1SQI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 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-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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-hydroxyphenylpyruvic acid dioxygenaseA, B393Rattus norvegicusMutation(s): 0 
Gene Names: Hpd
EC: 1.13.11.27
Find proteins for P32755 (Rattus norvegicus)
Explore P32755 
Go to UniProtKB:  P32755
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
869
Query on 869

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

Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
869IC50:  20   nM  Binding MOAD
869IC50 :  20   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.611α = 90
b = 107.481β = 90
c = 133.029γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
MLPHAREphasing
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance