5EM8

EGFR kinase domain with pyridone compound 13: 4-[(2-methoxyphenyl)amino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb5EM8/pdb

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


• Deposited: 2015-11-05 Released: 2015-12-30 
• Deposition Author(s): Eigenbrot, C., Yu, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Pyridones as Highly Selective, Noncovalent Inhibitors of T790M Double Mutants of EGFR.

Bryan, M.C., Burdick, D.J., Chan, B.K., Chen, Y., Clausen, S., Dotson, J., Eigenbrot, C., Elliott, R., Hanan, E.J., Heald, R., Jackson, P., La, H., Lainchbury, M., Malek, S., Mann, S.E., Purkey, H.E., Schaefer, G., Schmidt, S., Seward, E., Sideris, S., Wang, S., Yen, I., Yu, C., Heffron, T.P.

(2016) ACS Med Chem Lett 7: 100-104

• PubMed: 26819674 
• DOI: https://doi.org/10.1021/acsmedchemlett.5b00428
• Primary Citation of Related Structures:  
  5EM5, 5EM6, 5EM7, 5EM8


• PubMed Abstract: 
  

  The rapid advancement of a series of noncovalent inhibitors of T790M mutants of EGFR is discussed. The optimization of pyridone 1, a nonselective high-throughput screening hit, to potent molecules with high levels of selectivity over wtEGFR and the broader kinome is described herein.

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Organizational Affiliation: 

Genentech , South San Francisco, California 94080, United States.

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: 38.08 kDa 
• Atom Count: 2,449 
• Modelled Residue Count: 303 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	331	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
5Q4	B [auth A]	4-[(2-methoxyphenyl)amino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide C24 H27 N5 O3 DWKPGVACBGLMCU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5Q4	BindingDB:  5EM8	Ki: min: 19, max: 1090 (nM) from 2 assay(s)
		EC50: 1090 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.661	α = 90
b = 147.661	β = 90
c = 147.661	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Eigenbrot, C., Yu, C.

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2016-02-10
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Data collection, Derived calculations
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references