7M5Z

Crystal Structure of the MerTK Kinase Domain in Complex with Inhibitor MIPS15692


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 

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Ligand Structure Quality Assessment 


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Literature

Development of [ 18 F]MIPS15692, a radiotracer with in vitro proof-of-concept for the imaging of MER tyrosine kinase (MERTK) in neuroinflammatory disease.

Wong, S.W.Vivash, L.Mudududdla, R.Nguyen, N.Hermans, S.J.Shackleford, D.M.Field, J.Xue, L.Aprico, A.Hancock, N.C.Haskali, M.Stashko, M.A.Frye, S.V.Wang, X.Binder, M.D.Ackermann, U.Parker, M.W.Kilpatrick, T.J.Baell, J.B.

(2021) Eur J Med Chem 226: 113822-113822

  • DOI: https://doi.org/10.1016/j.ejmech.2021.113822
  • Primary Citation of Related Structures:  
    7M5Z

  • PubMed Abstract: 

    MER tyrosine kinase (MERTK) upregulation is associated with M2 polarization of microglia, which plays a vital role in neuroregeneration following damage induced by neuroinflammatory diseases such as multiple sclerosis (MS). Therefore, a radiotracer specific for MERTK could be of great utility in the clinical management of MS, for the detection and differentiation of neuroregenerative and neurodegenerative processes. This study aimed to develop an [ 18 F] ligand with high affinity and selectivity for MERTK as a potential positron emission tomography (PET) radiotracer. MIPS15691 and MIPS15692 were synthesized and kinase assays were utilized to determine potency and selectivity for MERTK. Both compounds were shown to be potent against MERTK, with respective IC 50 values of 4.6 nM and 4.0 nM, and were also MERTK-selective. Plasma and brain pharmacokinetics were measured in mice and led to selection of MIPS15692 over MIPS15691. X-ray crystallography was used to visualize how MIPS15692 is recognized by the enzyme. [ 18 F]MIPS15692 was synthesized using an automated iPHASE FlexLab module, with a molar activity (A m ) of 49 ± 26 GBq/μmol. The radiochemical purity of [ 18 F]MIPS15692 was >99% and the decay-corrected radiochemical yields (RCYs) were determined as 2.45 ± 0.85%. Brain MERTK protein density was measured by a saturation binding assay in the brain slices of a cuprizone mouse model of MS. High levels of specific binding of [ 18 F]MIPS15692 to MERTK were found, especially in the corpus callosum/hippocampus (CC/HC). The in vivo PET imaging study of [ 18 F]MIPS15692 suggested that its neuroPK is sub-optimal for clinical use. Current efforts are underway to optimize the neuroPK of our next generation PET radiotracers for maximal in vivo utility.


  • Organizational Affiliation

    Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase Mer
A, B
313Homo 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
YR7 (Subject of Investigation/LOI)
Query on YR7

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-(butylamino)-N-[1-(3-fluoropropyl)piperidin-4-yl]-4-{[(1r,4r)-4-hydroxycyclohexyl]amino}pyrimidine-5-carboxamide
C23 H39 F N6 O2
KOWRWJFANSWOCN-UAPYVXQJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.203α = 90
b = 91.272β = 90
c = 100.804γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description