Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 38.74 kDa 
• Atom Count: 2353 
• Residue Count: 292 
• Unique protein chains: 1

5Y25

EGFR kinase domain mutant (T790M/L858R) with covalent ligand NS-062

• DOI: 10.2210/pdb5Y25/pdb

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


• Deposited: 2017-07-24 Released: 2018-07-25 
• Deposition Author(s): Shiroishi, M., Abe, Y., Caaveiro, J.M.M., Sakamoto, S., Morimoto, S., Fuchida, H., Shindo, N., Ojida, A.
• Funding Organization(s): Network Joint Research Center for Materials and Devices (MEXT,Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 

Literature

Selective and reversible modification of kinase cysteines with chlorofluoroacetamides.

Shindo, N., Fuchida, H., Sato, M., Watari, K., Shibata, T., Kuwata, K., Miura, C., Okamoto, K., Hatsuyama, Y., Tokunaga, K., Sakamoto, S., Morimoto, S., Abe, Y., Shiroishi, M., Caaveiro, J.M.M., Ueda, T., Tamura, T., Matsunaga, N., Nakao, T., Koyanagi, S., Ohdo, S., Yamaguchi, Y., Hamachi, I., Ono, M., Ojida, A.

(2019) Nat Chem Biol 15: 250-258

• PubMed: 30643284 
• DOI: 10.1038/s41589-018-0204-3
• Primary Citation of Related Structures:  
  5Y25


• PubMed Abstract: 
  

Irreversible inhibition of disease-associated proteins with small molecules is a powerful approach for achieving increased and sustained pharmacological potency. Here, we introduce α-chlorofluoroacetamide (CFA) as a novel warhead of targeted covalent inhibitor (TCI). Despite weak intrinsic reactivity, CFA-appended quinazoline showed high reactivity toward Cys797 of epidermal growth factor receptor (EGFR). In cells, CFA-quinazoline showed higher target specificity for EGFR than the corresponding Michael acceptors in a wide concentration range (0.1-10 μM). The cysteine adduct of the CFA derivative was susceptible to hydrolysis and reversibly yielded intact thiol but was stable in solvent-sequestered ATP-binding pocket of EGFR. This environment-dependent hydrolysis can potentially reduce off-target protein modification by CFA-based drugs. Oral administration of CFA quinazoline NS-062 significantly suppressed tumor growth in a mouse xenograft model. Further, CFA-appended pyrazolopyrimidine irreversibly inhibited Bruton's tyrosine kinase with higher target specificity. These results demonstrate the utility of CFA as a new class warheads for TCI.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	332	Homo sapiens	Mutation(s): 2  Gene Names: EGFR, ERBB, ERBB1, HER1 EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens) Explore P00533  Go to UniProtKB:  P00533
NIH Common Fund Data Resources
PHAROS:  P00533 GTEx:  ENSG00000146648

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8LU	A	(2R)-N-[4-[(3-chloranyl-4-fluoranyl-phenyl)amino]-7-(3-morpholin-4-ylpropoxy)quinazolin-6-yl]-1-(2-fluoranylethanoyl)pyrrolidine-2-carboxamide C28 H31 Cl F2 N6 O4 NMRZVTKIRUUAHS-XMMPIXPASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.291	α = 90
b = 148.291	β = 90
c = 148.291	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-07-24 
• Released Date: 2018-07-25 
Deposition Author(s): Shiroishi, M., Abe, Y., Caaveiro, J.M.M., Sakamoto, S., Morimoto, S., Fuchida, H., Shindo, N., Ojida, A.

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Funding Organization	Location	Grant Number
Network Joint Research Center for Materials and Devices (MEXT,Japan)	Japan	--

Revision History 

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2019-08-07
  Changes: Data collection, Database references