5GMP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.797 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.ejmech.2016.12.006

  • PubMed Abstract: 
  • Structural optimization of pyrido[2,3-d]pyrimidin-7-ones was conducted to yield a series of new selective EGFR <sup>T790M </sup> inhibitors with improved pharmacokinetic properties. One of the most promising compound 9s potently suppressed EGFR <sup> ...

    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.,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China; School of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510632, China. Electronic address: ding_ke@gibh.ac.cn.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China. Electronic address: hxie@simm.ac.cn.,School of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510632, China. Electronic address: luxy2016@jnu.edu.cn.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.,Peking University Institute of Systems Biomedicine and Department of Biophysics, Peking University Health Science Center, Beijing 100191, China.,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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A
331Homo sapiensMutation(s): 1 
Gene Names: EGFR (ERBB, ERBB1, HER1)
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Go to Gene View: EGFR
Go to UniProtKB:  P00533
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F62
Query on F62

Download SDF File 
Download CCD File 
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
VJQPNQROUWVJQN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.797 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 145.343α = 90.00
b = 145.343β = 90.00
c = 145.343γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-14 
  • Released Date: 2017-06-28 
  • Deposition Author(s): Yan, X.E., Yun, C.H.

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-10-04
    Type: Data collection