5Z1D

MAP2K7 C276S mutant-inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Covalent Docking Identifies a Potent and Selective MKK7 Inhibitor.

Shraga, A.Olshvang, E.Davidzohn, N.Khoshkenar, P.Germain, N.Shurrush, K.Carvalho, S.Avram, L.Albeck, S.Unger, T.Lefker, B.Subramanyam, C.Hudkins, R.L.Mitchell, A.Shulman, Z.Kinoshita, T.London, N.

(2019) Cell Chem Biol 26: 98-108.e5

  • DOI: 10.1016/j.chembiol.2018.10.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The c-Jun NH2-terminal kinase (JNK) signaling pathway is central to the cell response to stress, inflammatory signals, and toxins. While selective inhibitors are known for JNKs and for various upstream MAP3Ks, no selective inhibitor is reported for M ...

    The c-Jun NH2-terminal kinase (JNK) signaling pathway is central to the cell response to stress, inflammatory signals, and toxins. While selective inhibitors are known for JNKs and for various upstream MAP3Ks, no selective inhibitor is reported for MKK7--one of two direct MAP2Ks that activate JNK. Here, using covalent virtual screening, we identify selective MKK7 covalent inhibitors. We optimized these compounds to low-micromolar inhibitors of JNK phosphorylation in cells. The crystal structure of a lead compound bound to MKK7 demonstrated that the binding mode was correctly predicted by docking. We asserted the selectivity of our inhibitors on a proteomic level and against a panel of 76 kinases, and validated an on-target effect using knockout cell lines. Lastly, we show that the inhibitors block activation of primary mouse B cells by lipopolysaccharide. These MKK7 tool compounds will enable better investigation of JNK signaling and may serve as starting points for therapeutics.


    Organizational Affiliation

    Program for Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Specialty Research & Development, Teva Pharmaceuticals, Inc., West Chester, PA 19380, USA.,Maurice and Vivienne Wohl Institute for Drug Discovery, Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot 76100, Israel.,Structural Proteomics Unit, Department of Life Sciences Core Facilities, The Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel.,Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan.,Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address: nir.london@weizmann.ac.il.,Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel.,Maurice and Vivienne Wohl Institute for Drug Discovery, Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot 76100, Israel; Pfizer, Research and Development, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dual specificity mitogen-activated protein kinase kinase 7
A
324Homo sapiensMutation(s): 0 
Gene Names: MAP2K7 (JNKK2, MEK7, MKK7, PRKMK7, SKK4)
EC: 2.7.12.2
Find proteins for O14733 (Homo sapiens)
Go to Gene View: MAP2K7
Go to UniProtKB:  O14733
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
95U
Query on 95U

Download SDF File 
Download CCD File 
A
N-[3-(6-methyl-1H-indazol-3-yl)phenyl]prop-2-enamide
C17 H15 N3 O
YCMAZDUWLKXRRU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.584α = 90.00
b = 63.827β = 90.00
c = 88.458γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Advisory, Data collection, Database references, Derived calculations