6YAQ | pdb_00006yaq

Crystal sttructure of ZmCKO8 in complex with inhibitor 1-(3-Chloro-5-trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.210 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6YAQ

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture.

Nisler, J.Kopecny, D.Pekna, Z.Koncitikova, R.Koprna, R.Murvanidze, N.Werbrouck, S.P.O.Havlicek, L.De Diego, N.Kopecna, M.Wimmer, Z.Briozzo, P.Morera, S.Zalabak, D.Spichal, L.Strnad, M.

(2021) J Exp Bot 72: 355-370

  • DOI: https://doi.org/10.1093/jxb/eraa437
  • Primary Citation Related Structures: 
    6YAO, 6YAP, 6YAQ

  • PubMed Abstract: 

    Increasing crop productivity is our major challenge if we are to meet global needs for food, fodder and fuel. Controlling the content of the plant hormone cytokinin is a method of improving plant productivity. Cytokinin oxidase/dehydrogenase (CKO/CKX) is a major target in this regard because it degrades cytokinins. Here, we describe the synthesis and biological activities of new CKX inhibitors derived mainly from diphenylurea. They were tested on four CKX isoforms from maize and Arabidopsis, where the best compounds showed IC50 values in the 10-8 M concentration range. The binding mode of the most efficient inhibitors was characterized from high-resolution crystal complexed structures. Although these compounds do not possess intrinsic cytokinin activity, we have demonstrated their tremendous potential for use in the plant tissue culture industry as well as in agriculture. We have identified a key substance, compound 19, which not only increases stress resistance and seed yield in Arabidopsis, but also improves the yield of wheat, barley and rapeseed grains under field conditions. Our findings reveal that modulation of cytokinin levels via CKX inhibition can positively affect plant growth, development and yield, and prove that CKX inhibitors can be an attractive target in plant biotechnology and agriculture.


  • Organizational Affiliation
    • Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Palacký University, Šlechtitelů 27, Olomouc, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 59.25 kDa 
  • Atom Count: 4,483 
  • Modeled Residue Count: 499 
  • Deposited Residue Count: 520 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytokinin dehydrogenase 8520Zea maysMutation(s): 0 
Gene Names: CKX8
EC: 1.5.99.12
UniProt
Find proteins for A0A1D6QQD6 (Zea mays)
Explore A0A1D6QQD6 
Go to UniProtKB:  A0A1D6QQD6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D6QQD6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 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
OHZ
(Subject of Investigation/LOI)

Query on OHZ



Download:Ideal Coordinates CCD File
B [auth A]1-(3-Chloro-5-trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea
C16 H14 Cl F3 N2 O3
MFPOPEHXGDSREH-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.210 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.518α = 90
b = 101.518β = 90
c = 128.171γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary