Crystal structure of EGFR 696-1022 T790M in complex with XTF-262

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


A structure-guided optimization of pyrido[2,3-d]pyrimidin-7-ones as selective inhibitors of EGFR(L858R/T790M) mutant with improved pharmacokinetic properties.

Yu, L.Huang, M.Xu, T.Tong, L.Yan, X.E.Zhang, Z.Xu, Y.Yun, C.Xie, H.Ding, K.Lu, X.

(2017) Eur J Med Chem 126: 1107-1117

  • DOI: https://doi.org/10.1016/j.ejmech.2016.12.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Structural optimization of pyrido[2,3-d]pyrimidin-7-ones was conducted to yield a series of new selective EGFR T790M inhibitors with improved pharmacokinetic properties. One of the most promising compound 9s potently suppressed EGFR L858R/T790M kinase and inhibited the proliferation of H1975 cells with IC 50 values of 2.0 nM and 40 nM, respectively. The compound dose-dependently induced reduction of the phosphorylation of EGFR and downstream activation of ERK in NCIH1975 cells. It also exhibited moderate plasma exposure after oral administration and an oral bioavailability value of 16%. Compound 9s may serve as a promising lead compound for further drug discovery overcoming the acquired resistance of non-small cell lung cancer (NSCLC) patients.

  • Organizational Affiliation

    Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor331Homo sapiensMutation(s): 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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on F62

Download Ideal Coordinates CCD File 
B [auth A]N-[3-[2-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]-5-methyl-7-oxidanylidene-pyrido[2,3-d]pyrimidin-8-yl]phenyl]prop-2-enamide
C29 H31 N7 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
F62 BindingDB:  5GMP IC50: min: 330, max: 386 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.343α = 90
b = 145.343β = 90
c = 145.343γ = 90
Software Package:
Software NamePurpose
DENZOdata 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: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Data collection
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description