5Y25

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.102 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1038/s41589-018-0204-3

  • 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 ...

    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 Engineering, Kyoto University, Kyoto, Japan.,Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.,Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo, Japan.,Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan. ojida@phar.kyushu-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A
332Homo sapiensMutation(s): 2 
Gene Names: EGFR (ERBB, ERBB1, HER1)
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Go to Gene View: EGFR
Go to UniProtKB:  P00533
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8LU
Query on 8LU

Download SDF File 
Download CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.102 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 148.291α = 90.00
b = 148.291β = 90.00
c = 148.291γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant 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
    Type: Data collection, Database references