4X21

The MAP kinase JNK3 as target for halogen bonding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Targeting the Gatekeeper MET146 of C-Jun N-Terminal Kinase 3 Induces a Bivalent Halogen/Chalcogen Bond.

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.

(2015) J Am Chem Soc 137: 14640-14652

  • DOI: 10.1021/jacs.5b07090
  • Primary Citation of Related Structures:  
    4X21

  • 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 ...

    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%).


    Organizational Affiliation

    Center for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen , Sand 1, 72076 Tübingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10A, B367Homo sapiensMutation(s): 0 
Gene Names: MAPK10JNK3JNK3APRKM10SAPK1B
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
PHAROS:  P53779
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3WH (Subject of Investigation/LOI)
Query on 3WH

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]N-ethyl-4-{[4-(1H-indol-3-yl)-5-iodopyrimidin-2-yl]amino}piperidine-1-carboxamide
C20 H23 I N6 O
AUFRUDIABNXVLI-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3WH Binding MOAD:  4X21 Kd: 36 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.94α = 90
b = 109.84β = 90
c = 43.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references
  • Version 2.0: 2020-06-03
    Changes: Atomic model, Data collection, Derived calculations