Crystal structure of human mitogen activated protein kinase 6 (MAPK6)

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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Crystal Structure and Inhibitor Identifications Reveal Targeting Opportunity for the Atypical MAPK Kinase ERK3.

Schroder, M.Filippakopoulos, P.Schwalm, M.P.Ferrer, C.A.Drewry, D.H.Knapp, S.Chaikuad, A.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21217953
  • Primary Citation of Related Structures:  
    7AK3, 7AQB

  • PubMed Abstract: 

    Extracellular signal-regulated kinase 3 (ERK3), known also as mitogen-activated protein kinase 6 (MAPK6), is an atypical member of MAPK kinase family, which has been poorly studied. Little is known regarding its function in biological processes, yet this atypical kinase has been suggested to play important roles in the migration and invasiveness of certain cancers. The lack of tools, such as a selective inhibitor, hampers the study of ERK3 biology. Here, we report the crystal structure of the kinase domain of this atypical MAPK kinase, providing molecular insights into its distinct ATP binding pocket compared to the classical MAPK ERK2, explaining differences in their inhibitor binding properties. Medium-scale small molecule screening identified a number of inhibitors, several of which unexpectedly exhibited remarkably high inhibitory potencies. The crystal structure of CLK1 in complex with CAF052, one of the most potent inhibitors identified for ERK3, revealed typical type-I binding mode of the inhibitor, which by structural comparison could likely be maintained in ERK3. Together with the presented structural insights, these diverse chemical scaffolds displaying both reversible and irreversible modes of action, will serve as a starting point for the development of selective inhibitors for ERK3, which will be beneficial for elucidating the important functions of this understudied kinase.

  • Organizational Affiliation

    Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 6
A, B
320Homo sapiensMutation(s): 1 
Gene Names: MAPK6ERK3PRKM6
UniProt & NIH Common Fund Data Resources
Find proteins for Q16659 (Homo sapiens)
Explore Q16659 
Go to UniProtKB:  Q16659
PHAROS:  Q16659
GTEx:  ENSG00000069956 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16659
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.317α = 90
b = 83.317β = 90
c = 181.066γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description