5TC0

Structure-based optimization of 1H-imidazole-2-carboxamides as Axl kinase inhibitors utilizing a Mer mutant surrogate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-based optimization of 1H-imidazole-2-carboxamides as Axl kinase inhibitors utilizing a Mer mutant surrogate.

Keung, W.Boloor, A.Brown, J.Kiryanov, A.Gangloff, A.Lawson, J.D.Skene, R.Hoffman, I.Atienza, J.Kahana, J.De Jong, R.Farrell, P.Balakrishna, D.Halkowycz, P.

(2017) Bioorg. Med. Chem. Lett. 27: 1099-1104

  • DOI: 10.1016/j.bmcl.2016.12.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Axl has been a target of interest in the oncology field for several years based on its role in various oncogenic processes. To date, no wild-type Axl crystal structure has been reported. Herein, we describe the structure-based optimization of a novel ...

    Axl has been a target of interest in the oncology field for several years based on its role in various oncogenic processes. To date, no wild-type Axl crystal structure has been reported. Herein, we describe the structure-based optimization of a novel chemotype of Axl inhibitors, 1H-imidazole-2-carboxamide, using a mutated kinase homolog, Mer(I650M), as a crystallographic surrogate. Iterative optimization of the initial lead compound (1) led to compound (21), a selective and potent inhibitor of wild-type Axl. Compound (21) will serve as a useful compound for further in vivo studies.


    Organizational Affiliation

    Medicinal Chemistry, Takeda California, 10410 Science Center Drive, San Diego, CA 92121, United States. Electronic address: walter.keung@takeda.com.,Medicinal Chemistry, Takeda California, 10410 Science Center Drive, San Diego, CA 92121, United States.,Discovery Biology, Takeda California, 10410 Science Center Drive, San Diego, CA 92121, United States.,Computational Sciences and Crystallography, Takeda California, 10410 Science Center Drive, San Diego, CA 92121, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase Mer
A, B
314Homo sapiensMutation(s): 0 
Gene Names: MERTK (MER)
EC: 2.7.10.1
Find proteins for Q12866 (Homo sapiens)
Go to Gene View: MERTK
Go to UniProtKB:  Q12866
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
79Y
Query on 79Y

Download SDF File 
Download CCD File 
A
N-(2-{4-[(2S)-4-(methylsulfonyl)morpholin-2-yl]-1,3-thiazol-2-yl}phenyl)-1H-imidazole-2-carboxamide
C18 H19 N5 O4 S2
MPCBXJASUBLGMA-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
79YIC50: 25 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.406α = 90.00
b = 91.503β = 99.47
c = 69.543γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release