8GC8

Bruton's tyrosine kinase L528W mutant in complex with 5-(piperidin-1-yl)-3-{[4-(piperidin-4-yl)phenyl]amino}pyrazine-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Kinase-impaired BTK mutations are susceptible to clinical-stage BTK and IKZF1/3 degrader NX-2127.

Montoya, S.Bourcier, J.Noviski, M.Lu, H.Thompson, M.C.Chirino, A.Jahn, J.Sondhi, A.K.Gajewski, S.Tan, Y.S.M.Yung, S.Urban, A.Wang, E.Han, C.Mi, X.Kim, W.J.Sievers, Q.Auger, P.Bousquet, H.Brathaban, N.Bravo, B.Gessner, M.Guiducci, C.Iuliano, J.N.Kane, T.Mukerji, R.Reddy, P.J.Powers, J.Sanchez Garcia de Los Rios, M.Ye, J.Barrientos Risso, C.Tsai, D.Pardo, G.Notti, R.Q.Pardo, A.Affer, M.Nawaratne, V.Totiger, T.M.Pena-Velasquez, C.Rhodes, J.M.Zelenetz, A.D.Alencar, A.Roeker, L.E.Mehta, S.Garippa, R.Linley, A.Soni, R.K.Skanland, S.S.Brown, R.J.Mato, A.R.Hansen, G.M.Abdel-Wahab, O.Taylor, J.

(2024) Science 383: eadi5798-eadi5798

  • DOI: https://doi.org/10.1126/science.adi5798
  • Primary Citation of Related Structures:  
    8GC7, 8GC8

  • PubMed Abstract: 

    Increasing use of covalent and noncovalent inhibitors of Bruton's tyrosine kinase (BTK) has elucidated a series of acquired drug-resistant BTK mutations in patients with B cell malignancies. Here we identify inhibitor resistance mutations in BTK with distinct enzymatic activities, including some that impair BTK enzymatic activity while imparting novel protein-protein interactions that sustain B cell receptor (BCR) signaling. Furthermore, we describe a clinical-stage BTK and IKZF1/3 degrader, NX-2127, that can bind and proteasomally degrade each mutant BTK proteoform, resulting in potent blockade of BCR signaling. Treatment of chronic lymphocytic leukemia with NX-2127 achieves >80% degradation of BTK in patients and demonstrates proof-of-concept therapeutic benefit. These data reveal an oncogenic scaffold function of mutant BTK that confers resistance across clinically approved BTK inhibitors but is overcome by BTK degradation in patients.


  • Organizational Affiliation

    Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK270Homo sapiensMutation(s): 1 
Gene Names: BTKAGMX1ATKBPK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
PHAROS:  Q06187
GTEx:  ENSG00000010671 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.38α = 90
b = 72.4β = 90
c = 104.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YXJClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2024-01-31 
  • Deposition Author(s): Gajewski, S.

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-02-14
    Changes: Database references
  • Version 1.2: 2024-02-21
    Changes: Database references