5LCJ

In-Gel Activity-Based Protein Profiling of a Clickable Covalent Erk 1/2 Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5LCJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-22 Released: 2016-07-20 
• Deposition Author(s): O'Reilly, M., Wright, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.212 
• R-Value Work: 0.162 
• R-Value Observed: 0.165 

Literature

In-gel activity-based protein profiling of a clickable covalent ERK1/2 inhibitor.

Lebraud, H., Wright, D.J., East, C.E., Holding, F.P., O'Reilly, M., Heightman, T.D.

(2016) Mol Biosyst 12: 2867-2874

• PubMed: 27385078 
• DOI: https://doi.org/10.1039/c6mb00367b
• Primary Citation of Related Structures:  
  5LCJ, 5LCK


• PubMed Abstract: 
  

  In-gel activity-based protein profiling (ABPP) offers rapid assessment of the proteome-wide selectivity and target engagement of a chemical tool. Here we demonstrate the use of the inverse electron demand Diels Alder (IEDDA) click reaction for in-gel ABPP by evaluating the selectivity profile and target engagement of a covalent ERK1/2 probe tagged with a trans-cyclooctene group. The chemical probe was shown to bind covalently to Cys166 of ERK2 using protein MS and X-ray crystallography, and displayed submicromolar GI50s in A375 and HCT116 cells. In both cell lines, the probe demonstrated target engagement and a good selectivity profile at low concentrations, which was lost at higher concentrations. The IEDDA cycloaddition enabled fast and quantitative fluorescent tagging for readout with a high background-to-noise ratio and thereby provides a promising alternative to the commonly used copper catalysed alkyne-azide cycloaddition.

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Organizational Affiliation: 

Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.33 kDa 
• Atom Count: 3,450 
• Modelled Residue Count: 346 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	368	Homo sapiens	Mutation(s): 0  Gene Names: MAPK1, ERK2, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
PHAROS:  P28482 GTEx:  ENSG00000100030

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6TS	B [auth A]	[(1~{R},4~{Z})-cyclooct-4-en-1-yl] ~{N}-[4-[4-[[5-chloranyl-4-[[2-(propanoylamino)phenyl]amino]pyrimidin-2-yl]amino]pyridin-2-yl]but-3-ynyl]carbamate C31 H34 Cl N7 O3 DLZIOTBNYZNPPK-YJMIJIGASA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.212 
• R-Value Work: 0.162 
• R-Value Observed: 0.165 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.729	α = 90
b = 70.807	β = 109.18
c = 60.208	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
iMOSFLM	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): O'Reilly, M., Wright, D.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2016-08-31
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Structure summary