9BHK

MerTK in complex with small molecule inhibitor 6-{1-[6-(3-hydroxy-3-methylbutoxy)-1,3-benzoxazol-2-yl]azetidin-3-yl}-3-[(1-methyl-1H-pyrazol-4-yl)amino]pyrazine-2-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb9BHK/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-04-20 Released: 2024-10-09 
• Deposition Author(s): Jakob, C.G., Gurbani, D., Qiu, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.229 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Discovery of Potent Azetidine-Benzoxazole MerTK Inhibitors with In Vivo Target Engagement.

Frey, R.R., Jana, N., Gorman, J.V., Wang, J., Smith, H.A., Bromberg, K.D., Thakur, A., Doktor, S.Z., Indulkar, A.S., Jakob, C.G., Upadhyay, A.K., Qiu, W., Manaves, V., Gambino Jr., F., Valentino, S.A., Montgomery, D., Zhou, Y., Li, T., Buchanan, F.G., Ferguson, D.C., Kurnick, M.D., Kapecki, N., Lai, A., Michaelides, M.R., Penning, T.D.

(2024) J Med Chem 67: 17033-17052

• PubMed: 39350472 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c01451
• Primary Citation of Related Structures:  
  9BHJ, 9BHK


• PubMed Abstract: 
  

  Inhibition of the receptor tyrosine kinase MerTK by small molecules has the potential to augment the immune response to tumors. Potent, selective inhibitors with high levels of in vivo target engagement are needed to fully evaluate the potential use of MerTK inhibitors as cancer therapeutics. We report the discovery and optimization of a series of pyrazinamide-based type 1.5 MerTK inhibitors bearing an azetidine-benzoxazole substituent. Compound 31 potently engages the target in vivo and demonstrates single agent activity in the immune-driven MC-38 murine syngeneic tumor model.

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Organizational Affiliation: 

Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.04 kDa 
• Atom Count: 2,430 
• Modelled Residue Count: 277 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Mer	A	323	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1APH (Subject of Investigation/LOI)	B [auth A]	6-{1-[6-(3-hydroxy-3-methylbutoxy)-1,3-benzoxazol-2-yl]azetidin-3-yl}-3-[(1-methyl-1H-pyrazol-4-yl)amino]pyrazine-2-carboxamide C24 H28 N8 O4 MALAUNPIQXEERD-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.229 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.385	α = 90
b = 80.385	β = 90
c = 135.383	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Jakob, C.G., Gurbani, D., Qiu, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Database references