5EKW

A. thaliana IGPD2 in complex with the racemate of the triazole-phosphonate inhibitor, C348


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide.

Bisson, C.Britton, K.L.Sedelnikova, S.E.Rodgers, H.F.Eadsforth, T.C.Viner, R.C.Hawkes, T.R.Baker, P.J.Rice, D.W.

(2016) Angew Chem Int Ed Engl 55: 13485-13489

  • DOI: 10.1002/anie.201607185
  • Primary Citation of Related Structures:  
    5DNL, 5DNX, 5EKW, 5EL9, 5ELW

  • PubMed Abstract: 
  • Programs of drug discovery generally exploit one enantiomer of a chiral compound for lead development following the principle that enantiomer recognition is central to biological specificity. However, chiral promiscuity has been identified for a number of enzyme families, which have shown that mirror-image packing can enable opposite enantiomers to be accommodated in an enzyme's active site ...

    Programs of drug discovery generally exploit one enantiomer of a chiral compound for lead development following the principle that enantiomer recognition is central to biological specificity. However, chiral promiscuity has been identified for a number of enzyme families, which have shown that mirror-image packing can enable opposite enantiomers to be accommodated in an enzyme's active site. Reported here is a series of crystallographic studies of complexes between an enzyme and a potent experimental herbicide whose chiral center forms an essential part of the inhibitor pharmacophore. Initial studies with a racemate at 1.85 Å resolution failed to identify the chirality of the bound inhibitor, however, by extending the resolution to 1.1 Å and by analyzing high-resolution complexes with the enantiopure compounds, we determined that both enantiomers make equivalent pseudosymmetric interactions in the active site, thus mimicking an achiral reaction intermediate.


    Organizational Affiliation

    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK. d.rice@sheffield.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Imidazoleglycerol-phosphate dehydratase 2, chloroplasticA205Arabidopsis thalianaMutation(s): 0 
Gene Names: HISN5BAt4g14910dl3495c
EC: 4.2.1.19
UniProt
Find proteins for O23346 (Arabidopsis thaliana)
Explore O23346 
Go to UniProtKB:  O23346
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5LD (Subject of Investigation/LOI)
Query on 5LD

Download Ideal Coordinates CCD File 
E [auth A][(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid
C5 H10 N3 O4 P
ZXKJPBBOMRHTCH-RXMQYKEDSA-N
 Ligand Interaction
5DL (Subject of Investigation/LOI)
Query on 5DL

Download Ideal Coordinates CCD File 
D [auth A][(2S)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid
C5 H10 N3 O4 P
ZXKJPBBOMRHTCH-YFKPBYRVSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
L [auth A], M [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
N [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.905α = 90
b = 112.905β = 90
c = 112.905γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2016-10-26
    Changes: Database references
  • Version 2.0: 2018-11-28
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-10-09
    Changes: Data collection