9D3V | pdb_00009d3v

CRYSTAL STRUCTURE OF EGFR(L858R/T790M/C797S) IN COMPLEX WITH AUR-3418


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.329 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.299 (Depositor), 0.222 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of a Novel Mutant-Selective Epidermal Growth Factor Receptor Inhibitor Using an In Silico Enabled Drug Discovery Platform.

Igawa, H.Konst, Z.A.Therrien, E.Shelley, M.Koldso, H.Bos, P.H.Negri, A.Verras, A.Guo, J.Dahlgren, M.K.Levinson, A.Parr, B.T.Kurhade, S.E.Latthe, P.Shetty, R.Santhanakrishnan, S.Amberg-Johnson, K.Futran, A.S.Atsriku, C.Pelletier, R.D.Liu, Z.Bell, J.A.Bhat, S.Svensson, M.Gerasyuto, A.I.

(2024) J Med Chem 67: 21811-21840

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01405
  • Primary Citation of Related Structures:  
    9D3V, 9D3W

  • PubMed Abstract: 

    Despite the success of first, second, and third generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) for non-small cell lung cancer with classical EGFR mutations (L858R or Exon 19 deletions), disease progression occurs due to the acquisition of T790M and C797S resistance. Herein, we report a physics-based computationally driven lead identification approach that identified structurally unique imidazo[3.2- b ]pyrazoles as reversible and wild-type-sparing EGFR TKIs of classical mutations bearing both T790M and C797S. During profiling of imidazo[3.2- b ]pyrazoles, we elucidated the bioactivation mechanism causing CYP3A4/5 time-dependent inhibition (TDI) and found key modifications to mitigate the TDI. Compound 31 inhibited EGFR L858R/T790M/C797S in biochemical assays with a K i = 2.1 nM and EGFR del19/T790M/C797S in a Ba/F3 cellular assay with an IC 50 = 56.9 nM. The deuterated analogue of 31 ( 38 ) demonstrated dose-dependent tumor growth inhibition in a Ba/F3 EGFR del19/T790M/C797S CDX model by 47% at 50 mg/kg BID and 92% at 100 mg/kg BID.


  • Organizational Affiliation
    • Schrödinger Inc., New York, New York 10036, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor330Homo sapiensMutation(s): 6 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.329 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.299 (Depositor), 0.222 (DCC) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.736α = 90
b = 145.736β = 90
c = 145.736γ = 90
Software Package:
Software NamePurpose
PRIME-Xrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-03-05 
  • Deposition Author(s): Bell, J.A.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release