6GJB

Erk2 signalling protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report



Literature

Quantitation of ERK1/2 inhibitor cellular target occupancies with a reversible slow off-rate probe.

Lebraud, H.Surova, O.Courtin, A.O'Reilly, M.Valenzano, C.R.Nordlund, P.Heightman, T.D.

(2018) Chem Sci 9: 8608-8618

  • DOI: 10.1039/c8sc02754d
  • Primary Citation of Related Structures:  
    6GJB, 6GJD

  • PubMed Abstract: 
  • Target engagement is a key concept in drug discovery and its direct measurement can provide a quantitative understanding of drug efficacy and/or toxicity. Failure to demonstrate target occupancy in relevant cells and tissues has been recognised as a cont ...

    Target engagement is a key concept in drug discovery and its direct measurement can provide a quantitative understanding of drug efficacy and/or toxicity. Failure to demonstrate target occupancy in relevant cells and tissues has been recognised as a contributing factor to the low success rate of clinical drug development. Several techniques are emerging to quantify target engagement in cells; however, in situ measurements remain challenging, mainly due to technical limitations. Here, we report the development of a non-covalent clickable probe, based on SCH772984, a slow off-rate ERK1/2 inhibitor, which enabled efficient pull down of ERK1/2 protein via click reaction with tetrazine tagged agarose beads. This was used in a competition setting to measure relative target occupancy by selected ERK1/2 inhibitors. As a reference we used the cellular thermal shift assay, a label-free biophysical assay relying solely on ligand-induced thermodynamic stabilization of proteins. To validate the EC 50 values measured by both methods, the results were compared with IC 50 data for the phosphorylation of RSK, a downstream substrate of ERK1/2 used as a functional biomarker of ERK1/2 inhibition. We showed that a slow off-rate reversible probe can be used to efficiently pull down cellular proteins, significantly extending the potential of the approach beyond the need for covalent or photoaffinity warheads.


    Organizational Affiliation

    Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . Email: honorine.lebraud@astx.com ; Email: tom.heightman@astx.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1 A368Homo sapiensMutation(s): 0 
Gene Names: MAPK1ERK2PRKM1PRKM2
EC: 2.7.11.24
Find proteins for P28482 (Homo sapiens)
Explore P28482 
Go to UniProtKB:  P28482
NIH Common Fund Data Resources
PHAROS:  P28482
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F0H
Query on F0H

Download Ideal Coordinates CCD File 
A
[(1~{R},4~{Z})-cyclooct-4-en-1-yl] ~{N}-[4-[4-[[4-[1-[(1~{S})-1-(4-chloranyl-3-fluoranyl-phenyl)-2-oxidanyl-ethyl]-2-oxidanylidene-pyridin-4-yl]pyrimidin-2-yl]amino]pyridin-2-yl]but-3-ynyl]carbamate
C35 H34 Cl F N6 O4
ORLWNASDTJFKIF-ABXFUJLBSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F0HIC50:  8   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.804α = 90
b = 70.596β = 109.2
c = 60.023γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-05-16 
  • Released Date: 2019-01-02 
  • Deposition Author(s): O'Reilly, M.

Revision History 

  • Version 1.0: 2019-01-02
    Type: Initial release