9ZQV | pdb_00009zqv

Crystal structure of wild-type Bruton's Tyrosine Kinase (BTK) in the apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9ZQV

This is version 1.1 of the entry. See complete history

Literature

Molecular and Structural Basis of Pan-Resistance to BTK Degraders and Inhibitors.

Sievers, Q.Lu, H.Cool, A.Gajewski, S.Kong, T.Noviski, M.A.Whelan, S.Wang, Y.Mendoza Navarrete, L.Mi, X.Ficici, E.Mukerji, R.Iuliano, J.N.Ye, J.Sanchez Garcia De Los Rios, M.Bousquet, H.Tan, M.Brathaban, N.Narasappa, N.Lu, Y.W.Elechko, J.Maron, M.I.Phelps, C.B.Rahman, J.Notti, R.Q.Sekeres, S.Lamkin, E.N.Bravo, E.Alencar, A.Ewalt, M.D.Islam, P.Mato, A.R.Roeker, L.Bhatt, S.Taylor, J.Thompson, M.C.Hansen, G.M.Abdel-Wahab, O.

(2026) Cancer Discov 

  • DOI: https://doi.org/10.1158/2159-8290.CD-26-0251
  • Primary Citation Related Structures: 
    9YT9, 9ZQV

  • PubMed Abstract: 

    Early-phase clinical trials of Bruton's tyrosine kinase (BTK) degraders have demonstrated efficacy in patients with BTK inhibitor-resistant chronic lymphocytic leukemia (CLL). How clinical resistance to BTK degraders arises is unknown. Here we sequenced serial CLL samples from patients enrolled in the phase I trials of zelebrudomide and bexobrutideg and observed recurrent expansion of preexisting BTK A428D mutations at relapse. Unlike previously studied BTK inhibitor resistance mutations, BTK A428D conferred pan-resistance to BTK inhibitors and degraders. In the absence of BTK-directed therapies, however, cells bearing BTK A428D exhibited a competitive disadvantage. A crystal structure of BTK A428D revealed that the mutant aspartate clashes with the adenine ring of ATP and the adenine-mimetic moiety of BTK inhibitors and degraders. Combining BTK degraders with venetoclax mitigated the expansion of BTK A428D. These results provide the molecular basis for clinical resistance to BTK degraders and will inform the development of next-generation BTK degrader therapies.


  • Organizational Affiliation
    • Memorial Sloan Kettering Cancer Center New York, NY United States.

Macromolecule Content 

  • Total Structure Weight: 31.96 kDa 
  • Atom Count: 2,503 
  • Modeled Residue Count: 270 
  • Deposited Residue Count: 270 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK270Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000010671 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
D [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.1α = 90
b = 76.92β = 90
c = 106.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-07-15 
  • Deposition Author(s): Gajewski, S.

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-15
    Type: Initial release
  • Version 1.1: 2026-08-05
    Changes: Database references