6YLL

Biochemical, Cellular and Structural Characterization of Novel ERK3 Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb6YLL/pdb

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


• Deposited: 2020-04-07 Released: 2020-09-23 
• Deposition Author(s): Graedler, U.

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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 

Starting Model: experimental

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

• PubMed: 32927028 
• 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.

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Organizational Affiliation: 

Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.73 kDa 
• Atom Count: 4,358 
• Modelled Residue Count: 538 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 6	A, B	319	Homo sapiens	Mutation(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 GTEx:  ENSG00000069956

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OYB (Subject of Investigation/LOI)	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

Binding Affinity Annotations
ID	Source	Binding Affinity
OYB	BindingDB:  6YLL	Kd: min: 130, max: 890 (nM) from 3 assay(s)
		IC50: min: 300, max: 549 (nM) from 3 assay(s)

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 = 85.12	α = 90
b = 85.12	β = 90
c = 181.26	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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