Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.50 kDa 
• Atom Count: 2333 
• Modelled Residue Count: 274 
• Deposited Residue Count: 324 
• Unique protein chains: 1

5Z1D

MAP2K7 C276S mutant-inhibitor

• PDB DOI: 10.2210/pdb5Z1D/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2017-12-26 Released: 2019-01-02 
• Deposition Author(s): Kinoshita, T., London, N.

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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 

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

• PubMed: 30449673 
• DOI: 10.1016/j.chembiol.2018.10.011
• Primary Citation of Related Structures:  
  5Z1D, 5Z1E


• 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. 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.

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Organizational Affiliation: 

Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 7	A	324	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
95U	B [auth A]	N-[3-(6-methyl-1H-indazol-3-yl)phenyl]prop-2-enamide C17 H15 N3 O YCMAZDUWLKXRRU-UHFFFAOYSA-N
EPE	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

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 = 54.584	α = 90
b = 63.827	β = 90
c = 88.458	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-12-26 
• Released Date: 2019-01-02 
Deposition Author(s): Kinoshita, T., London, N.

Revision History  

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