6JRK

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

• PDB DOI: https://doi.org/10.2210/pdb6JRK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2019-04-04 Released: 2020-04-15 
• Deposition Author(s): Zhu, S.J., Yun, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.200 

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

• PubMed: 31298540 
• 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.08 kDa 
• Atom Count: 2,316 
• Modelled Residue Count: 283 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	331	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C6O	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 
• R-Value Work: 0.196 
• R-Value Observed: 0.200 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.542	α = 90
b = 146.542	β = 90
c = 146.542	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Zhu, S.J., Yun, C.H.

Revision History  

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