6S90

BTK in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design of Potent and Selective Covalent Inhibitors of Bruton's Tyrosine Kinase Targeting an Inactive Conformation.

Pulz, R.Angst, D.Dawson, J.Gessier, F.Gutmann, S.Hersperger, R.Hinniger, A.Janser, P.Koch, G.Revesz, L.Vulpetti, A.Waelchli, R.Zimmerlin, A.Cenni, B.

(2019) ACS Med Chem Lett 10: 1467-1472

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00317
  • Primary Citation of Related Structures:  
    6S90

  • PubMed Abstract: 

    Bruton's tyrosine kinase (BTK) is a member of the TEC kinase family and is selectively expressed in a subset of immune cells. It is a key regulator of antigen receptor signaling in B cells and of Fc receptor signaling in mast cells and macrophages. A BTK inhibitor will likely have a positive impact on autoimmune diseases which are caused by autoreactive B cells and immune-complex driven inflammation. We report the design, optimization, and characterization of potent and selective covalent BTK inhibitors. Starting from the selective reversible inhibitor 3 binding to an inactive conformation of BTK, we designed covalent irreversible compounds by attaching an electrophilic warhead to reach Cys481. The first prototype 4 covalently modified BTK and showed an excellent kinase selectivity including several Cys-containing kinases, validating the design concept. In addition, this compound blocked FcγR-mediated hypersensitivity in vivo . Optimization of whole blood potency and metabolic stability resulted in compounds such as 8 , which maintained the excellent kinase selectivity and showed improved BTK occupancy in vivo .


  • Organizational Affiliation

    Global Discovery Chemistry, Autoimmunity, Transplantation & Inflammation, Chemical Biology & Therapeutics, and PK Sciences, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK
A, B
266Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L0Z (Subject of Investigation/LOI)
Query on L0Z

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-~{tert}-butyl-~{N}-[2-methyl-3-[6-[4-(4-methylpiperazin-1-yl)carbonylphenyl]-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]phenyl]benzamide
C36 H38 N6 O2
IGVLLOMIUXKXBM-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
L0Z Binding MOAD:  6S90 IC50: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.83α = 90
b = 39.36β = 111.18
c = 105.19γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AutoPROCdata 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: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references