6YG2

Target information

RCSB PDB
6YG2
Title
Crystal structure of MKK7 (MAP2K7) in complex with ibrutnib, with covalent and allosteric binding modes
Method
X-RAY DIFFRACTION
Resolution
2
Classification
TRANSFERASE
Organism
Homo sapiens
Protein
Dual specificity mitogen-activated protein kinase kinase 7 (O14733)    Looking for covalent inhibitors of this target ?
Year
2020
Publication Title
Catalytic Domain Plasticity of MKK7 Reveals Structural Mechanisms of Allosteric Activation and Diverse Targeting Opportunities.
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.

External Link
RCSB PDB





Ligand information

HET
8E8
Chain ID
A
HET Number
514
Molecular Formula
C25H24N6O2
Structure
2D structure
IUPAC Name
1-[(3R)-3-[4-amino-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]-1-piperidyl]prop-2-en-1-one
InChI
InChI=1S/C25H24N6O2/c1-2-21(32)30-14-6-7-18(15-30)31-25-22(24(26)27-16-28-25)23(29-31)17-10-12-20(13-11-17)33-19-8-4-3-5-9-19/h2-5,8-13,16,18H,1,6-7,14-15H2,(H2,26,27,28)/t18-/m1/s1
InChI Key
XYFPWWZEPKGCCK-GOSISDBHSA-N
Canonical SMILES
C=CC(=O)N1C[C@@H](CCC1)n2nc(c(c23)c(N)ncn3)-c4ccc(cc4)Oc5ccccc5
Bioactivity data
CI000729

Covalent Binding

Warhead
Michael Acceptor
Reaction Mechanism
Michael Addition
Residue
CYS : 218
Residue Chain
A
Interactions
Pharmacophore Model