6HRT

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[9.4.0.02,7]pentadeca-1(15),2(7),3,11,13-pentaen-5-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2019.03.001
  • Primary Citation of Related Structures:  

  • 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 sub ...

    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.,Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, 340 Kingsland Street, Nutley 07110, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase BTK
A
283Homo sapiensMutation(s): 4 
Gene Names: BTK (AGMX1, ATK, BPK)
EC: 2.7.10.2
Find proteins for Q06187 (Homo sapiens)
Go to Gene View: BTK
Go to UniProtKB:  Q06187
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GMW
Query on GMW

Download SDF File 
Download CCD File 
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[9.4.0.0^{2,7}]pentadeca-1(15),2(7),3,11,13-pentaen-5-one
C37 H37 F N6 O5
ACFBKRAWAGNCMP-DEOSSOPVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.778α = 90.00
b = 107.001β = 90.00
c = 38.359γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-03
    Type: Data collection, Database references
  • Version 1.2: 2019-05-15
    Type: Data collection, Refinement description