3I5Z

Crystal structure of ERK2 bound to (S)-N-(2-hydroxy-1-phenylethyl)-4-(5-methyl-2-(phenylamino)pyrimidin-4-yl)-1H-pyrrole-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Z48Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Structure-guided design of potent and selective pyrimidylpyrrole inhibitors of extracellular signal-regulated kinase (ERK) using conformational control.

Aronov, A.M.Tang, Q.Martinez-Botella, G.Bemis, G.W.Cao, J.Chen, G.Ewing, N.P.Ford, P.J.Germann, U.A.Green, J.Hale, M.R.Jacobs, M.Janetka, J.W.Maltais, F.Markland, W.Namchuk, M.N.Nanthakumar, S.Poondru, S.Straub, J.ter Haar, E.Xie, X.

(2009) J Med Chem 52: 6362-6368

  • DOI: https://doi.org/10.1021/jm900630q
  • Primary Citation of Related Structures:  
    3I4B, 3I5Z, 3I60

  • PubMed Abstract: 

    The Ras/Raf/MEK/ERK signal transduction, an oncogenic pathway implicated in a variety of human cancers, is a key target in anticancer drug design. A novel series of pyrimidylpyrrole ERK inhibitors has been identified. Discovery of a conformational change for lead compound 2, when bound to ERK2 relative to antitarget GSK3, enabled structure-guided selectivity optimization, which led to the discovery of 11e, a potent, selective, and orally bioavailable inhibitor of ERK.


  • Organizational Affiliation

    Vertex Pharmaceuticals Inc., 130 Waverly Street, Cambridge, Massachusetts 02139-4242, USA. alex_aronov@vrtx.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1380Homo sapiensMutation(s): 0 
Gene Names: ERK2MAPK1PRKM1PRKM2
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.948α = 90
b = 70.751β = 90
c = 118.46γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Z48Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description