9KRY | pdb_00009kry

Crystal structure Of MerTK kinase domain in complex With compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.284 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure-Based Design of Potent and Selective MerTK Inhibitors by Modulating the Conformation of alpha C Helix.

Peng, Y.H.Li, M.C.Yen, W.C.Yeh, T.K.Hsueh, C.C.Kuo, F.M.Lai, Y.L.Chang, L.Lee, L.C.Chen, P.Y.Yen, K.J.Chang, T.Y.Sun, H.Y.Chang, C.Y.Hsieh, S.H.Yang, C.M.Hsieh, H.P.Wu, S.Y.

(2025) J Med Chem 68: 10877-10896

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c03092
  • Primary Citation of Related Structures:  
    9KRY, 9KRZ, 9KS9

  • PubMed Abstract: 

    Tumor-associated macrophages play an important role in cancer progression and immunosuppression, making their receptors promising therapeutic targets. MerTK, a TAM receptor, regulates macrophage efferocytosis and polarization, and its inhibition holds potential for tumor growth suppression and immune modulation. However, Tyro3, another TAM receptor, is involved in neurogenesis, highlighting the need to selectively target MerTK while avoiding Tyro3 inhibition to prevent neurotoxicity. In this study, we present a novel strategy for designing MerTK-selective inhibitors by modulating the conformational dynamics of its αC helix. By integrating structural biology, medicinal chemistry, protein stabilization assays, and molecular docking studies, we identified compound 11 , which demonstrates potent inhibition and selectivity for MerTK. Pharmacokinetic evaluations and in vivo studies further reveal compound 11 as a promising candidate for further development. Our findings not only advance the understanding of the MerTK-specific mechanism but also propose a strategy for designing selective kinase inhibitors targeting the αC helix conformation.


  • Organizational Affiliation
    • Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Miaoli County, Zhunan Town 350, Taiwan, R.O.C.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase Mer
A, B
294Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L6J (Subject of Investigation/LOI)
Query on A1L6J

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
~{N}-[4-[5-(3-aminophenyl)-6-(1-methylpyrazol-4-yl)furo[2,3-d]pyrimidin-4-yl]oxyphenyl]-2-(4-fluorophenyl)-1-methyl-3-oxidanylidene-pyrazole-4-carboxamide
C33 H25 F N8 O4
ROQFVBHLGRGANE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.284 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.994α = 90
b = 91.279β = 100.77
c = 69.227γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release