8EME

EGFR(T790M/V948R) in complex with ZNL-0056

• PDB DOI: https://doi.org/10.2210/pdb8EME/pdb

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


• Deposited: 2022-09-27 Released: 2023-10-18 
• Deposition Author(s): Beyett, T.S., Eck, M.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 0.318 
• R-Value Work: 0.283 
• R-Value Observed: 0.285 

Literature

Molecular Bidents with Two Electrophilic Warheads as a New Pharmacological Modality

Li, Z., Jiang, J., Ficarro, S.B., Beyett, T.S., To, C., Tavares, I., Zhu, Y., Li, J., Eck, M.J., Janne, P.A., Marto, J.A., Zhang, T., Che, J., Gray, N.S.

(2024) ACS Cent Sci 

• DOI: https://doi.org/10.1021/acscentsci.3c01245

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 75.93 kDa 
• Atom Count: 4,461 
• Modelled Residue Count: 549 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A [auth B], B [auth A]	331	Homo sapiens	Mutation(s): 2  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
ZNL (Subject of Investigation/LOI)	C [auth B]	N-{7-methyl-1-[(3S)-1-(prop-2-enoyl)azepan-3-yl]-1H-benzimidazol-2-yl}-5-(prop-2-enamido)thiophene-3-carboxamide C25 H27 N5 O3 S DZTGCJZKRUDIGP-SFHVURJKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 0.318 
• R-Value Work: 0.283 
• R-Value Observed: 0.285 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.874	α = 90
b = 99.992	β = 100.8
c = 87.023	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Beyett, T.S., Eck, M.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R01CA116020-16

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Database references