8WD4 | pdb_00008wd4

EGFR(L858R/T790/C797S) in complex with compound 5j

• PDB DOI: https://doi.org/10.2210/pdb8WD4/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-09-14 Released: 2023-12-20 
• Deposition Author(s): Nishikawa, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.230 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Synthesis, activity, and their relationships of 2,4-diaminonicotinamide derivatives as EGFR inhibitors targeting C797S mutation.

Kageji, H., Momose, T., Nagamoto, Y., Togashi, N., Yasumatsu, I., Nishikawa, Y., Kihara, K., Hiramoto, K., Minami, M., Kasanuki, N., Isoyama, T., Naito, H.

(2023) Bioorg Med Chem Lett 98: 129575-129575

• PubMed: 38065292 
• DOI: https://doi.org/10.1016/j.bmcl.2023.129575
• Primary Citation Related Structures: 
  8WD4


• PubMed Abstract: 
  

  The C797S mutation is one of the major factors behind resistance to the third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors. Herein, we describe the discovery of the 2,4-diaminonicotinamide derivative 5j, which shows potent inhibitory activity against EGFR del19/T790M/C797S and L858R/T790M/C797S. We also report the structure-activity relationship of the 2,4-diaminonicotinamide derivatives and the co-crystal structure of 5j and EGFR del19/T790M/C797S.

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Organizational Affiliation: 
• R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. Electronic address: [e-mail].
R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.
Daiichi Sankyo RD Novare Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.
Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.98 kDa 
• Atom Count: 2,471 
• Modeled Residue Count: 299 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	329	Homo sapiens	Mutation(s): 3  Gene Names: EGFR 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W7W (Subject of Investigation/LOI)	B [auth A]	~{N}-[3,3-bis(fluoranyl)propyl]-4-[[(2~{S})-butan-2-yl]amino]-6-[[2-(1-cyclopropylsulfonylpyrazol-4-yl)pyrimidin-4-yl]amino]pyridine-3-carboxamide C23 H28 F2 N8 O3 S MXDOLPJSGCLVEB-AWEZNQCLSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.230 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.327	α = 90
b = 145.327	β = 90
c = 145.327	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Nishikawa, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release
  
• Version 1.1: 2024-01-03
  Changes: Database references