Bruton's tyrosine kinase in complex with compound 1

Experimental Data Snapshot

  • Resolution: 1.51 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Discovery of BIIB068: A Selective, Potent, Reversible Bruton's Tyrosine Kinase Inhibitor as an Orally Efficacious Agent for Autoimmune Diseases.

Ma, B.Bohnert, T.Otipoby, K.L.Tien, E.Arefayene, M.Bai, J.Bajrami, B.Bame, E.Chan, T.R.Humora, M.MacPhee, J.M.Marcotte, D.Mehta, D.Metrick, C.M.Moniz, G.Polack, E.Poreci, U.Prefontaine, A.Sheikh, S.Schroeder, P.Smirnakis, K.Zhang, L.Zheng, F.Hopkins, B.T.

(2020) J Med Chem 63: 12526-12541

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00702
  • Primary Citation of Related Structures:  
    6VXQ, 6W06, 6W07

  • PubMed Abstract: 

    Autoreactive B cell-derived antibodies form immune complexes that likely play a pathogenic role in autoimmune diseases. In systemic lupus erythematosus (SLE), these antibodies bind Fc receptors on myeloid cells and induce proinflammatory cytokine production by monocytes and NETosis by neutrophils. Bruton's tyrosine kinase (BTK) is a non-receptor tyrosine kinase that signals downstream of Fc receptors and plays a transduction role in antibody expression following B cell activation. Given the roles of BTK in both the production and sensing of autoreactive antibodies, inhibitors of BTK kinase activity may provide therapeutic value to patients suffering from autoantibody-driven immune disorders. Starting from an in-house proprietary screening hit followed by structure-based rational design, we have identified a potent, reversible BTK inhibitor, BIIB068 ( 1 ), which demonstrated good kinome selectivity with good overall drug-like properties for oral dosing, was well tolerated across preclinical species at pharmacologically relevant doses with good ADME properties, and achieved >90% inhibition of BTK phosphorylation (pBTK) in humans.

  • Organizational Affiliation

    Research & Development, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK293Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
PHAROS:  Q06187
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S9A (Subject of Investigation/LOI)
Query on S9A

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[[2-methyl-4-[2-[(1-methylpyrazol-4-yl)amino]pyrimidin-4-yl]phenyl]methyl]-3-propan-2-yloxy-azetidine-1-carboxamide
C23 H29 N7 O2
Query on DMS

Download Ideal Coordinates CCD File 
C2 H6 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
S9A Binding MOAD:  6W07 IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.51 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.658α = 90
b = 103.895β = 90
c = 38.23γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description