6AP6

Crystal Structure of DAD2 in complex with tolfenamic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibition of strigolactone receptors byN-phenylanthranilic acid derivatives: Structural and functional insights.

Hamiaux, C.Drummond, R.S.M.Luo, Z.Lee, H.W.Sharma, P.Janssen, B.J.Perry, N.B.Denny, W.A.Snowden, K.C.

(2018) J Biol Chem 293: 6530-6543

  • DOI: https://doi.org/10.1074/jbc.RA117.001154
  • Primary Citation of Related Structures:  
    6AP6, 6AP7, 6AP8

  • PubMed Abstract: 

    The strigolactone (SL) family of plant hormones regulates a broad range of physiological processes affecting plant growth and development and also plays essential roles in controlling interactions with parasitic weeds and symbiotic fungi. Recent progress elucidating details of SL biosynthesis, signaling, and transport offers many opportunities for discovering new plant-growth regulators via chemical interference. Here, using high-throughput screening and downstream biochemical assays, we identified N -phenylanthranilic acid derivatives as potent inhibitors of the SL receptors from petunia (DAD2), rice (OsD14), and Arabidopsis (AtD14). Crystal structures of DAD2 and OsD14 in complex with inhibitors further provided detailed insights into the inhibition mechanism, and in silico modeling of 19 other plant strigolactone receptors suggested that these compounds are active across a large range of plant species. Altogether, these results provide chemical tools for investigating SL signaling and further define a framework for structure-based approaches to design and validate optimized inhibitors of SL receptors for specific plant targets.


  • Organizational Affiliation

    From the New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand, cyril.hamiaux@plantandfood.co.nz.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable strigolactone esterase DAD2
A, B
269Petunia x hybridaMutation(s): 1 
Gene Names: DAD2
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TLF (Subject of Investigation/LOI)
Query on TLF

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-[(3-chloro-2-methylphenyl)amino]benzoic acid
C14 H12 Cl N O2
YEZNLOUZAIOMLT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TLF Binding MOAD:  6AP6 Kd: 4300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.86α = 95.76
b = 55.83β = 95.13
c = 69.23γ = 108.46
Software Package:
Software NamePurpose
iMOSFLMdata processing
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2018-03-21 
  • Deposition Author(s): Hamiaux, C.

Funding OrganizationLocationGrant Number
AGMARDTNew Zealand1323
MarsdenNew ZealandPAF1301

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description