7ER2

Crystal structure of EGFR 696-1022 T790M/C797S in complex with LS_2_40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Optimization of Brigatinib as New Wild-Type Sparing Inhibitors of EGFR T790M/C797S Mutants.

Li, S.Zhang, T.Zhu, S.J.Lei, C.Lai, M.Peng, L.Tong, L.Pang, Z.Lu, X.Ding, J.Ren, X.Yun, C.H.Xie, H.Ding, K.

(2022) ACS Med Chem Lett 13: 196-202

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00555
  • Primary Citation of Related Structures:  
    7ER2

  • PubMed Abstract: 

    A series of brigatinib derivatives were designed and synthesized as new potent and selective EGFR T790M/C797S inhibitors. One of the most potent and selective compounds 18k strongly suppressed the EGFR L858R/T790M/C797S and EGFR 19Del/T790M/C797S kinases with IC 50 values of 0.7 and 3.6 nM, respectively, which were over 54-fold more potent than the lead compound. 18k also demonstrated promising EGFR T790M/C797S mutant selectivity, and was 94-fold less potent against the wild type EGFR. A cocrystal structure of EGFR T790M/C797S with a close derivative 18f was solved to provide insight on the inhibitor's binding mode. Moreover, compound 18k was orally bioavailable and demonstrated highly desirable PK properties, making it a promising lead compound for further structural optimization.


  • Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 855 Xingye Avenue East, Guangzhou 511436, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor331Homo sapiensMutation(s): 2 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JAU (Subject of Investigation/LOI)
Query on JAU

Download Ideal Coordinates CCD File 
B [auth A]5-chloranyl-N2-[3-chloranyl-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]-N4-(2-dimethylphosphorylphenyl)pyrimidine-2,4-diamine
C28 H36 Cl2 N7 O P
YVGYDPFKZQBIRJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JAU BindingDB:  7ER2 IC50: min: 0.6, max: 38 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.200 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.926α = 90
b = 145.926β = 90
c = 145.926γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description