5EL9

A. thaliana IGPD2 in complex with the triazole-phosphonate inhibitor, (S)-C348, to 1.1A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Imidazoleglycerol-phosphate dehydratase 2, chloroplastic205Arabidopsis thalianaMutation(s): 0 
Gene Names: HISN5BAt4g14910dl3495c
EC: 4.2.1.19
UniProt
Find proteins for O23346 (Arabidopsis thaliana)
Explore O23346 
Go to UniProtKB:  O23346
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO23346
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5DL
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
TRS
Query on TRS

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

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

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5DL Binding MOAD:  5EL9 Ki: 23 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.62α = 90
b = 112.62β = 90
c = 112.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

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 1.3: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description