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

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41589-018-0204-3
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor332Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8LU (Subject of Investigation/LOI)
Query on 8LU

Download Ideal Coordinates CCD File 
B [auth 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
Experimental Data & Validation

Experimental Data

  • 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 = 148.291α = 90
b = 148.291β = 90
c = 148.291γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description