4X21

The MAP kinase JNK3 as target for halogen bonding

Summary for 4X21

• Entry DOI: 10.2210/pdb4x21/pdb
• Related: 2P33
• Descriptor: Mitogen-activated protein kinase 10, N-ethyl-4-{[4-(1H-indol-3-yl)-5-iodopyrimidin-2-yl]amino}piperidine-1-carboxamide, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: mapk, halogen bond complex, transferase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 85573.30

Authors

Lange, A.,Buettner, F.M.,Guenther, M.B.,Zimmermann, M.O.,Hennig, S.,Laufer, S.A.,Stehle, T.,Boeckler, F. (deposition date: 2014-11-25, release date: 2015-11-11, Last modification date: 2024-01-10)

Primary citation

Lange, A.,Gunther, M.,Buttner, F.M.,Zimmermann, M.O.,Heidrich, J.,Hennig, S.,Zahn, S.,Schall, C.,Sievers-Engler, A.,Ansideri, F.,Koch, P.,Laemmerhofer, M.,Stehle, T.,Laufer, S.A.,Boeckler, F.M.
Targeting the Gatekeeper MET146 of C-Jun N-Terminal Kinase 3 Induces a Bivalent Halogen/Chalcogen Bond.
J.Am.Chem.Soc., 137:14640-14652, 2015

PubMed Abstract: We target the gatekeeper MET146 of c-Jun N-terminal kinase 3 (JNK3) to exemplify the applicability of X···S halogen bonds in molecular design using computational, synthetic, structural and biophysical techniques. In a designed series of aminopyrimidine-based inhibitors, we unexpectedly encounter a plateau of affinity. Compared to their QM-calculated interaction energies, particularly bromine and iodine fail to reach the full potential according to the size of their σ-hole. Instead, mutation of the gatekeeper residue into leucine, alanine, or threonine reveals that the heavier halides can significantly influence selectivity in the human kinome. Thus, we demonstrate that, although the choice of halogen may not always increase affinity, it can still be relevant for inducing selectivity. Determining the crystal structure of the iodine derivative in complex with JNK3 (4X21) reveals an unusual bivalent halogen/chalcogen bond donated by the ligand and the back-pocket residue MET115. Incipient repulsion from the too short halogen bond increases the flexibility of Cε of MET146, whereas the rest of the residue fails to adapt being fixed by the chalcogen bond. This effect can be useful to induce selectivity, as the necessary combination of methionine residues only occurs in 9.3% of human kinases, while methionine is the predominant gatekeeper (39%).

PubMed: 26505827
DOI: 10.1021/jacs.5b07090

Experimental method

X-RAY DIFFRACTION (1.95 Å)