6JRK | pdb_00006jrk

The structure of co-crystals of 8r-B-EGFR WT complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.236 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

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This is version 1.1 of the entry. See complete history. 


Literature

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.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor331Homo sapiensMutation(s): 3 
Gene Names: EGFR, ERBB, ERBB1, HER1
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C6O
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
REZLHNFSSBBSFC-DEOSSOPVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.236 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.542α = 90
b = 146.542β = 90
c = 146.542γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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