4RX5

Bruton's tyrosine kinase (BTK) with pyridazinone compound 23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of highly potent and selective Bruton's tyrosine kinase inhibitors: Pyridazinone analogs with improved metabolic stability.

Young, W.B.Barbosa, J.Blomgren, P.Bremer, M.C.Crawford, J.J.Dambach, D.Eigenbrot, C.Gallion, S.Johnson, A.R.Kropf, J.E.Lee, S.H.Liu, L.Lubach, J.W.Macaluso, J.Maciejewski, P.Mitchell, S.A.Ortwine, D.F.Di Paolo, J.Reif, K.Scheerens, H.Schmitt, A.Wang, X.Wong, H.Xiong, J.M.Xu, J.Yu, C.Zhao, Z.Currie, K.S.

(2016) Bioorg Med Chem Lett 26: 575-579

  • DOI: 10.1016/j.bmcl.2015.11.076
  • Primary Citation of Related Structures:  
    4RX5

  • PubMed Abstract: 
  • BTK inhibitor GDC-0834 (1) was found to be rapidly metabolized in human studies, resulting in a suspension of clinical trials. The primary route of metabolism was through cleavage of the acyclic amide bond connecting the terminal tetrahydrobenzothiop ...

    BTK inhibitor GDC-0834 (1) was found to be rapidly metabolized in human studies, resulting in a suspension of clinical trials. The primary route of metabolism was through cleavage of the acyclic amide bond connecting the terminal tetrahydrobenzothiophene with the central linker aryl ring. SAR studies were focused on reducing metabolic cleavage of this amide, and resulted in the identification of several central aryl linker substituents that conferred improved stability. The most promising substituted aryl linkers were then incorporated into an optimized pyridazinone scaffold, resulting in the identification of lead analog 23, possessing improved potency, metabolic stability and preclinical properties.


    Organizational Affiliation

    Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTKA271Homo sapiensMutation(s): 0 
Gene Names: BTKAGMX1ATKBPK
EC: 2.7.10.2
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
NIH Common Fund Data Resources
PHAROS  Q06187
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3YO
Query on 3YO

Download Ideal Coordinates CCD File 
A
N-(6-fluoro-2-methyl-3-{5-[(5-methyl-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-2-yl)amino]-6-oxo-1,6-dihydropyridazin-3-yl}phenyl)-1-benzothiophene-2-carboxamide
C27 H24 F N7 O2 S
MZSDTUIZKGUVHK-UHFFFAOYSA-N
 Ligand Interaction
PG0
Query on PG0

Download Ideal Coordinates CCD File 
A
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3YOIC50:  3   nM  Binding MOAD
3YOIC50:  3   nM  BindingDB
3YOIC50:  91   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.3α = 90
b = 108.3β = 90
c = 42.422γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-12-08 
  • Released Date: 2015-12-02 
  • Deposition Author(s): Eigenbrot, C., Yu, C.

Revision History 

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references