6J6M | pdb_00006j6m

Co-crystal structure of BTK kinase domain with Zanubrutinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.164 (Depositor), 0.165 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6J6M

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Zanubrutinib (BGB-3111), a Novel, Potent, and Selective Covalent Inhibitor of Bruton's Tyrosine Kinase.

Guo, Y.Liu, Y.Hu, N.Yu, D.Zhou, C.Shi, G.Zhang, B.Wei, M.Liu, J.Luo, L.Tang, Z.Song, H.Guo, Y.Liu, X.Su, D.Zhang, S.Song, X.Zhou, X.Hong, Y.Chen, S.Cheng, Z.Young, S.Wei, Q.Wang, H.Wang, Q.Lv, L.Wang, F.Xu, H.Sun, H.Xing, H.Li, N.Zhang, W.Wang, Z.Liu, G.Sun, Z.Zhou, D.Li, W.Liu, L.Wang, L.Wang, Z.

(2019) J Med Chem 62: 7923-7940

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00687
  • Primary Citation Related Structures: 
    6J6M

  • PubMed Abstract: 

    Aberrant activation of Bruton's tyrosine kinase (BTK) plays an important role in pathogenesis of B-cell lymphomas, suggesting that inhibition of BTK is useful in the treatment of hematological malignancies. The discovery of a more selective on-target covalent BTK inhibitor is of high value. Herein, we disclose the discovery and preclinical characterization of a potent, selective, and irreversible BTK inhibitor as our clinical candidate by using in vitro potency, selectivity, pharmacokinetics (PK), and in vivo pharmacodynamic for prioritizing compounds. Compound BGB-3111 ( 31a , Zanubrutinib) demonstrates (i) potent activity against BTK and excellent selectivity over other TEC, EGFR and Src family kinases, (ii) desirable ADME, excellent in vivo pharmacodynamic in mice and efficacy in OCI-LY10 xenograft models.

Macromolecule Content 

  • Total Structure Weight: 31.89 kDa 
  • Atom Count: 2,734 
  • Modeled Residue Count: 267 
  • Deposited Residue Count: 269 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK269Homo 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
PHAROS:  Q06187
GTEx:  ENSG00000010671 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BA0

Query on BA0



Download:Ideal Coordinates CCD File
B [auth A](7S)-2-(4-phenoxyphenyl)-7-(1-propanoylpiperidin-4-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide
C27 H31 N5 O3
WVLVCHIIZKJCHR-QFIPXVFZSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
C [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.164 (Depositor), 0.165 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.924α = 90
b = 71.988β = 90
c = 104.429γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary