6OMU | pdb_00006omu

Structure of human Bruton's Tyrosine Kinase in complex with Evobrutinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Evobrutinib: An Oral, Potent, and Highly Selective, Covalent Bruton's Tyrosine Kinase (BTK) Inhibitor for the Treatment of Immunological Diseases.

Caldwell, R.D.Qiu, H.Askew, B.C.Bender, A.T.Brugger, N.Camps, M.Dhanabal, M.Dutt, V.Eichhorn, T.Gardberg, A.S.Goutopoulos, A.Grenningloh, R.Head, J.Healey, B.Hodous, B.L.Huck, B.R.Johnson, T.L.Jones, C.Jones, R.C.Mochalkin, I.Morandi, F.Nguyen, N.Meyring, M.Potnick, J.R.Santos, D.C.Schmidt, R.Sherer, B.Shutes, A.Urbahns, K.Follis, A.V.Wegener, A.A.Zimmerli, S.C.Liu-Bujalski, L.

(2019) J Med Chem 62: 7643-7655

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00794
  • Primary Citation Related Structures: 
    6OMU

  • PubMed Abstract: 

    Bruton's tyrosine kinase (BTK) inhibitors such as ibrutinib hold a prominent role in the treatment of B cell malignancies. However, further refinement is needed to this class of agents, particularly in terms of adverse events (potentially driven by kinase promiscuity), which preclude their evaluation in nononcology indications. Here, we report the discovery and preclinical characterization of evobrutinib, a potent, obligate covalent inhibitor with high kinase selectivity. Evobrutinib displayed sufficient preclinical pharmacokinetic and pharmacodynamic characteristics which allowed for in vivo evaluation in efficacy models. Moreover, the high selectivity of evobrutinib for BTK over epidermal growth factor receptor and other Tec family kinases suggested a low potential for off-target related adverse effects. Clinical investigation of evobrutinib is ongoing in several autoimmune diseases, including multiple sclerosis, rheumatoid arthritis, and systemic lupus erythematosus.


  • Organizational Affiliation
    • EMD Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany) , 45 A Middlesex Turnpike , Billerica , Massachusetts 01821 , United States.

Macromolecule Content 

  • Total Structure Weight: 32.06 kDa 
  • Atom Count: 2,785 
  • Modeled Residue Count: 271 
  • Deposited Residue Count: 271 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK271Homo 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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MZJ

Query on MZJ



Download:Ideal Coordinates CCD File
C [auth A]1-[4-({[6-amino-5-(4-phenoxyphenyl)pyrimidin-4-yl]amino}methyl)piperidin-1-yl]prop-2-en-1-one
C25 H27 N5 O2
QUIWHXQETADMGN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.173α = 90
b = 104.52β = 90
c = 37.983γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description