Biochemical, Cellular and Structural Characterization of Novel ERK3 Inhibitors

Experimental Data Snapshot

  • Resolution: 2.52 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

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Biochemical, cellular and structural characterization of novel and selective ERK3 inhibitors.

Gradler, U.Busch, M.Leuthner, B.Raba, M.Burgdorf, L.Lehmann, M.Linde, N.Esdar, C.

(2020) Bioorg Med Chem Lett 30: 127551-127551

  • DOI: https://doi.org/10.1016/j.bmcl.2020.127551
  • Primary Citation of Related Structures:  
    6YKY, 6YLC, 6YLL

  • PubMed Abstract: 

    Triazolo[4,5-d]pyrimidin-5-amines were identified from kinase selectivity screening as novel ERK3 inhibitors with sub-100 nanomolar potencies in a biochemical assay using MK5 as substrate and with an attractive kinase selectivity profile. ERK3 crystal structures clarified the inhibitor binding mode in the ATP pocket with impact on A-loop, GC-loop and αC-helix conformations suggesting a potential structural link towards MK5 interaction via the FHIEDE motif. The inhibitors also showed sub-100 nM potencies in a cellular ERK3 NanoBRET assay and with excellent correlation to the biochemical IC 50 s. This novel series provides valuable tool compounds to further investigate the biological function and activation mechanism of ERK3.

  • Organizational Affiliation

    Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany. Electronic address: ulrich.graedler@merckgroup.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 6
A, B, C, D
319Homo 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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.52 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.978α = 90
b = 100.883β = 90
c = 195.522γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2020-09-23 
  • Deposition Author(s): Graedler, U.

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description