SDF to InChI Converter
In short: Convert SDF or MOL blocks into standard InChI strings for indexing and search. It is free, works in your web browser and needs no download.
Paste an SDF or MOL block and convert it into a standard InChI string.
Input and output formats
| Input: SDF | Output: InChI | |
|---|---|---|
| Full name | SDF (Structure Data File) | InChI (IUPAC International Chemical Identifier) |
| What it holds | One or more MOL records, each with optional data fields, split by $$$$. | A layered text identifier built from the structure. The standard InChI is the same in every program. |
| File or form | .sdf | Text starting with InChI=1S/ |
File Format Explained
SDF stores molecule records with MOL-style atom and bond blocks plus optional property fields. It is common for compound libraries and screening datasets.
InChI is a standardized IUPAC identifier that represents a molecule in layered text form. Converting SDF to InChI helps create stable identifiers for search, indexing, and deduplication.
If an SDF contains multiple records, convert and verify records carefully. Structure salts, mixtures, stereochemistry, and missing hydrogens can affect the resulting InChI.
About SDF files
An SDF (structure-data file) is essentially many MOL records joined together. Each record is followed by optional data fields such as > <NAME> or > <CAS> and ends with a line containing $$$$. Compound libraries, PubChem downloads, and supplier catalogues commonly use SDF because one file can hold thousands of molecules with their properties.
Why generate InChI
Standard InChI gives every structure a canonical identifier, independent of atom order and drawing. That is useful for merging libraries, removing duplicates, and matching compounds against public databases.
How to use it
- Open the .sdf file in a plain-text editor.
- Copy a record (from its header through
$$$$) and paste it in. - Convert and copy the InChI, or shorten it with InChI to InChIKey.
Troubleshooting
- Records with unusual elements, query atoms, or R-groups may not produce a standard InChI.
- Large files are easier to handle a few records at a time.
- Keep the original spacing; SDF connection tables are column-based.
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