5TD2 | pdb_00005td2

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: 2.68 Å
  • R-Value Free: 
    0.300 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 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: https://doi.org/10.1016/j.bmcl.2016.12.024
  • Primary Citation of Related Structures:  
    5TC0, 5TD2

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase Mer
A, B
285Homo sapiensMutation(s): 0 
Gene Names: MERTKMER
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12866 (Homo sapiens)
Explore Q12866 
Go to UniProtKB:  Q12866
PHAROS:  Q12866
GTEx:  ENSG00000153208 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12866
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7AE
Query on 7AE

Download Ideal Coordinates CCD File 
C [auth A]N-[2-{4-[(2S)-4-(methylsulfonyl)morpholin-2-yl]-1,3-thiazol-2-yl}-4-(morpholin-4-yl)phenyl]-1H-imidazole-2-carboxamide
C22 H26 N6 O5 S2
WWTNLDQWEKRXNB-IBGZPJMESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free:  0.300 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.157α = 90
b = 91.942β = 99.51
c = 69.655γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
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 7AEClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Refinement description