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 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/jm900630q
  • Structures With Same Primary Citation

  • 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 ch ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 1A380Homo sapiensMutation(s): 0 
Gene Names: ERK2MAPK1PRKM1PRKM2
EC: 2.7.11.24
Find proteins for P28482 (Homo sapiens)
Explore P28482 
Go to UniProtKB:  P28482
NIH Common Fund Data Resources
PHAROS  P28482
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z48
Query on Z48

Download CCD File 
A
N-[(1S)-2-hydroxy-1-phenylethyl]-4-[5-methyl-2-(phenylamino)pyrimidin-4-yl]-1H-pyrrole-2-carboxamide
C24 H23 N5 O2
PFHKAGAZRDERTK-OAQYLSRUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Z48Ki :  2   nM  PDBBind
Z48Ki:  4   nM  BindingDB
Z48Ki:  2   nM  Binding MOAD
Z48Ki:  2   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • 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



Entry History 

Deposition Data

  • Deposited Date: 2009-07-06 
  • Released Date: 2010-01-12 
  • Deposition Author(s): Jacobs, M.D., Xie, X.

Revision History 

  • 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