4WKQ | pdb_00004wkq

1.85 angstrom structure of EGFR kinase domain with gefitinib

• PDB DOI: https://doi.org/10.2210/pdb4WKQ/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-10-03 Released: 2014-11-05 
• Deposition Author(s): Yosaatmadja, Y., Squire, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.225 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

1.85 angstrom structure of EGFR kinase domain with gefitinib

Yosaatmadja, Y., Squire, C.J., McKeage, M., Flanagan, J.U.

To be published.

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: 38.24 kDa 
• Atom Count: 2,503 
• Modeled Residue Count: 297 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	330	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IRE	B [auth A]	Gefitinib C22 H24 Cl F N4 O3 XGALLCVXEZPNRQ-UHFFFAOYSA-N
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
IRE	BindingDB:  4WKQ	Ki: min: 0.4, max: 26 (nM) from 8 assay(s)
		Kd: min: 0.52, max: 940 (nM) from 26 assay(s)
		IC50: min: 0.1, max: 1000 (nM) from 118 assay(s)
		EC50: min: 35, max: 2162 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.225 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.714	α = 90
b = 143.714	β = 90
c = 143.714	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Yosaatmadja, Y., Squire, C.J.

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.3: 2024-03-27
  Changes: Data collection