6DI1

CRYSTAL STRUCTURE OF BTK IN COMPLEX WITH COVALENT FRAGMENT LIGAND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a novel series of pyridine and pyrimidine carboxamides as potent and selective covalent inhibitors of Btk.

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

(2018) Bioorg. Med. Chem. Lett. 28: 3419-3424

  • DOI: 10.1016/j.bmcl.2018.09.033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Btk is an attractive target for the treatment of a range of Bcell malignancies as well as several autoimmune diseases such as murine lupus and rheumatoid arthritis. Several covalent irreversible inhibitors of Btk are currently in development includin ...

    Btk is an attractive target for the treatment of a range of Bcell malignancies as well as several autoimmune diseases such as murine lupus and rheumatoid arthritis. Several covalent irreversible inhibitors of Btk are currently in development including ibrutinib which was approved for treatment of B-cell malignancies. Herein, we describe our efforts using X-ray guided structure based design (SBD) to identify a novel chemical series of covalent Btk inhibitors. The resulting pyridine carboxamides were potent and selective inhibitors of Btk having excellent enzymatic and cellular inhibitory activity.


    Organizational Affiliation

    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. Electronic address: richard.caldwell@emdserono.com.,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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GJD
Query on GJD

Download SDF File 
Download CCD File 
A
4-amino-2-[(3S)-3-(propanoylamino)pyrrolidin-1-yl]pyrimidine-5-carboxamide
C12 H18 N6 O2
RFNYKYSEMVFRHS-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.250α = 90.00
b = 104.170β = 90.00
c = 38.120γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-05-22 
  • Released Date: 2018-10-17 
  • Deposition Author(s): Jiang, X.

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references