7CBX

Crystal structure of MAP2K7 complexed with a covalent inhibitor 12

• PDB DOI: https://doi.org/10.2210/pdb7CBX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-06-15 Released: 2020-09-30 
• Deposition Author(s): Kinoshita, T., Murakawa, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.224 
• R-Value Work: 0.182 

Literature

Structural basis for producing selective MAP2K7 inhibitors.

Murakawa, Y., Valter, S., Barr, H., London, N., Kinoshita, T.

(2020) Bioorg Med Chem Lett 30: 127546-127546

• PubMed: 32931911 
• DOI: https://doi.org/10.1016/j.bmcl.2020.127546
• Primary Citation of Related Structures:  
  7CBX


• PubMed Abstract: 
  

  Mitogen-activated protein kinase kinase 7 (MAP2K7) in the c-Jun N-terminal kinase signal cascade is an attractive drug target for a variety of diseases. The selectivity of MAP2K7 inhibitors against off-target kinases is a major barrier in drug development. We report a crystal structure of MAP2K7 complexed with a potent covalent inhibitor bearing an acrylamide moiety as an electrophile, which discloses a structural basis for producing selective and potent MAP2K7 inhibitors.

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Organizational Affiliation: 

Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.29 kDa 
• Atom Count: 2,393 
• Modelled Residue Count: 281 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 7	A	323	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FU6 (Subject of Investigation/LOI)	B [auth A]	3-(1H-indazol-3-yl)-5-(prop-2-enoylamino)-N-prop-2-ynyl-benzamide C20 H16 N4 O2 QLVGPPRZJNJOLD-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.224 
• R-Value Work: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.965	α = 90
b = 70.517	β = 90
c = 84.346	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Kinoshita, T., Murakawa, Y.

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description