MOL to InChIKey Converter
In short: Convert MOL or SDF structure blocks into standard InChIKey identifiers. It is free, works in your web browser and needs no download.
Paste a MOL or SDF block and convert it into a standard InChIKey value.
Input and output formats
| Input: MOL file | Output: InChIKey | |
|---|---|---|
| Full name | MOL file (MDL Molfile) | InChIKey |
| What it holds | An atom list with 2D or 3D coordinates and a bond table for one molecule. | 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 | .mol | Text like XXXXXXXXXXXXXX-YYYYYYYYYY-Z |
File Format Explained
MOL is a structure file with atom and bond blocks. It can preserve drawn coordinates and editable molecular topology.
InChIKey is a fixed-length key generated from an InChI. It is designed for fast lookup, database matching, and duplicate detection across chemical collections.
Use MOL when you need an editable structure file. Use InChIKey when you need a compact identifier for search or matching.
When an InChIKey is the right output
If you have a structure as a MOL file and want to find it online, register it in a spreadsheet, or check whether two files describe the same compound, an InChIKey is the most practical identifier. It is a fixed-length string, so it fits neatly in a database column and works as a search-engine query.
How to use it
- Export or open your structure as a .mol file.
- Copy the full text, from the first header line to
M END. - Paste and convert, then copy the 27-character key.
Example uses
- Duplicate checking: generate keys for a folder of MOL files and sort them; identical keys mean identical structures, even if atoms were numbered differently.
- Literature search: search the key in a search engine to find database entries and papers mentioning the compound.
- Stereo comparison: compare the first block to see whether two stereoisomers share a skeleton.
Need the full identifier as well? Use MOL to InChI. Have SMILES instead? Use SMILES to InChIKey.
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