EGFR(T790M/V948R) in complex with LN2380

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Structural Basis for EGFR Mutant Inhibition by Trisubstituted Imidazole Inhibitors.

Heppner, D.E.Gunther, M.Wittlinger, F.Laufer, S.A.Eck, M.J.

(2020) J Med Chem 63: 4293-4305

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00200
  • Primary Citation of Related Structures:  
    6V5N, 6V5P, 6V66, 6V6K, 6V6O, 6VH4, 6VHN, 6VHP

  • PubMed Abstract: 

    Acquired drug resistance in epidermal growth factor receptor (EGFR) mutant non-small-cell lung cancer is a persistent challenge in cancer therapy. Previous studies of trisubstituted imidazole inhibitors led to the serendipitous discovery of inhibitors that target the drug resistant EGFR(L858R/T790M/C797S) mutant with nanomolar potencies in a reversible binding mechanism. To dissect the molecular basis for their activity, we determined the binding modes of several trisubstituted imidazole inhibitors in complex with the EGFR kinase domain with X-ray crystallography. These structures reveal that the imidazole core acts as an H-bond acceptor for the catalytic lysine (K745) in the "αC-helix out" inactive state. Selective N-methylation of the H-bond accepting nitrogen ablates inhibitor potency, confirming the role of the K745 H-bond in potent, noncovalent inhibition of the C797S variant. Insights from these studies offer new strategies for developing next generation inhibitors targeting EGFR in non-small-cell lung cancer.

  • Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor327Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QQM (Subject of Investigation/LOI)
Query on QQM

Download Ideal Coordinates CCD File 
J [auth D]
L [auth A]
N [auth B]
P [auth C]
R [auth E]
J [auth D],
L [auth A],
N [auth B],
P [auth C],
R [auth E],
T [auth F],
U [auth G],
X [auth H]
C27 H28 F N5 O3
Query on CL

Download Ideal Coordinates CCD File 
I [auth D]
K [auth A]
M [auth B]
O [auth C]
Q [auth E]
I [auth D],
K [auth A],
M [auth B],
O [auth C],
Q [auth E],
S [auth F],
V [auth G],
W [auth H]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.55α = 90
b = 102.36β = 101.3
c = 173.569γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA201049

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2020-07-15
    Changes: Derived calculations
  • Version 1.3: 2022-02-23
    Changes: Database references, Experimental preparation
  • Version 1.4: 2023-10-11
    Changes: Data collection, Refinement description