5P9J

BTK1 COCRYSTALLIZED WITH IBRUTINIB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ability of Bruton's Tyrosine Kinase Inhibitors to Sequester Y551 and Prevent Phosphorylation Determines Potency for Inhibition of Fc Receptor but not B-Cell Receptor Signaling.

Bender, A.T.Gardberg, A.Pereira, A.Johnson, T.Wu, Y.Grenningloh, R.Head, J.Morandi, F.Haselmayer, P.Liu-Bujalski, L.

(2017) Mol. Pharmacol. 91: 208-219

  • DOI: 10.1124/mol.116.107037
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bruton's tyrosine kinase (Btk) is expressed in a variety of hematopoietic cells. Btk has been demonstrated to regulate signaling downstream of the B-cell receptor (BCR), Fc receptors (FcRs), and toll-like receptors. It has become an attractive drug t ...

    Bruton's tyrosine kinase (Btk) is expressed in a variety of hematopoietic cells. Btk has been demonstrated to regulate signaling downstream of the B-cell receptor (BCR), Fc receptors (FcRs), and toll-like receptors. It has become an attractive drug target because its inhibition may provide significant efficacy by simultaneously blocking multiple disease mechanisms. Consequently, a large number of Btk inhibitors have been developed. These compounds have diverse binding modes, and both reversible and irreversible inhibitors have been developed. Reported herein, we have tested nine Btk inhibitors and characterized on a molecular level how their interactions with Btk define their ability to block different signaling pathways. By solving the crystal structures of Btk inhibitors bound to the enzyme, we discovered that the compounds can be classified by their ability to trigger sequestration of Btk residue Y551. In cells, we found that sequestration of Y551 renders it inaccessible for phosphorylation. The ability to sequester Y551 was an important determinant of potency against FcεR signaling as Y551 sequestering compounds were more potent for inhibiting basophils and mast cells. This result was true for the inhibition of FcγR signaling as well. In contrast, Y551 sequestration was less a factor in determining potency against BCR signaling. We also found that Btk activity is regulated differentially in basophils and B cells. These results elucidate important determinants for Btk inhibitor potency against different signaling pathways and provide insight for designing new compounds with a broader inhibitory profile that will likely result in greater efficacy.


    Organizational Affiliation

    TIP Immunology (A.T.B., A.P., Y.W., R.G.) and Discovery Technologies (A.G., T.J., J.H., F.M., L.L.-B.), EMD Serono Research and Development Institute, Billerica, Massachusetts; and TIP Immunology, Merck, Darmstadt, Germany (P.H.).,TIP Immunology (A.T.B., A.P., Y.W., R.G.) and Discovery Technologies (A.G., T.J., J.H., F.M., L.L.-B.), EMD Serono Research and Development Institute, Billerica, Massachusetts; and TIP Immunology, Merck, Darmstadt, Germany (P.H.) andrew.bender@emdserono.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase BTK
A
279Homo sapiensMutation(s): 0 
Gene Names: BTK (AGMX1, ATK, BPK)
EC: 2.7.10.2
Find proteins for Q06187 (Homo sapiens)
Go to Gene View: BTK
Go to UniProtKB:  Q06187
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8E8
Query on 8E8

Download SDF File 
Download CCD File 
A
1-[(3~{R})-3-[4-azanyl-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one
Ibrutinib (bound form)
C25 H26 N6 O2
ROGRQCNRPWIQJN-GOSISDBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.250α = 90.00
b = 104.610β = 90.00
c = 38.100γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-09-20 
  • Released Date: 2017-05-24 
  • Deposition Author(s): Gardberg, A.S.

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Structure summary