8GC8 | pdb_00008gc8

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

• PDB DOI: https://doi.org/10.2210/pdb8GC8/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-03-01 Released: 2024-01-31 
• Deposition Author(s): Gajewski, S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 38301010 
• DOI: https://doi.org/10.1126/science.adi5798
• Primary Citation 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.

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Organizational Affiliation: 
• Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA.
Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Nurix Therapeutics, San Francisco, CA, USA.
Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
K.G. Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY, USA.
Division of Hematology-Oncology, Department of Medicine at Zucker School of Medicine at Hofstra/Northwell, CLL Research and Treatment Center, Lake Success, NY, USA.
Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Gene Editing and Screening Core Facility, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA.
Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.28 kDa 
• Atom Count: 2,212 
• Modeled Residue Count: 253 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A	270	Homo sapiens	Mutation(s): 1  Gene Names: BTK, AGMX1, ATK, BPK 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YXJ (Subject of Investigation/LOI)	B [auth A]	5-(piperidin-1-yl)-3-[4-(piperidin-4-yl)anilino]pyrazine-2-carboxamide C21 H28 N6 O VGSQWWPMYSJONU-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.38	α = 90
b = 72.4	β = 90
c = 104.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• 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