3W2S

EGFR kinase domain with compound4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure-Based Approach for the Discovery of Pyrrolo[3,2-d]pyrimidine-Based EGFR T790M/L858R Mutant Inhibitors.

Sogabe, S., Kawakita, Y., Igaki, S., Iwata, H., Miki, H., Cary, D.R., Takagi, T., Takagi, S., Ohta, Y., Ishikawa, T.

(2013) ACS Med Chem Lett 4: 201-205

  • DOI: 10.1021/ml300327z
  • Primary Citation of Related Structures:  
    3W2O, 3W2P, 3W2Q, 3W2R, 3W2S

  • PubMed Abstract: 

    • The epidermal growth factor receptor (EGFR) family plays a critical role in vital cellular processes and in various cancers. Known EGFR inhibitors exhibit distinct antitumor responses against the various EGFR mutants associated with nonsmall-cell lung cancer ...

    The epidermal growth factor receptor (EGFR) family plays a critical role in vital cellular processes and in various cancers. Known EGFR inhibitors exhibit distinct antitumor responses against the various EGFR mutants associated with nonsmall-cell lung cancer. The L858R mutation enhances clinical sensitivity to gefitinib and erlotinib as compared with wild type and reduces the relative sensitivity to lapatinib. In contrast, the T790M mutation confers drug resistance to gefitinib and erlotinib. We determined crystal structures of the wild-type and T790M/L858R double mutant EGFR kinases with reversible and irreversible pyrrolo[3,2-d]pyrimidine inhibitors based on analogues of TAK-285 and neratinib. In these structures, M790 adopts distinct conformations to accommodate different inhibitors, whereas R858 allows conformational variations of the activation loop. These results provide structural insights for understanding the structure-activity relationships that should contribute to the development of potent inhibitors against drug-sensitive or -resistant EGFR mutations.

    Organizational Affiliation: 

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epidermal growth factor receptorA330Homo sapiensMutation(s): 0 
Gene Names: EGFR, ERBB, ERBB1, HER1
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
NIH Common Fund Data Resources
PHAROS:  P00533
GTEx:  ENSG00000146648
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
W2R
Query on W2R
Download Ideal Coordinates CCD File 
 B [auth A]1-{3-[2-chloro-4-({5-[2-(2-hydroxyethoxy)ethyl]-5H-pyrrolo[3,2-d]pyrimidin-4-yl}amino)phenoxy]phenyl}-3-cyclohexylurea
C29 H33 Cl N6 O4
WDGCQQKABPWBPZ-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
 C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
W2RIC50:  6.900000095367432   nM  BindingDB
W2RIC50 :  6.900000095367432   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.759α = 90
b = 68.446β = 90
c = 105.02γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Database references
  • Version 1.2: 2019-12-25
    Changes: Database references