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 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.3 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTK283Homo sapiensMutation(s): 4 
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
Expand
  • 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[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
Binding Affinity Annotations 
IDSourceBinding Affinity
GMW BindingDB:  6HRT IC50: min: 0.91, max: 26 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
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
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GMWClick on this verticalbar to view details

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