4Z3V

Fragment-Based Discovery of a Small Molecule Reversible Inhibitor of Bruton's Tyrosine Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fragment-Based Discovery of a Small Molecule Inhibitor of Bruton's Tyrosine Kinase.

Smith, C.R.Dougan, D.R.Komandla, M.Kanouni, T.Knight, B.Lawson, J.D.Sabat, M.Taylor, E.R.Vu, P.Wyrick, C.

(2015) J Med Chem 58: 5437-5444

  • DOI: 10.1021/acs.jmedchem.5b00734
  • Primary Citation of Related Structures:  
    4ZLY, 4ZLZ, 4Z3V

  • PubMed Abstract: 
  • The discovery and optimization of a series of 4-aminocinnoline-3-carboxamide inhibitors of Bruton's tyrosine kinase are reported. A fragment-based screening approach incorporating X-ray co-crystallography was used to identify a cinnoline fragment and ...

    The discovery and optimization of a series of 4-aminocinnoline-3-carboxamide inhibitors of Bruton's tyrosine kinase are reported. A fragment-based screening approach incorporating X-ray co-crystallography was used to identify a cinnoline fragment and characterize its binding mode in the ATP binding site of Btk. Optimization of the fragment hit resulted in the identification of a lead compound which reduced paw swelling in a dose- and exposure-dependent fashion in a rat model of collagen-induced arthritis.


    Organizational Affiliation

    Takeda California, 10410 Science Center Drive, San Diego, California 92121, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTKA283Homo 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
4L6
Query on 4L6

Download Ideal Coordinates CCD File 
A
4-amino-8-(5-methyl-1H-indazol-6-yl)cinnoline-3-carboxamide
C17 H14 N6 O
PTHVKCSYXICMAR-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
A
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4L6IC50:  4   nM  Binding MOAD
4L6EC50:  28   nM  BindingDB
4L6IC50:  4000   nM  BindingDB
4L6IC50:  2   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.092α = 90
b = 104.1β = 90
c = 38.078γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-03-31 
  • Released Date: 2015-07-01 
  • Deposition Author(s): Dougan, D.R.

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references, Other