9KL4 | pdb_00009kl4

Crystal structure of EGFR complexed with N-[4-[4-amino-6-ethynyl-5-(3-quinolyl)pyrrolo[2,3-d]pyrimidin-7-yl]norbornan-1-yl]pyrimidine-5-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.238 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

TAS3351 is a brain penetrable EGFR-TKI that overcomes T790M and C797S resistant mutations.

Kasuga, H.Kataoka, Y.Yamamoto, F.Miyamoto, R.Tsuji, S.Suzuki, T.Mizuarai, S.

(2026) Commun Med (Lond) 

  • DOI: https://doi.org/10.1038/s43856-026-01546-1
  • Primary Citation Related Structures: 
    9KL4, 9KLW

  • PubMed Abstract: 

    Activating mutations in the epidermal growth factor receptor (EGFR), particularly exon 19 deletions and L858R mutation, are frequently observed in non-small cell lung cancer (NSCLC) and confer sensitivity to EGFR-tyrosine kinase inhibitors (EGFR-TKIs). Among these EGFR-TKIs, osimertinib is currently the standard of care for patients with NSCLC harboring the activating mutations. However, resistant mutations often arise, leading to resistance to osimertinib. The resistant mutation that most frequently occurs in EGFR during osimertinib treatment is the C797S mutation. Another major resistant mutation arising in EGFR during treatment with other EGFR-TKIs, such as gefitinib and afatinib, is the T790M mutation. Currently, no approved EGFR-TKIs are effective in patients who simultaneously develop the T790M and C797S mutations. Additionally, brain metastasis often causes disease progression due to reduced drug penetration into the brain. We conducted preclinical evaluations of TAS3351, a fourth-generation EGFR-TKI, including biochemical, structural, and in vitro/in vivo pharmacological assays. We also evaluated the efflux transporter susceptibility and brain penetrability of TAS3351 in male mice. Here, we demonstrate that TAS3351 overcomes resistance due to T790M and C797S mutations while sparing wild-type EGFR activity. Furthermore, TAS3351 is not a substrate of P-glycoprotein (P-gp) and the breast cancer-resistant protein (BCRP) and exhibits significant brain penetrability, resulting in anti-tumor efficacy in mice with intracranial allografts. These findings indicate that TAS3351 is a promising therapeutic candidate for patients with NSCLC whose tumors have relapsed or are refractory to treatment due to the C797S and T790M mutations, and the brain metastases.


  • Organizational Affiliation
    • Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Japan. h-kasuga@taiho.co.jp.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor330Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L53 (Subject of Investigation/LOI)
Query on A1L53

Download Ideal Coordinates CCD File 
B [auth A]N-[4-[4-amino-6-ethynyl-5-(3-quinolyl)pyrrolo[2,3-d]pyrimidin-7-yl]norbornan-1-yl]pyrimidine-5-carboxamide
C29 H24 N8 O
JTIOULFGKCXQAT-ISILISOKSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.238 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.92α = 90
b = 146.92β = 90
c = 146.92γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2026-04-15
    Changes: Database references