7YC9 | pdb_00007yc9

Co-crystal structure of BTK kinase domain with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.187 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7YC9

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of BGB-8035, a Highly Selective Covalent Inhibitor of Bruton's Tyrosine Kinase for B-Cell Malignancies and Autoimmune Diseases.

Guo, Y.Hu, N.Liu, Y.Zhang, W.Yu, D.Shi, G.Zhang, B.Yin, L.Wei, M.Yuan, X.Luo, L.Wang, F.Song, X.Xin, L.Wei, Q.Li, Y.Guo, Y.Chen, S.Zhang, T.Zhang, S.Zhou, X.Zhang, C.Su, D.Liu, J.Cheng, Z.Zhang, J.Xing, H.Sun, H.Li, X.Zhao, Y.He, M.Wu, Y.Guo, Y.Sun, X.Tian, A.Zhou, C.Young, S.Liu, X.Wang, L.Wang, Z.

(2023) J Med Chem 66: 4025-4044

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01938
  • Primary Citation Related Structures: 
    7YC9

  • PubMed Abstract: 

    Bruton's tyrosine kinase (BTK) plays an essential role in B-cell receptor (BCR)-mediated signaling as well as the downstream signaling pathway for Fc receptors (FcRs). Targeting BTK for B-cell malignancies by interfering with BCR signaling has been clinically validated by some covalent inhibitors, but suboptimal kinase selectivity may lead to some adverse effects, which also makes the clinical development of autoimmune disease therapy more challenging. The structure-activity relationship (SAR) starting from zanubrutinib ( BGB - 3111 ) leads to a series of highly selective BTK inhibitors, in which BGB - 8035 is located in the ATP binding pocket and has similar hinge binding to ATP but exhibits high selectivity over other kinases (EGFR, Tec, etc.). With an excellent pharmacokinetic profile as well as demonstrated efficacy studies in oncology and autoimmune disease models, BGB - 8035 has been declared a preclinical candidate. However, BGB - 8035 showed an inferior toxicity profile compared to that of BGB - 3111 .


  • Organizational Affiliation
    • Department of Medicinal Chemistry, BeiGene (Beijing) Co., Ltd., Beijing 102206, P.R. China.

Macromolecule Content 

  • Total Structure Weight: 31.93 kDa 
  • Atom Count: 2,598 
  • Modeled Residue Count: 264 
  • 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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IS4
(Subject of Investigation/LOI)

Query on IS4



Download:Ideal Coordinates CCD File
B [auth A](7~{S})-2-(4-bromanyl-3,5-dimethoxy-phenyl)-7-(1-propanoylpiperidin-4-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide
C23 H30 Br N5 O4
GQJVVSVHZDAEOE-HNNXBMFYSA-N
EDO

Query on EDO



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.187 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.232α = 90
b = 58.177β = 90
c = 95.258γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-05-17 
  • Deposition Author(s): Zhou, X.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary