Crystal Structure of DAD2 bound to quinazolinone derivative

Experimental Data Snapshot

  • Resolution: 1.63 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

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Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode.

Hamiaux, C.Larsen, L.Lee, H.W.Luo, Z.Sharma, P.Hawkins, B.C.Perry, N.B.Snowden, K.C.

(2019) Biochem J 476: 1843-1856

  • DOI: https://doi.org/10.1042/BCJ20190288
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Strigolactones (SLs) are multifunctional plant hormones regulating essential physiological processes affecting growth and development. In vascular plants, SLs are recognized by α/β hydrolase-fold proteins from the D14/DAD2 (Dwarf14/Decreased Apical Dominance 2) family in the initial step of the signaling pathway. We have previously discovered that N -phenylanthranilic acid derivatives (e.g. tolfenamic acid) are potent antagonists of SL receptors, prompting us to design quinazolinone and quinazolinedione derivatives (QADs and QADDs, respectively) as second-generation antagonists. Initial in silico docking studies suggested that these compounds would bind to DAD2, the petunia SL receptor, with higher affinity than the first-generation compounds. However, only one of the QADs/QADDs tested in in vitro assays acted as a competitive antagonist of SL receptors, with reduced affinity and potency compared with its N -phenylanthranilic acid 'parent'. X-ray crystal structure analysis revealed that the binding mode of the active QADD inside DAD2's cavity was not that predicted in silico , highlighting a novel inhibition mechanism for SL receptors. Despite a ∼10-fold difference in potency in vitro , the QADD and tolfenamic acid had comparable activity in planta , suggesting that the QADD compensates for lower potency with increased bioavailability. Altogether, our results establish this QADD as a novel lead compound towards the development of potent and bioavailable antagonists of SL receptors.

  • Organizational Affiliation

    The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand cyril.hamiaux@plantandfood.co.nz.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable strigolactone esterase DAD2
A, B
264Petunia x hybridaMutation(s): 1 
Gene Names: DAD2
EC: 3.1
Find proteins for J9U5U9 (Petunia hybrida)
Explore J9U5U9 
Go to UniProtKB:  J9U5U9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9U5U9
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.63 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.63α = 95.69
b = 56.83β = 94.59
c = 68.8γ = 108.74
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-06-26 
  • Deposition Author(s): Hamiaux, C.

Funding OrganizationLocationGrant Number
Royal Society of New ZealandNew ZealandPAF1301

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description