SDF to InChIKey Converter
In short: Convert SDF or MOL blocks to standard InChIKey identifiers for database matching. It is free, works in your web browser and needs no download.
Paste an SDF or MOL block and convert it into a standard InChIKey.
Input and output formats
| Input: SDF | Output: InChIKey | |
|---|---|---|
| Full name | SDF (Structure Data File) | InChIKey |
| What it holds | One or more MOL records, each with optional data fields, split by $$$$. | A 27 character hash of the InChI, made for web and database search. It cannot be turned back into a structure without a lookup database. |
| File or form | .sdf | Text like XXXXXXXXXXXXXX-YYYYYYYYYY-Z |
File Format Explained
SDF is a structure-data format that can store atom/bond blocks and compound properties. It is widely used for chemical datasets and screening libraries.
InChIKey is a compact hashed identifier derived from an InChI. It is especially useful for database matching, indexing, and checking whether two records likely describe the same compound.
InChIKey is search-friendly but not fully reversible. Keep the source SDF if you need coordinates, atom blocks, or property fields later.
Using InChIKeys with compound libraries
When you receive a compound library as SDF, an InChIKey for each record gives you a short, searchable fingerprint of the structure. Keys fit neatly in spreadsheets and databases and make it easy to spot the same compound listed under different names or IDs.
How to use it
- Copy one or more SDF records, each ending with
$$$$. - Paste and convert.
- Copy the resulting 27-character keys into your spreadsheet next to the compound IDs.
Practical uses
- Deduplication: sort by InChIKey; identical keys indicate the same structure, including stereochemistry.
- Finding stereoisomers: group by the first 14-character block to collect compounds that share a skeleton but differ in stereo or isotopes.
- Cross-referencing: search keys in public databases to find literature, suppliers, or safety data.
Note: salts and mixtures in SDF records produce keys for the whole record, so a hydrochloride salt and its free base have different keys. Strip counter-ions first if you want to match parent compounds. For the full identifier, use SDF to InChI.
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