1TG5

Crystal structures of plant 4-hydroxyphenylpyruvate dioxygenases complexed with DAS645


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    1SQD, 1SQI, 1TFZ, 1TG5

  • 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-hydroxyphenylpyruvate dioxygenase (HPPD; EC 1 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-hydroxyphenylpyruvate dioxygenase A424Arabidopsis thalianaMutation(s): 0 
Gene Names: HPDAt1g06570F12K11.9PDS1
EC: 1.13.11.27
Find proteins for P93836 (Arabidopsis thaliana)
Explore P93836 
Go to UniProtKB:  P93836
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
645
Query on 645

Download Ideal Coordinates CCD File 
A
[1-TERT-BUTYL-3-(2,4-DICHLOROPHENYL)-5-HYDROXY-1H-PYRAZOL-4-YL][2-CHLORO-4-(METHYLSULFONYL)PHENYL]METHANONE
C21 H19 Cl3 N2 O4 S
HVZVWLVEDDWLOA-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
645IC50:  12   nM  Binding MOAD
645IC50 :  12   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.464α = 90
b = 83.871β = 102.28
c = 63.301γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2012-05-09
    Changes: Structure summary
  • Version 1.4: 2018-04-04
    Changes: Data collection