7VRA

The crystal structure of EGFR T790M/C797S with the inhibitor HC5476


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Conformational Constrained 4-(1-Sulfonyl-3-indol)yl-2-phenylaminopyrimidine Derivatives as New Fourth-Generation Epidermal Growth Factor Receptor Inhibitors Targeting T790M/C797S Mutations.

Chen, H.Lai, M.Zhang, T.Chen, Y.Tong, L.Zhu, S.Zhou, Y.Ren, X.Ding, J.Xie, H.Lu, X.Ding, K.

(2022) J Med Chem 65: 6840-6858

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00168
  • Primary Citation of Related Structures:  
    7VRA, 7VRE

  • PubMed Abstract: 

    Tertiary C797S mutation of epidermal growth factor receptor (EGFR)-mediated resistance in non-small-cell-lung-cancer (NSCLC) patients is still an unmet clinical need. Several classes of adenosine 5'-triphosphate-competitive or allosteric EGFR T790M/C797S inhibitors and degraders have been developed, but none of them have received approval from the regulatory agencies. Herein, we report the structure-based design of conformational constrained 4-(1-ethylsufonyl-3-indolyl)-2-phenylaminopyrimidines as new EGFR T790M/C797S inhibitors by using a macrocyclization strategy. Representative compound 18j potently inhibited EGFR 19del/T790M/C797S and EGFR L858R/T790M/C797S mutants with IC 50 values of 15.8 and 23.6 nM and suppressed Ba/F3-EGFR L858R/T790M/C797S and Ba/F3-EGFR 19del/T790M/C797S cells with IC 50 values of 0.036 and 0.052 μM, respectively, which is 10-20-fold more potent than brigatinib. 18j also potently inhibited the EGFR 19del/T790M/C797S -mutated PC-9-OR NSCLC cell proliferation with an IC 50 value of 0.644 μM but was less potent for parental Ba/F3 and A431 cells. This study provides a new lead compound for drug discovery to combat EGFR C797S -mediated resistance in NSCLC patients.


  • 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 and the 1st Affiliated Hospital (Huaqiao Hospital), 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): 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I0A (Subject of Investigation/LOI)
Query on I0A

Download Ideal Coordinates CCD File 
B [auth A]25-chloro-11-(ethylsulfonyl)-44-morpholino-11H-5,12-dioxa-3-aza-1(3,6)-indola-2(4,2)-pyrimidina-4(1,3)-benzenacyclododecaphane
C30 H34 Cl N5 O5 S
KBYYUDNRZUURRS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.973α = 90
b = 144.973β = 90
c = 144.973γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-06-08 
  • Deposition Author(s): Zhu, S.J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81903539

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description