Reactivity axis
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Here we describe the "clean" axis in the exported subsets of ZINC15.
Traditionally, ZINC standard subsets included: A, B, C, D, E.
ZINC "clean" subsets were just A, B, C, D.
The Clean Axis
| Class | Nickname | Description | How computed |
|---|---|---|---|
| A | Anodyne | No flags of any kind set | no pattern matches whatsoever |
| B | Unnecessarily complex | The worst feature is the molecules are over decorated e.g. too many chlorides | complex, requires representative in A. This is really reserved for future use, and gives us the opportunity to split "super clean" into A (representatives) and B (versions of A) |
| C | Chromophore | Worst problem is a chromophore that could interfere with some asays | extended conjugated system, pattern_type = 5 |
| D | Any PAINS | Any pains pattern not covered in E,F,G,H | pattern_type= 8 (call it mild PAINS, or pains we don't necessarly believe in because there is no clear MOA) |
| E | mildly electrophilic or nucleophilic | aldhydes, thiols, michael acceptors, epoxides | pattern_type in (1,2) |
| F | strongly electrophilic or nucleophilic | alpha halo ketones, alkyl halides. Note includes cancer drugs. | pattern_type in (3,4) |
| G | unstable in buffer | typically reagents, but could be used for covalent binding. e.g. boronic acids | pattern_type = 10 |
| H | nonsensical | idea from the PAINS papers | pattern_type = 14. This is a container, but generally we are not expecting to find any of these in ZINC. |
other concepts mentioned, must be fit in: chelation, redox, covalent, amphiphilicity
poor derivatizability, optimizability
we never build protomers of H, G, F.
we need to classify pains by assumed mechanism
397 pains never hit any compound in zinc