The structure of co-crystals of 8r-B-EGFR T790M/C797S complex

Experimental Data Snapshot

  • Resolution: 2.94 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

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Structure-Based Design of 5-Methylpyrimidopyridone Derivatives as New Wild-Type Sparing Inhibitors of the Epidermal Growth Factor Receptor Triple Mutant (EGFRL858R/T790M/C797S).

Shen, J.Zhang, T.Zhu, S.J.Sun, M.Tong, L.Lai, M.Zhang, R.Xu, W.Wu, R.Ding, J.Yun, C.H.Xie, H.Lu, X.Ding, K.

(2019) J Med Chem 62: 7302-7308

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00576
  • Primary Citation of Related Structures:  
    6JRJ, 6JRK

  • PubMed Abstract: 

    Tertiary EGFR C797S mutation induced resistance against osimertinib ( 1 ) is an emerging "unmet clinical need" for non-small-cell lung cancer (NSCLC) patients. A series of 5-methylpyrimidopyridone derivatives were designed and synthesized as new selective EGFR L858R/T790M/C797S inhibitors. A representative compound, 8r-B , exhibited an IC 50 of 27.5 nM against the EGFR L858R/T790M/C797S mutant, while being a significantly less potent for EGFR WT (IC 50 > 1.0 μM). Cocrystallographic structure determination and computational investigation were conducted to elucidate its target selectivity.

  • Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy , Jinan University , 601 Huangpu Avenue West , Guangzhou 510632 , China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor331Homo sapiensMutation(s): 5 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C6O

Download Ideal Coordinates CCD File 
B [auth A]6-(2-chloranyl-3-fluoranyl-phenyl)-5-methyl-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[(3S)-1-propanoylpiperidin-3-yl]pyrido[2,3-d]pyrimidin-7-one
C34 H39 Cl F N7 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.94 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.072α = 90
b = 148.072β = 90
c = 148.072γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Advisory, Data collection, Database references