7N4S

Bruton's tyrosine kinase in complex with compound 65


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Utilizing structure based drug design and metabolic soft spot identification to optimize the in vitro potency and in vivo pharmacokinetic properties leading to the discovery of novel reversible Bruton's tyrosine kinase inhibitors.

Hopkins, B.T.Bame, E.Bell, N.Bohnert, T.Bowden-Verhoek, J.K.Bui, M.Cancilla, M.T.Conlon, P.Cullen, P.Erlanson, D.A.Fan, J.Fuchs-Knotts, T.Hansen, S.Heumann, S.Jenkins, T.J.Gua, C.Liu, Y.Liu, Y.Lulla, M.Marcotte, D.Marx, I.McDowell, B.Mertsching, E.Negrou, E.Romanowski, M.J.Scott, D.Silvian, L.Yang, W.Zhong, M.

(2021) Bioorg Med Chem 44: 116275-116275

  • DOI: https://doi.org/10.1016/j.bmc.2021.116275
  • Primary Citation of Related Structures:  
    7N4Q, 7N4R, 7N4S

  • PubMed Abstract: 

    Bruton's tyrosine kinase (BTK) is an essential node on the BCR signaling in B cells, which are clinically validated to play a critical role in B-cell lymphomas and various auto-immune diseases such as Multiple Sclerosis (MS), Pemphigus, and rheumatoid arthritis (RA). Although non-selective irreversible BTK inhibitors have been approved for oncology, due to the emergence of drug resistance in B-cell lymphoma associated with covalent inhibitor, there an unmet medical need to identify reversible, selective, potent BTK inhibitor as viable therapeutics for patients. Herein, we describe the identification of Hits and subsequence optimization to improve the physicochemical properties, potency and kinome selectivity leading to the discovery of a novel class of BTK inhibitors. Utilizing Met ID and structure base design inhibitors were synthesized with increased in vivo metabolic stability and oral exposure in rodents suitable for advancing to lead optimization.


  • Organizational Affiliation

    Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA. Electronic address: Brian.Hopkins@biogen.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0B0 (Subject of Investigation/LOI)
Query on 0B0

Download Ideal Coordinates CCD File 
B [auth A](3R,3'R)-3-anilino-1'-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)[1,3'-bipiperidin]-2-one
C22 H26 N6 O
BYRYLAFNCJLOIQ-IEBWSBKVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.372α = 90
b = 104.158β = 90
c = 38.016γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description