, and other annotations. Each record typically contains a structure block (MDL MOL-style) followed by tagged data fields, making it convenient for storing datasets of many compounds in a single file.

This format is widely used in chemistry and bioinformatics workflows, for example when moving compound collections between databases, modeling tools, and screening pipelines. Because it is plain text, it is also easy to generate and parse, and can be inspected with any text editor for troubleshooting.

In practice, users open .sd files with cheminformatics tools that can interpret MDL MOL/SD/SDF. Open Babel specifically documents read/write support for MDL MOL/SD/SDF and recognizes extensions including .sd and .sdf.

Common MIME types: chemical/x-mdl-sdfile

Common .SD issues

The .SD file opens as unreadable text or in the wrong app

An SDfile is plain text, so the OS may default to a text editor instead of a chemistry tool, and a text editor won’t visualize structures.

Open it with a cheminformatics tool that supports MDL SD/SDF (for example, Open Babel).
If your workflow expects .sdf, convert the file to .sdf using a proper converter rather than renaming the extension.

Import fails or only some molecules load

SDfiles can contain multiple records; importers may stop on a malformed record, unexpected tags, or nonstandard variations.

Try reading/converting the file with Open Babel, which supports MDL MOL/SD/SDF and can often handle variations.
Inspect the file as text around the point of failure to look for truncated records or missing separators, then re-download or re-export the dataset.

File type identification (MIME) is inconsistent across systems

MIME type mapping can vary by platform and desktop environment; Linux often relies on the freedesktop shared MIME database and local overrides.

On Linux, update or check your shared-mime-info database and file associations if your desktop misidentifies .sd files.
When sharing files, consider using the more explicit .sdf extension if your collaborators’ tools expect it.

FAQ

Is .sd the same as .sdf?

Often, yes. In chemistry, “SD file” refers to the SDF/SDfile Structure-Data Format, and many tools treat .sd and .sdf as the same format.

How can I tell if my .sd file is an SDfile (SDF) in practice?

Open it in a text editor: SDfiles are plain text and typically contain a MOL-style structure block followed by tagged property fields (common in SDF/SDfile datasets).

Can I convert an .sd file by renaming it to .sdf (or another extension)?

No. Renaming only changes the filename; use a converter such as Open Babel to convert between SD/SDF and other chemical formats.

What MIME type is commonly associated with SDfile/SDF?

A commonly used MIME type for SDF/SDfile is chemical/x-mdl-sdfile, though MIME handling can vary by platform and may not be formally consistent everywhere.

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