4QYY

Discovery of Novel, Dual Mechanism ERK Inhibitors by Affinity Selection Screening of an Inactive Kinase State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Novel, Dual Mechanism ERK Inhibitors by Affinity Selection Screening of an Inactive Kinase.

Deng, Y.Shipps, G.W.Cooper, A.English, J.M.Annis, D.A.Carr, D.Nan, Y.Wang, T.Zhu, H.Y.Chuang, C.C.Dayananth, P.Hruza, A.W.Xiao, L.Jin, W.Kirschmeier, P.Windsor, W.T.Samatar, A.A.

(2014) J.Med.Chem. 57: 8817-8826

  • DOI: 10.1021/jm500847m

  • PubMed Abstract: 
  • An affinity-based mass spectrometry screening technology was used to identify novel binders to both nonphosphorylated and phosphorylated ERK2. Screening of inactive ERK2 identified a pyrrolidine analogue 1 that bound to both nonphosphorylated and pho ...

    An affinity-based mass spectrometry screening technology was used to identify novel binders to both nonphosphorylated and phosphorylated ERK2. Screening of inactive ERK2 identified a pyrrolidine analogue 1 that bound to both nonphosphorylated and phosphorylated ERK2 and inhibited ERK2 kinase activity. Chemical optimization identified compound 4 as a novel, potent, and highly selective ERK1,2 inhibitor which not only demonstrated inhibition of phosphorylation of ERK substrate p90RSK but also demonstrated inhibition of ERK1,2 phosphorylation on the activation loop. X-ray cocrystallography revealed that upon binding of compound 4 to ERK2, Tyr34 undergoes a rotation (flip) along with a shift in the poly-Gly rich loop to create a new binding pocket into which 4 can bind. This new binding mode represents a novel mechanism by which high affinity ATP-competitive compounds may achieve excellent kinase selectivity.


    Organizational Affiliation

    Merck Research Laboratories , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 1
A
365Rattus norvegicusMutation(s): 0 
Gene Names: Mapk1 (Erk2, Mapk, Prkm1)
EC: 2.7.11.24
Find proteins for P63086 (Rattus norvegicus)
Go to UniProtKB:  P63086
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
3G7
Query on 3G7

Download SDF File 
Download CCD File 
A
(3R)-1-{2-[4-(4-acetylphenyl)piperazin-1-yl]-2-oxoethyl}-N-(3-chloro-4-hydroxyphenyl)pyrrolidine-3-carboxamide
C25 H29 Cl N4 O4
YPNCCYRKEHPJMN-LJQANCHMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3G7IC50: 50 - 4200 nM (99) BINDINGDB
3G7Kd: 50 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.202α = 90.00
b = 91.409β = 90.00
c = 63.316γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
StructureStudiodata collection
BUSTERrefinement
MOLREPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-17
    Type: Database references