6YAQ

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 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 10.1093/jxb/eraa437
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytokinin dehydrogenase 8A520Zea maysMutation(s): 0 
Gene Names: CKX8ZEAMMB73_Zm00001d053578
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
OHZ Binding MOAD:  6YAQ IC50: 59 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • 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