5CQJ

Crystal structure of E. coli undecaprenyl pyrophosphate synthase in complex with clomiphene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Antagonism screen for inhibitors of bacterial cell wall biogenesis uncovers an inhibitor of undecaprenyl diphosphate synthase.

Farha, M.A.Czarny, T.L.Myers, C.L.Worrall, L.J.French, S.Conrady, D.G.Wang, Y.Oldfield, E.Strynadka, N.C.Brown, E.D.

(2015) Proc.Natl.Acad.Sci.USA 112: 11048-11053

  • DOI: 10.1073/pnas.1511751112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Drug combinations are valuable tools for studying biological systems. Although much attention has been given to synergistic interactions in revealing connections between cellular processes, antagonistic interactions can also have tremendous value in ...

    Drug combinations are valuable tools for studying biological systems. Although much attention has been given to synergistic interactions in revealing connections between cellular processes, antagonistic interactions can also have tremendous value in elucidating genetic networks and mechanisms of drug action. Here, we exploit the power of antagonism in a high-throughput screen for molecules that suppress the activity of targocil, an inhibitor of the wall teichoic acid (WTA) flippase in Staphylococcus aureus. Well-characterized antagonism within the WTA biosynthetic pathway indicated that early steps would be sensitive to this screen; however, broader interactions with cell wall biogenesis components suggested that it might capture additional targets. A chemical screening effort using this approach identified clomiphene, a widely used fertility drug, as one such compound. Mechanistic characterization revealed the target was the undecaprenyl diphosphate synthase, an enzyme that catalyzes the synthesis of a polyisoprenoid essential for both peptidoglycan and WTA synthesis. The work sheds light on mechanisms contributing to the observed suppressive interactions of clomiphene and in turn reveals aspects of the biology that underlie cell wall synthesis in S. aureus. Further, this effort highlights the utility of antagonistic interactions both in high-throughput screening and in compound mode of action studies. Importantly, clomiphene represents a lead for antibacterial drug discovery.


    Organizational Affiliation

    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8N 3Z5; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON, Canada L8N 3Z5;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
A, B
253Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ispU (rth, uppS, yaeS)
EC: 2.5.1.31
Find proteins for P60472 (Escherichia coli (strain K12))
Go to UniProtKB:  P60472
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
53Q
Query on 53Q

Download SDF File 
Download CCD File 
A
Clomifene
1-[(E)-2-chloro-1,2-diphenylethenyl]-4-methoxybenzene, clomiphene
C21 H17 Cl O
CRZZNHLZXLMEPA-QZQOTICOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
53QIC50: 7500 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.312α = 90.00
b = 68.488β = 90.00
c = 111.630γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Database references
  • Version 1.2: 2015-09-09
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Database references, Derived calculations, Refinement description