Discovery of affinity-based probes for Btk occupancy assay

Experimental Data Snapshot

  • Resolution: 2.23 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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Discovery of Affinity-Based Probes for Btk Occupancy Assays.

Qiu, H.Caldwell, R.Liu-Bujalski, L.Goutopoulos, A.Jones, R.Potnick, J.Sherer, B.Bender, A.Grenningloh, R.Xu, D.Gardberg, A.Mochalkin, I.Johnson, T.Viacava Follis, A.Head, J.Morandi, F.

(2019) ChemMedChem 14: 217-223

  • DOI: https://doi.org/10.1002/cmdc.201800714
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Bruton's tyrosine kinase (Btk) is an attractive target for the treatment of a wide array of B-cell malignancies and autoimmune diseases. Small-molecule covalent irreversible Btk inhibitors targeting Cys481 have been developed for the treatment of such diseases. In clinical trials, probe molecules are required in occupancy studies to measure the level of engagement of the protein by these covalent irreversible inhibitors. The result of this pharmacodynamic (PD) activity provides guidance for appropriate dosage selection to optimize inhibition of the drug target and correlation of target inhibition with disease treatment efficacy. This information is crucial for successful evaluation of drug candidates in clinical trials. Based on the pyridine carboxamide scaffold of a novel solvent-accessible pocket (SAP) series of covalent irreversible Btk inhibitors, we successfully developed a potent and selective affinity-based biotinylated probe 12 (2-[(4-{4-[5-(1-{5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamido}-3,6,9,12-tetraoxapentadecan-15-amido)pentanoyl]piperazine-1-carbonyl}phenyl)amino]-6-[1-(prop-2-enoyl)piperidin-4-yl]pyridine-3-carboxamide). Compound 12 has been used in Btk occupancy assays for preclinical studies to determine the therapeutic efficacy of Btk inhibition in two mouse lupus models driven by TLR7 activation and type I interferon.

  • Organizational Affiliation

    EMD Serono Research & Development Institute, 45A Middlesex Turnpike, Billerica, MA, 01821, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK271Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
GTEx:  ENSG00000010671 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KHD (Subject of Investigation/LOI)
Query on KHD

Download Ideal Coordinates CCD File 
B [auth A]N-(3-{[2-amino-3-(4-phenoxyphenyl)pyridin-4-yl]oxy}phenyl)propanamide
C26 H23 N3 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.23 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.02α = 90
b = 104.412β = 90
c = 38.018γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release