6GJD

Erk2 signalling protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1368Homo sapiensMutation(s): 0 
Gene Names: MAPK1ERK2PRKM1PRKM2
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28482
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F0E (Subject of Investigation/LOI)
Query on F0E

Download Ideal Coordinates CCD File 
L [auth A]cyclooctyl ~{N}-[3-[[4-[5-[[(3~{R})-1-[2-oxidanylidene-2-[4-(4-pyrimidin-2-ylphenyl)piperazin-1-yl]ethyl]pyrrolidin-3-yl]carbonylamino]-1~{H}-indazol-3-yl]pyridin-2-yl]carbonylamino]propyl]carbamate
C46 H55 N11 O5
FWLOTDDRDKLCPO-UUWRZZSWSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
B [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.77α = 90
b = 70.996β = 109.42
c = 60.12γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary