Experimental Data Snapshot

  • Resolution: 3.25 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 

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Start Selective and Rigidify: The Discovery Path toward a Next Generation of EGFR Tyrosine Kinase Inhibitors.

Engelhardt, H.Bose, D.Petronczki, M.Scharn, D.Bader, G.Baum, A.Bergner, A.Chong, E.Dobel, S.Egger, G.Engelhardt, C.Ettmayer, P.Fuchs, J.E.Gerstberger, T.Gonnella, N.Grimm, A.Grondal, E.Haddad, N.Hopfgartner, B.Kousek, R.Krawiec, M.Kriz, M.Lamarre, L.Leung, J.Mayer, M.Patel, N.D.Simov, B.P.Reeves, J.T.Schnitzer, R.Schrenk, A.Sharps, B.Solca, F.Stadtmuller, H.Tan, Z.Wunberg, T.Zoephel, A.McConnell, D.B.

(2019) J Med Chem 62: 10272-10293

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01169
  • Primary Citation of Related Structures:  
    6S9B, 6S9C, 6S9D

  • PubMed Abstract: 

    The epidermal growth factor receptor (EGFR), when carrying an activating mutation like del19 or L858R, acts as an oncogenic driver in a subset of lung tumors. While tumor responses to tyrosine kinase inhibitors (TKIs) are accompanied by marked tumor shrinkage, the response is usually not durable. Most patients relapse within two years of therapy often due to acquisition of an additional mutation in EGFR kinase domain that confers resistance to TKIs. Crucially, oncogenic EGFR harboring both resistance mutations, T790M and C797S, can no longer be inhibited by currently approved EGFR TKIs. Here, we describe the discovery of BI-4020 , which is a noncovalent, wild-type EGFR sparing, macrocyclic TKI. BI-4020 potently inhibits the above-described EGFR variants and induces tumor regressions in a cross-resistant EGFR del19 T790M C797S xenograft model. Key was the identification of a highly selective but moderately potent benzimidazole followed by complete rigidification of the molecule through macrocyclization.

  • Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor326Homo sapiensMutation(s): 5 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L1H (Subject of Investigation/LOI)
Query on L1H

Download Ideal Coordinates CCD File 
B [auth A]3-fluoranyl-~{N}-[1-(2-methyl-2-oxidanyl-propyl)benzimidazol-2-yl]-5-pyridin-3-yl-benzamide
C23 H21 F N4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.25 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.597α = 90
b = 144.597β = 90
c = 144.597γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2019-11-20 
  • Deposition Author(s): Bader, G.

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Database references