6DI5

CRYSTAL STRUCTURE OF BTK IN COMPLEX WITH COVALENT INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of potent, highly selective covalent irreversible BTK inhibitors from a fragment hit.

Qiu, H.Liu-Bujalski, L.Caldwell, R.D.Follis, A.V.Gardberg, A.Goutopoulos, A.Grenningloh, R.Head, J.Johnson, T.Jones, R.Mochalkin, I.Morandi, F.Neagu, C.Sherer, B.

(2018) Bioorg. Med. Chem. Lett. 28: 2939-2944

  • DOI: 10.1016/j.bmcl.2018.07.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bruton's Tyrosine Kinase (BTK) is a member of the TEC kinase family that is expressed in cells of hematopoietic lineage (e.g., in B cells, macrophages, monocytes, and mast cells). Small molecule covalent irreversible BTK inhibitor targeting Cys481 wi ...

    Bruton's Tyrosine Kinase (BTK) is a member of the TEC kinase family that is expressed in cells of hematopoietic lineage (e.g., in B cells, macrophages, monocytes, and mast cells). Small molecule covalent irreversible BTK inhibitor targeting Cys481 within the ATP-binding pocket, for example ibrutinib, has been applied in the treatment of B-cell malignancies. Starting from a fragment hit, we discovered a novel series of potent covalent irreversible BTK inhibitors that occupy selectivity pocket of the active site of the BTK kinase domain. Guided by X-ray structures and a fragment-based drug design (FBDD) approach, we generated molecules showing comparable cellular potency to ibrutinib and higher kinome selectivity against undesirable off-targets like EGFR.


    Organizational Affiliation

    EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica 01821, MA, USA. Electronic address: hui.qiu@emdserono.com.,F. Hoffmann-La Roche AG, Konzern-Hauptsitz, Grenzacherstrasse 124, CH-4070 Basel, Switzerland.,Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, USA.,EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica 01821, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase BTK
A
271Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GJ7
Query on GJ7

Download SDF File 
Download CCD File 
A
2-(4-phenoxyphenoxy)-6-[(1S,4S)-5-propanoyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]pyridine-3-carboxamide
C26 H26 N4 O4
DQFJRLJIIQKNPY-ROUUACIJSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.033α = 90.00
b = 107.696β = 90.00
c = 39.320γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-05-22 
  • Released Date: 2018-09-05 
  • Deposition Author(s): Gardberg, A.

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release