9UBI | pdb_00009ubi

Crystal structure of FERONIA kinase and Ferovicin inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.203 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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Literature

Unveiling FERONIA receptor kinase-mediated cellular mechanisms with a small-molecule inhibitor.

Sun, M.Lu, B.Yang, Y.Fan, J.Ren, W.Chu, X.Gao, Y.Wu, J.Wang, J.Ke, H.Liu, Z.Dai, S.Lei, X.Li, C.

(2025) Proc Natl Acad Sci U S A 122: e2515322122-e2515322122

  • DOI: https://doi.org/10.1073/pnas.2515322122
  • Primary Citation of Related Structures:  
    9UBI

  • PubMed Abstract: 

    Since its initial identification as the receptor for Rapid Alkalinization Factor 1 (RALF1), FERONIA (FER) receptor kinase has emerged as a central signaling hub coordinating plant development, stress adaptation, and immune responses. Nevertheless, fundamental questions persist regarding the precise mechanisms of FER-mediated signal transduction and its context-dependent functional specialization in multicellular processes. Here, we develop Ferovicin (FRV), a small-molecule inhibitor that specifically disrupts FER kinase activity, thereby enabling mechanistic dissection of FER. Cocrystallization and mutational analysis show that FRV selectively binds to the ATP-binding pocket of the kinase domain of FER and inhibits its kinase activity. Assisted by the FRV tool and quantitative phosphoproteomics, we characterized a series of signaling pathways and networks regulated by RALF1 and FER. Notably, our analysis reveals that RALF1 activates FER through phosphorylation at Ser695, which subsequently inhibits H + -ATPase1/2 via phosphorylation at Ser899. This mechanism leads to apoplastic alkalinization and regulates cell expansion in the root meristem. Given the conservation of FRV binding sites in FER proteins across land plant species, FRV will serve as a valuable tool for dissecting FER signaling mechanisms as well as facilitating agricultural applications.


  • Organizational Affiliation
    • Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-like protein kinase FERONIAA [auth B],
B [auth A]
327Arabidopsis thalianaMutation(s): 0 
Gene Names: FERAAK1SIRSRNAt3g51550F26O13.190
EC: 2.7.11.1
UniProt
Find proteins for Q9SCZ4 (Arabidopsis thaliana)
Explore Q9SCZ4 
Go to UniProtKB:  Q9SCZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SCZ4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OT5 (Subject of Investigation/LOI)
Query on OT5

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
1-[6-(3,5-dichloro-4-hydroxyphenyl)-4-({trans-4-[(dimethylamino)methyl]cyclohexyl}amino)-1,5-naphthyridin-3-yl]ethanone
C25 H28 Cl2 N4 O2
DKZYXHCYPUVGAF-JCNLHEQBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.203 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.794α = 90
b = 83.114β = 93.376
c = 61.993γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22193073

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references