4JRV

Crystal structure of EGFR kinase domain in complex with compound 4c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Protein Kinase Inhibitor Design by Targeting the Asp-Phe-Gly (DFG) Motif: The Role of the DFG Motif in the Design of Epidermal Growth Factor Receptor Inhibitors

Peng, Y.H.Shiao, H.Y.Tu, C.H.Liu, P.M.Hsu, J.T.Amancha, P.K.Wu, J.S.Coumar, M.S.Chen, C.H.Wang, S.Y.Lin, W.H.Sun, H.Y.Chao, Y.S.Lyu, P.C.Hsieh, H.P.Wu, S.Y.

(2013) J.Med.Chem. 56: 3889-3903

  • DOI: 10.1021/jm400072p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Asp-Phe-Gly (DFG) motif plays an important role in the regulation of kinase activity. Structure-based drug design was performed to design compounds able to interact with the DFG motif; epidermal growth factor receptor (EGFR) was selected as an ex ...

    The Asp-Phe-Gly (DFG) motif plays an important role in the regulation of kinase activity. Structure-based drug design was performed to design compounds able to interact with the DFG motif; epidermal growth factor receptor (EGFR) was selected as an example. Structural insights obtained from the EGFR/2a complex suggested that an extension from the meta-position on the phenyl group (ring-5) would improve interactions with the DFG motif. Indeed, introduction of an N,N-dimethylamino tail resulted in 4b, which showed almost 50-fold improvement in inhibition compared to 2a. Structural studies confirmed this N,N-dimethylamino tail moved toward the DFG motif to form a salt bridge with the side chain of Asp831. That the interactions with the DFG motif greatly contribute to the potency of 4b is strongly evidenced by synthesizing and testing compounds 2a, 3g, and 4f: when the charge interactions are absent, the inhibitory activity decreased significantly.


    Organizational Affiliation

    Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A
328Homo sapiensMutation(s): 0 
Gene Names: EGFR (ERBB, ERBB1, HER1)
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Go to Gene View: EGFR
Go to UniProtKB:  P00533
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KJV
Query on KJV

Download SDF File 
Download CCD File 
A
4-(dimethylamino)-N-[3-(4-{[(1S)-2-hydroxy-1-phenylethyl]amino}-6-phenylfuro[2,3-d]pyrimidin-5-yl)phenyl]butanamide
C32 H33 N5 O3
KPTUKIAZZFDEOC-AREMUKBSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KJVIC50: 29 nM (100) BINDINGDB
KJVIC50: 29 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 146.391α = 90.00
b = 146.391β = 90.00
c = 146.391γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-03-22 
  • Released Date: 2013-06-19 
  • Deposition Author(s): Peng, Y.H., Wu, J.S.

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release