5TC0

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

• PDB DOI: https://doi.org/10.2210/pdb5TC0/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-13 Released: 2017-01-25 
• Deposition Author(s): Hoffman, I.D., Lawson, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.262 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

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

• PubMed: 28082036 
• 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.

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Organizational Affiliation: 

Medicinal Chemistry, Takeda California, 10410 Science Center Drive, San Diego, CA 92121, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.42 kDa 
• Atom Count: 4,002 
• Modelled Residue Count: 488 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Mer	A, B	314	Homo sapiens	Mutation(s): 0  Gene Names: MERTK, MER 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
79Y	C [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
79Y	Binding MOAD:  5TC0	IC50: 25 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.262 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.406	α = 90
b = 91.503	β = 99.47
c = 69.543	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Hoffman, I.D., Lawson, J.D.

Revision History  

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