5YU9

Crystal structure of EGFR 696-1022 T790M in complex with Ibrutinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Ibrutinib targets mutant-EGFR kinase with a distinct binding conformation.

Wang, A.Yan, X.E.Wu, H.Wang, W.Hu, C.Chen, C.Zhao, Z.Zhao, P.Li, X.Wang, L.Wang, B.Ye, Z.Wang, J.Wang, C.Zhang, W.Gray, N.S.Weisberg, E.L.Chen, L.Liu, J.Yun, C.H.Liu, Q.

(2016) Oncotarget 7: 69760-69769

  • DOI: 10.18632/oncotarget.11951

  • PubMed Abstract: 
  • Ibrutinib, a clinically approved irreversible BTK kinase inhibitor for Mantle Cell Lymphoma (MCL) and Chronic Lymphocytic Leukemia (CLL) etc, has been reported to be potent against EGFR mutant kinase and currently being evaluated in clinic for Non Sm ...

    Ibrutinib, a clinically approved irreversible BTK kinase inhibitor for Mantle Cell Lymphoma (MCL) and Chronic Lymphocytic Leukemia (CLL) etc, has been reported to be potent against EGFR mutant kinase and currently being evaluated in clinic for Non Small Cell Lung Cancer (NSCLC). Through EGFR wt/mutant engineered isogenic BaF3 cell lines we confirmed the irreversible binding mode of Ibrutinib with EGFR wt/mutant kinase via Cys797. However, comparing to typical irreversible EGFR inhibitor, such as WZ4002, the washing-out experiments revealed a much less efficient covalent binding for Ibrutinib. The biochemical binding affinity examination in the EGFR L858R/T790M kinase revealed that, comparing to more efficient irreversible inhibitor WZ4002 (Kd: 0.074 μM), Ibrutinib exhibited less efficient binding (Kd: 0.18 μM). An X-ray crystal structure of EGFR (T790M) in complex with Ibrutinib exhibited a unique DFG-in/c-Helix-out inactive binding conformation, which partially explained the less efficiency of covalent binding and provided insight for further development of highly efficient irreversible binding inhibitor for the EGFR mutant kinase. These results also imply that, unlike the canonical irreversible inhibitor, sustained effective concentration might be required for Ibrutinib in order to achieve the maximal efficacy in the clinic application against EGFR driven NSCLC.


    Organizational Affiliation

    Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, P. R. China.,Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Institute of Systems Biomedicine, Department of Biophysics, Beijing Key Laboratory of Tumor Systems Biology and Center for Molecular and Translational Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, P. R. China.,Collaborative Innovation Center of Cancer Medicine, National Institute of Biological Sciences, Beijing 102206, P. R. China.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,University of Science and Technology of China, Anhui, Hefei 230036, P. R. China.,Hefei Science Center, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.,High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, Hefei 230031, P. R. China.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A, B, C, D
331Homo sapiensMutation(s): 1 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1E8
Query on 1E8

Download SDF File 
Download CCD File 
A, B, C, D
1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one
Imbruvica, PCI-32765
C25 H24 N6 O2
XYFPWWZEPKGCCK-GOSISDBHSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 168.194α = 90.00
b = 74.385β = 118.32
c = 120.460γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DENZOdata reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-11-21 
  • Released Date: 2017-12-27 
  • Deposition Author(s): Yan, X.E., Yun, C.H.

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release