6YLL

Biochemical, Cellular and Structural Characterization of Novel ERK3 Inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

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Literature

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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 6
A, B
319Homo sapiensMutation(s): 1 
Gene Names: MAPK6, ERK3, PRKM6
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16659 (Homo sapiens)
Explore Q16659 
Go to UniProtKB:  Q16659
PHAROS:  Q16659
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16659
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OYB (Subject of Investigation/LOI)
Query on OYB
Download Ideal Coordinates CCD File 
C [auth A]~{N}4-[3-(4-methoxyphenyl)-[1,2,3]triazolo[4,5-d]pyrimidin-5-yl]cyclohexane-1,4-diamine
C17 H21 N7 O
OYCSZJFCBXZCDD-HAQNSBGRSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.12α = 90
b = 85.12β = 90
c = 181.26γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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