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
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 (PAINS)
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

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