4QYY | pdb_00004qyy

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 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm500847m
  • Primary Citation Related Structures: 
    4QYY

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 43 kDa 
  • Atom Count: 2,994 
  • Modeled Residue Count: 337 
  • Deposited Residue Count: 365 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1365Rattus norvegicusMutation(s): 0 
Gene Names: Mapk1Erk2MapkPrkm1
EC: 2.7.11.24
UniProt
Find proteins for P63086 (Rattus norvegicus)
Explore P63086 
Go to UniProtKB:  P63086
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63086
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
3G7 BindingDB:  4QYY IC50: min: 50, max: 2600 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.259 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.202α = 90
b = 91.409β = 90
c = 63.316γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
MOLREPphasing
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description