5J9Y

EGFR-T790M in complex with pyrazolopyrimidine inhibitor 1b

• PDB DOI: https://doi.org/10.2210/pdb5J9Y/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-04-11 Released: 2016-08-17 
• Deposition Author(s): Becker, C., Engel, J., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Insight into the Inhibition of Drug-Resistant Mutants of the Receptor Tyrosine Kinase EGFR.

Engel, J., Becker, C., Lategahn, J., Keul, M., Ketzer, J., Muhlenberg, T., Kollipara, L., Schultz-Fademrecht, C., Zahedi, R.P., Bauer, S., Rauh, D.

(2016) Angew Chem Int Ed Engl 55: 10909-10912

• PubMed: 27496389 
• DOI: https://doi.org/10.1002/anie.201605011
• Primary Citation of Related Structures:  
  5J9Y, 5J9Z


• PubMed Abstract: 
  

  Targeting acquired drug resistance represents the major challenge in the treatment of EGFR-driven non-small-cell lung cancer (NSCLC). Herein, we describe the structure-based design, synthesis, and biological evaluation of a novel class of covalent EGFR inhibitors that exhibit excellent inhibition of EGFR-mutant drug-resistant cells. Protein X-ray crystallography combined with detailed kinetic studies led to a deeper understanding of the mode of inhibition of EGFR-T790M and provided insight into the key principles for effective inhibition of the recently discovered tertiary mutation at EGFR-C797S.

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Organizational Affiliation: 

Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.36 kDa 
• Atom Count: 2,452 
• Modelled Residue Count: 300 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	323	Homo sapiens	Mutation(s): 0  Gene Names: EGFR, ERBB, ERBB1, HER1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6HL	B [auth A]	(R)-1-(3-(4-amino-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl)prop-2-en-1-one C23 H22 N6 O WAJKANXMXJLTKT-MRXNPFEDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6HL	BindingDB:  5J9Y	IC50: min: 1.9, max: 7900 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.39	α = 90
b = 144.39	β = 90
c = 144.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Becker, C., Engel, J., Rauh, D.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2016-09-07
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary