4HJO

Crystal structure of the inactive EGFR tyrosine kinase domain with erlotinib

• PDB DOI: https://doi.org/10.2210/pdb4HJO/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-10-13 Released: 2012-11-14 
• Deposition Author(s): Park, J.H., Lemmon, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.253 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 

Starting Model: experimental

Literature

Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain.

Park, J.H., Liu, Y., Lemmon, M.A., Radhakrishnan, R.

(2012) Biochem J 448: 417-423

• PubMed: 23101586 
• DOI: https://doi.org/10.1042/BJ20121513
• Primary Citation of Related Structures:  
  4HJO


• PubMed Abstract: 
  

  Erlotinib and gefitinib, tyrosine kinase inhibitors used to block EGFR (epidermal growth factor receptor) signalling in cancer, are thought to bind only the active conformation of the EGFR-TKD (tyrosine kinase domain). Through parallel computational and crystallographic studies, we show in the present study that erlotinib also binds the inactive EGFR-TKD conformation, which may have significant implications for its use in EGFR-mutated cancers.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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: 38.95 kDa 
• Atom Count: 2,264 
• Modelled Residue Count: 278 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	337	Homo sapiens	Mutation(s): 1  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
AQ4	B [auth A]	[6,7-BIS(2-METHOXY-ETHOXY)QUINAZOLINE-4-YL]-(3-ETHYNYLPHENYL)AMINE C22 H23 N3 O4 AAKJLRGGTJKAMG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AQ4	BindingDB:  4HJO	Ki: min: 0.1, max: 136 (nM) from 6 assay(s)
		Kd: min: 0.35, max: 970 (nM) from 16 assay(s)
		IC50: min: 0.03, max: 260 (nM) from 71 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.253 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.967	α = 90
b = 114.284	β = 90
c = 84.918	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Park, J.H., Lemmon, M.A.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description