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 
  • R-Value Observed: 0.195 

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:  
    5Z1E, 5Z1D

  • 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 MKK7--one of two direct MAP2Ks that activate JNK ...

    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: 

    Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address: nir.london@weizmann.ac.il.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 7A324Homo sapiensMutation(s): 0 
Gene Names: MAP2K7, JNKK2, MEK7, MKK7, PRKMK7, SKK4
EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for O14733 (Homo sapiens)
Explore O14733 
Go to UniProtKB:  O14733
PHAROS:  O14733
GTEx:  ENSG00000076984
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
95U
Query on 95U
Download Ideal Coordinates CCD File 
 B [auth A]N-[3-(6-methyl-1H-indazol-3-yl)phenyl]prop-2-enamide
C17 H15 N3 O
YCMAZDUWLKXRRU-UHFFFAOYSA-N		 Ligand Interaction
EPE
Query on EPE
Download Ideal Coordinates CCD File 
 C [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-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 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.584α = 90
b = 63.827β = 90
c = 88.458γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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