EGFR(T790M/V948R) in complex with LN2899

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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This is version 1.3 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 receptorA [auth D],
B [auth A],
C [auth B],
D [auth C]
327Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QP1 (Subject of Investigation/LOI)
Query on QP1

Download Ideal Coordinates CCD File 
G [auth D],
I [auth A],
K [auth B],
M [auth C]
C27 H28 F N5 O3 S
Query on EDO

Download Ideal Coordinates CCD File 
F [auth D],
J [auth B]
C2 H6 O2
Query on CL

Download Ideal Coordinates CCD File 
E [auth D],
H [auth A],
L [auth B],
N [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.48α = 90
b = 102.448β = 102.78
c = 87.422γ = 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: 2022-02-23
    Changes: Database references, Experimental preparation
  • Version 1.3: 2023-10-11
    Changes: Data collection, Refinement description