7C8L

Hybrid designing of potent inhibitors of Striga strigolactone receptor ShHTL7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Rational design of Striga hermonthica-specific seed germination inhibitors.

Zarban, R.A.Hameed, U.F.S.Jamil, M.Ota, T.Wang, J.Y.Arold, S.T.Asami, T.Al-Babili, S.

(2022) Plant Physiol 188: 1369-1384

  • DOI: https://doi.org/10.1093/plphys/kiab547
  • Primary Citation of Related Structures:  
    7C8L

  • PubMed Abstract: 

    The obligate hemiparasitic weed Striga hermonthica grows on cereal roots and presents a severe threat to global food security by causing enormous yield losses, particularly in sub-Saharan Africa. The rapidly increasing Striga seed bank in infested soils provides a major obstacle in controlling this weed. Striga seeds require host-derived strigolactones (SLs) for germination, and corresponding antagonists could be used as germination inhibitors. Recently, we demonstrated that the common detergent Triton X-100 is a specific inhibitor of Striga seed germination by binding noncovalently to its receptor, S. hermonthica HYPO-SENSITIVE TO LIGHT 7 (ShHTL7), without blocking the rice (Oryza sativa) SL receptor DWARF14 (OsD14). Moreover, triazole ureas, the potent covalently binding antagonists of rice SL perception with much higher activity toward OsD14, showed inhibition of Striga but were less specific. Considering that Triton X-100 is not suitable for field application and by combining structural elements of Triton and triazole urea, we developed two hybrid compounds, KK023-N1 and KK023-N2, as potential Striga-specific germination inhibitors. Both compounds blocked the hydrolysis activity of ShHTL7 but did not affect that of OsD14. Binding of KK023-N1 diminished ShHTL7 interaction with S. hermonthica MORE AXILLARY BRANCHING 2, a major component in SL signal transduction, and increased ShHTL7 thermal specificity. Docking studies indicate that KK023-N1 binding is not covalent but is caused by hydrophobic interactions. Finally, in vitro and greenhouse tests revealed specific inhibition of Striga seed germination, which led to a 38% reduction in Striga infestation in pot experiments. These findings reveal that KK023-N1 is a potential candidate for combating Striga and a promising basis for rational design and development of further Striga-specific herbicides.


  • Organizational Affiliation

    Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, The BioActives Lab, Thuwal, 23955-6900, Saudi Arabia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hyposensitive to light 7276Striga hermonthicaMutation(s): 0 
UniProt
Find proteins for A0A0M3PNA2 (Striga hermonthica)
Explore A0A0M3PNA2 
Go to UniProtKB:  A0A0M3PNA2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3PNA2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EGC (Subject of Investigation/LOI)
Query on EGC

Download Ideal Coordinates CCD File 
B [auth A]2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOX Y}-ETHOXY)-ETHANOL
C32 H58 O10
VJYAJQFKKLYARJ-UHFFFAOYSA-N
FP6 (Subject of Investigation/LOI)
Query on FP6

Download Ideal Coordinates CCD File 
F [auth A]pyrrolidine-1-carbaldehyde
C5 H9 N O
AGRIQBHIKABLPJ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.474α = 90
b = 92.474β = 90
c = 80.256γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references, Structure summary
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description