1TFZ

Structural basis for herbicidal inhibitor selectivity revealed by comparison of crystal structures of plant and mammalian 4-hydroxyphenylpyruvate dioxygenases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for herbicidal inhibitor selectivity revealed by comparison of crystal structures of plant and Mammalian 4-hydroxyphenylpyruvate dioxygenases

Yang, C.Pflugrath, J.W.Camper, D.L.Foster, M.L.Pernich, D.J.Walsh, T.A.

(2004) Biochemistry 43: 10414-10423

  • DOI: 10.1021/bi049323o
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A high degree of selectivity toward the target site of the pest organism is a desirable attribute for new safer agrochemicals. To assist in the design of novel herbicides, we determined the crystal structures of the herbicidal target enzyme 4-hydroxy ...

    A high degree of selectivity toward the target site of the pest organism is a desirable attribute for new safer agrochemicals. To assist in the design of novel herbicides, we determined the crystal structures of the herbicidal target enzyme 4-hydroxyphenylpyruvate dioxygenase (HPPD; EC 1.13.11.27) from the plant Arabidopsis thaliana with and without an herbicidal benzoylpyrazole inhibitor that potently inhibits both plant and mammalian HPPDs. We also determined the structure of a mammalian (rat) HPPD in complex with the same nonselective inhibitor. From a screening campaign of over 1000 HPPD inhibitors, six highly plant-selective inhibitors were found. One of these had remarkable (>1600-fold) selectivity toward the plant enzyme and was cocrystallized with Arabidopsis HPPD. Detailed comparisons of the plant and mammalian HPPD-ligand structures suggest a structural basis for the high degree of plant selectivity of certain HPPD inhibitors and point to design strategies to obtain potent and selective inhibitors of plant HPPD as agrochemical leads.


    Organizational Affiliation

    Rigaku/MSC Inc., 9009 New Trails Drive, The Woodlands, Texas 77381, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-hydroxyphenylpyruvate dioxygenase
A
424Arabidopsis thalianaMutation(s): 0 
Gene Names: HPD (PDS1)
EC: 1.13.11.27
Find proteins for P93836 (Arabidopsis thaliana)
Go to Gene View: HPD
Go to UniProtKB:  P93836
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
869
Query on 869

Download SDF File 
Download CCD File 
A
(1-TERT-BUTYL-5-HYDROXY-1H-PYRAZOL-4-YL)[6-(METHYLSULFONYL)-4'-METHOXY-2-METHYL-1,1'-BIPHENYL-3-YL]METHANONE
(1-TERT-BUTYL-5-HYDROXY-1H-PYRAZOL-4-YL)-(6-METHANESULFONYL-4'-METHOXY-2-METHYL-BIPHENYL-3-YL)-METHANONE
C23 H26 N2 O5 S
AVFXBZIGDFPGBY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
869IC50: 7 nM BINDINGMOAD
869IC50: 7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.400α = 90.00
b = 83.700β = 102.40
c = 63.300γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
CrystalCleardata collection
REFMACrefinement
d*TREKdata reduction
CrystalCleardata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection