Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Savvas Savvides
Gesendet: Mittwoch, 23. August 2017 21:54
An: [log in to unmask]
Betreff: Re: [ccp4bb] A question about Cys and fluoro benzene ring

it is possible that the sulfhydryl of the cysteine might have reacted with the methyl fluoro benzyl group via nucleophilic aromatic substitution. Fluorine is not the best leaving group among the halides but it would certainly allow this especially if the ligand-protein incubation time was sufficient and if the the pH of the reaction is above 7. This would get the Cys-SH closer to the cysteinyl moiety (S:-). The pKa of the Cys-SH group is just under 8.5 and in your case it might even be lower depending on local structure environment, resulting in an even better nucleophile.

Your electron density indeed suggests that the sulfur from the Cys-SH is covalently bonded to the benzyl ring and this would happen at the carbon that originally carried the fluorine. You will have to remodel your ligand, keeping in mind that the fluorine will no longer be part of your ligand model. The methyl group will of course be retained.

It might also be useful to try to confirm the reactivity of the ligand of interest with the protein (reminiscent of a suicide or covalent inhibitor against cysteine proteases?) via some kind of an orthogonal method (e.g. mass spectrometry). This would even tell you if the particular cysteine in your structure is truly the relevant covalent target. In this way you can even compare washed and dissolved crystals of your protein-ligand complex with the complex in solution.

best wishes

Savvas