Crystal Structure of a Double Mutant Rat Erk2 Complexed With a Type II Quinazoline Inhibitor

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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Sequence determinants of a specific inactive protein kinase conformation.

Hari, S.B.Merritt, E.A.Maly, D.J.

(2013) Chem Biol 20: 806-815

  • DOI: https://doi.org/10.1016/j.chembiol.2013.05.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Only a small percentage of protein kinases have been shown to adopt a distinct inactive ATP-binding site conformation, called the Asp-Phe-Gly-out (DFG-out) conformation. Given the high degree of homology within this enzyme family, we sought to understand the basis of this disparity on a sequence level. We identified two residue positions that sensitize mitogen-activated protein kinases (MAPKs) to inhibitors that stabilize the DFG-out inactive conformation. After characterizing the structure and dynamics of an inhibitor-sensitive MAPK mutant, we demonstrated the generality of this strategy by sensitizing a kinase (apoptosis signal-regulating kinase 1) not in the MAPK family to several DFG-out stabilizing ligands, using the same residue positions. The use of specific inactive conformations may aid the study of noncatalytic roles of protein kinases, such as binding partner interactions and scaffolding effects.

  • Organizational Affiliation

    Department of Chemistry, University of Washington, Seattle, WA 98195, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1359Rattus norvegicusMutation(s): 2 
Gene Names: Erk2MapkMapk1Prkm1
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on G17

Download Ideal Coordinates CCD File 
B [auth A]N-{3-[2-(cyclopropylamino)quinazolin-6-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide
C26 H21 F3 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
G17 Binding MOAD:  4I5H Ki: 2 (nM) from 1 assay(s)
PDBBind:  4I5H Ki: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.24α = 90
b = 77.24β = 90
c = 121.791γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations