Reactivity axis: Difference between revisions

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{| class="wikitable"
{| class="wikitable"
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! Class !! Nickname !! Description || How computed
! Class !! Nickname !! Description || How computed || Examples
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| A ||  Anodyne ||  No flags of any kind set || no pattern matches whatsoever
| A ||  Anodyne ||  No flags of any kind set || pattern_origin_fk is null || example
|-
|-
| 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)
| B || Reserved1 || Future Use || no matches || example
|-
|-
| C || Chromophore || Worst problem is a chromophore that could interfere with some asays || extended conjugated system, pattern_type = 5
| C || PAINS sans mechanism || Worst problem is, PAINS without a clear mechanism matches || pattern_origin_fk =2 || example
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| 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)
| D || Reserved2 || Future Use || no matches || example
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|-
| E || mildly electrophilic or nucleophilic || aldhydes, thiols, michael acceptors, epoxides || pattern_type in (1,2)
| E || mildly reactive || mildly electrophilic or nucleophilic group, including PAINS where these mechanisms have been assigned.  ||  pattern_type_fk in (1,2) || aldhydes, thiols, michael acceptors, epoxides
|-
|-
| F || strongly electrophilic or nucleophilic || alpha halo ketones, alkyl halides.  Note includes cancer drugs. || pattern_type in (3,4)
| F || Reserved3 || Future Use || no matches || example
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| G || unstable in buffer || typically reagents, but could be used for covalent binding. e.g. boronic acids || pattern_type = 10
| G || reactive || electrophile or nucleophile, including PAINS where these mechanisms have been assigned || pattern_type in (3,4) || alpha halo ketones, alkyl halides. Note includes cancer drugs.
|-
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| 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.
| H || Reserved4 || Future use || no matches || example
|-
| I || Unstable || Highly reactive || pattern_origin=7 || typically reagents, but could be used for covalent binding. e.g. boronic acids
|}
|}


Revision as of 17:51, 28 July 2015

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 Examples
A Anodyne No flags of any kind set pattern_origin_fk is null example
B Reserved1 Future Use no matches example
C PAINS sans mechanism Worst problem is, PAINS without a clear mechanism matches pattern_origin_fk =2 example
D Reserved2 Future Use no matches example
E mildly reactive mildly electrophilic or nucleophilic group, including PAINS where these mechanisms have been assigned. pattern_type_fk in (1,2) aldhydes, thiols, michael acceptors, epoxides
F Reserved3 Future Use no matches example
G reactive electrophile or nucleophile, including PAINS where these mechanisms have been assigned pattern_type in (3,4) alpha halo ketones, alkyl halides. Note includes cancer drugs.
H Reserved4 Future use no matches example
I Unstable Highly reactive pattern_origin=7 typically reagents, but could be used for covalent binding. e.g. boronic acids

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

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