View SDF files in your browser
Many molecules in one file, each with its data, as PubChem, ChEMBL and screening libraries hand them out. Open an SDF right here in 3D. Nothing leaves your device.
Or drop it anywhere on this page
What you'll see
Your molecule opens in 3D, a protein's chains as a cartoon and a small molecule's atoms as balls and sticks, with its parts beside it and what you pick on the other side.
- Turn, zoom and move it • Double click to center on a point
- Cartoon, balls and sticks or spacefill • By element, chain or residue
- Inspect an atom • Its residue, chain, charge and B-factor
- Export • PNG, GLB, USDZ, STL and OBJ
About SDF
An SDF is the molfile's way of holding many molecules: MDL Information Systems made it for its chemical databases, and PubChem, ChEMBL, ZINC and drug makers' screening libraries share thousands or millions of molecules in one. Docking and conformer apps write their results in it too.
Each record is a molfile, its atoms and bonds, then data fields like > <PUBCHEM_IUPAC_NAME> with their values, and it ends with $$$$.
Filepeek reads it in your browser and puts each molecule on a page of its own, up to the first 200, in balls and sticks or spacefill. Inspect lists a molecule's data fields, or an atom's element and bonds once you click it, and Export saves the view as PNG or the molecule as GLB, USDZ, STL or OBJ. A 2D SDF, its molecules saved flat as drawings, opens as their structures instead, one at a time with its fields under it.
Structure-data file
.sdf • .sd
Format
- MIME type
- chemical/x-mdl-sdfile
- Made by
- MDL Information Systems
Inside the file
- Holds
- Molecules, one or millions
- Each
- A molfile, then its data fields
- Ends with
- $$$$
- Markup
- Plain text
Opens in every browser
Filepeek opens SDF files in 3D in Chrome, Edge, Firefox and Safari. On their own, browsers download them or show them as text.
- YouChromeOpens through Filepeek
- YouEdgeOpens through Filepeek
- YouFirefoxOpens through Filepeek
- YouSafariOpens through Filepeek
Apps that open SDF
- WindowsNo app built in opens it • DataWarrior and Avogadro read it
- MacNo app built in opens it • DataWarrior and Avogadro read it
- iPhone and iPadNo app built in opens it • Save it here as USDZ to see it in your room
- AndroidNo app built in opens it • Save it here as GLB for 3D apps
Questions
How do I see the other molecules?
The picker at the top steps through them, each by its name. A file of more than 200 shows the first 200, and Show details says how many it holds.
Where are a molecule's data fields?
In 3D, pick the molecule in the Scene panel, and Inspect lists its fields, like its name, formula, weight or a docking score, as the file gives them. A 2D SDF lists them under its drawing.
Why does PubChem's SDF open as drawings?
PubChem hands out each compound as a 2D drawing or a 3D conformer. The 2D SDF has every atom at a depth of zero, so Filepeek draws each molecule as a structure, with its fields under it. The 3D conformer's SDF opens in 3D.
Is every .sdf file a molecule?
No. SQL Server Compact's databases are .sdf files too. Filepeek tells them apart by what's inside, and shows what a database is.
Can I save it for 3D printing?
Yes. Choose Export, then Save as STL or OBJ for the style on show, or GLB for 3D apps and USDZ for an iPhone or iPad.