Crystal structure of MKK7 (MAP2K7) in complex with ibrutnib, with covalent and allosteric binding modes

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Catalytic Domain Plasticity of MKK7 Reveals Structural Mechanisms of Allosteric Activation and Diverse Targeting Opportunities.

Schroder, M.Tan, L.Wang, J.Liang, Y.Gray, N.S.Knapp, S.Chaikuad, A.

(2020) Cell Chem Biol 27: 1285-1295.e4

  • DOI: https://doi.org/10.1016/j.chembiol.2020.07.014
  • Primary Citation of Related Structures:  
    6YFZ, 6YG0, 6YG1, 6YG2, 6YG3, 6YG4, 6YG5, 6YG6, 6YG7, 6YZ4

  • PubMed Abstract: 

    MKK7 (MEK7) is a key regulator of the JNK stress signaling pathway and targeting MKK7 has been proposed as a chemotherapeutic strategy. Detailed understanding of the MKK7 structure and factors that affect its activity is therefore of critical importance. Here, we present a comprehensive set of MKK7 crystal structures revealing insights into catalytic domain plasticity and the role of the N-terminal regulatory helix, conserved in all MAP2Ks, mediating kinase activation. Crystal structures harboring this regulatory helix revealed typical structural features of active kinase, providing exclusively a first model of the MAP2K active state. A small-molecule screening campaign yielded multiple scaffolds, including type II irreversible inhibitors a binding mode that has not been reported previously. We also observed an unprecedented allosteric pocket located in the N-terminal lobe for the approved drug ibrutinib. Collectively, our structural and functional data expand and provide alternative targeting strategies for this important MAP2K kinase.

  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt 60438, Germany; Structural Genomics Consortium, BMLS, Goethe-University Frankfurt, Frankfurt 60438, Germany. Electronic address: chaikuad@pharmchem.uni-frankfurt.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 7307Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O14733 (Homo sapiens)
Explore O14733 
Go to UniProtKB:  O14733
PHAROS:  O14733
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14733
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8E8 (Subject of Investigation/LOI)
Query on 8E8

Download Ideal Coordinates CCD File 
O [auth A]1-[(3~{R})-3-[4-azanyl-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one
C25 H26 N6 O2
1E8 (Subject of Investigation/LOI)
Query on 1E8

Download Ideal Coordinates CCD File 
N [auth A]1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one
C25 H24 N6 O2
Query on DMS

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A]
C2 H6 O S
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.111α = 90
b = 74.955β = 90
c = 86.666γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2020-10-28
    Changes: Database references