CRYSTAL STRUCTURE OF BTK KINASE DOMAIN COMPLEXED WITH 12-(6-tert-butyl-8-fluoro-1-oxo-phthalazin-2-yl)-9-hydroxy-6-methyl-4-[[5-(morpholine-4-carbonyl)-2-pyridyl]amino]-6-azatricyclo[,7]pentadeca-1(15),2(7),3,11,13-pentaen-5-one

Experimental Data Snapshot

  • Resolution: 1.36 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


A potent seven-membered cyclic BTK (Bruton's tyrosine Kinase) chiral inhibitor conceived by structure-based drug design to lock its bioactive conformation.

Lopez-Tapia, F.Lou, Y.Brotherton-Pleiss, C.Kuglstatter, A.So, S.S.Kondru, R.

(2019) Bioorg Med Chem Lett 29: 1074-1078

  • DOI: https://doi.org/10.1016/j.bmcl.2019.03.001
  • Primary Citation of Related Structures:  
    6HRP, 6HRT

  • PubMed Abstract: 

    A seven-membered cyclic chiral analog of potent lead BTK inhibitor 1 was envisioned by structure-based design to lock the molecule into its bioactive conformation. For the elaboration of the seven-membered ring, compound 1 pyridone 6-position was substituted with the purpose to prevent formation of reactive metabolites. Eventually, the cyclic chiral compound 3 maintained the high potency of 1, and most importantly showed no activity at either GSH or TDI assays suggesting no formation of reactive metabolites. The anticipated bound conformation of 3 to BTK was confirmed by X-ray crystallography. Synthetically, the crucial seven-membered ring formation was obtained by using TosMIC as a connective reagent.

  • Organizational Affiliation

    Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, 340 Kingsland Street, Nutley 07110, United States. Electronic address: ftapia@cc.hawaii.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK283Homo sapiensMutation(s): 4 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GMW (Subject of Investigation/LOI)
Query on GMW

Download Ideal Coordinates CCD File 
B [auth A](9~{S})-12-(6-~{tert}-butyl-8-fluoranyl-1-oxidanylidene-phthalazin-2-yl)-6-methyl-4-[(5-morpholin-4-ylcarbonylpyridin-2-yl)amino]-9-oxidanyl-6-azatricyclo[^{2,7}]pentadeca-1(15),2(7),3,11,13-pentaen-5-one
C37 H37 F N6 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
GMW BindingDB:  6HRT IC50: min: 0.91, max: 26 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.36 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.778α = 90
b = 107.001β = 90
c = 38.359γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata 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: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-15
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references