4JQ7

Crystal structure of EGFR kinase domain in complex with compound 2a

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report



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:  
    4JQ7, 4JQ8, 4JR3, 4JRV

  • 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epidermal growth factor receptorA328Homo sapiensMutation(s): 0 
Gene Names: EGFR, ERBB, ERBB1, HER1
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
NIH Common Fund Data Resources
PHAROS  P00533
GTEx  ENSG00000146648
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KJQ
Query on KJQ
Download Ideal Coordinates CCD File 
A
(2S)-2-[(5,6-diphenylfuro[2,3-d]pyrimidin-4-yl)amino]-2-phenylethanol
C26 H21 N3 O2
CCGBAJCQZPJWCS-OAQYLSRUSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KJQIC50:  223   nM  BindingDB
KJQIC50 :  393   nM  PDBBind
KJQIC50:  393   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.933α = 90
b = 145.933β = 90
c = 145.933γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2013-03-20 
  • 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