8CM2

Crystal structure of maize cytokinin oxidase/dehydrogenase 4 (CKO/CKX4) in complex with inhibitor 2-[[3,5-dichloro-2-(2-hydroxyethyl)phenyl]carbamoylamino]-4-(trifluoromethoxy)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Cytokinin oxidase/dehydrogenase inhibitors: progress towards agricultural practice.

Nisler, J.Klimes, P.Koncitikova, R.Kadlecova, A.Voller, J.Chalaki, M.Karampelias, M.Murvanidze, N.Werbrouck, S.P.O.Kopecny, D.Havlicek, L.De Diego, N.Briozzo, P.Morera, S.Zalabak, D.Spichal, L.

(2024) J Exp Bot 75: 4873-4890

  • DOI: https://doi.org/10.1093/jxb/erae239

  • PubMed Abstract: 

    Cytokinin oxidase/dehydrogenase (CKX) inhibitors reduce the degradation of cytokinins in plants and thereby may improve the efficiency of agriculture and plant tissue culture-based practices. Here, we report a synthesis and structure-activity relationship study of novel urea derivatives concerning their CKX inhibitory activity. The best compounds showed sub-nanomolar IC50 values with maize ZmCKX1, the lowest value yet documented. Other CKX isoforms of maize (Zea mays) and Arabidopsis were also inhibited very effectively. The binding mode of four compounds was characterized based on high-resolution crystal complex structures. Using the soil nematode Caenorhabditis elegans, and human skin fibroblasts, key CKX inhibitors with low toxicity were identified. These compounds enhanced the shoot regeneration of Lobelia, Drosera, and Plectranthus, as well as the growth of Arabidopsis and Brassica napus. At the same time, a key compound (namely 82), activated a cytokinin primary response gene ARR5:GUS and cytokinin sensor TCSv2:GUS, without activating the Arabidopsis cytokinin receptors AHK3 and AHK4. This strongly implies that the effect of compound 82 is due to the upregulation of cytokinin signalling. Overall, this work presents highly effective and easily prepared CKX inhibitors with a low risk of environmental toxicity for further investigation of their potential in agriculture and biotechnology.


  • Organizational Affiliation

    Isotope Laboratory, Institute of Experimental Botany, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytokinin dehydrogenase 4541Zea maysMutation(s): 0 
Gene Names: CKX4
EC: 1.5.99.12
UniProt
Find proteins for E3T1W8 (Zea mays)
Explore E3T1W8 
Go to UniProtKB:  E3T1W8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3T1W8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
V1X (Subject of Investigation/LOI)
Query on V1X

Download Ideal Coordinates CCD File 
B [auth A]2-[[3,5-bis(chloranyl)-2-(2-hydroxyethyl)phenyl]carbamoylamino]-4-(trifluoromethyloxy)benzamide
C17 H14 Cl2 F3 N3 O4
ZBQIFPAPLDHKHL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.53α = 90
b = 79.53β = 90
c = 203.31γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic21-07661S
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCZ.02.1.01/0.0/0.0/16_019/0000827

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references
  • Version 1.2: 2024-09-04
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Structure summary