3SH0

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1065


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antibacterial drug leads targeting isoprenoid biosynthesis.

Zhu, W.Zhang, Y.Sinko, W.Hensler, M.E.Olson, J.Molohon, K.J.Lindert, S.Cao, R.Li, K.Wang, K.Wang, Y.Liu, Y.L.Sankovsky, A.de Oliveira, C.A.Mitchell, D.A.Nizet, V.McCammon, J.A.Oldfield, E.

(2013) Proc.Natl.Acad.Sci.USA 110: 123-128

  • DOI: 10.1073/pnas.1219899110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • With the rise in resistance to antibiotics such as methicillin, there is a need for new drugs. We report here the discovery and X-ray crystallographic structures of 10 chemically diverse compounds (benzoic, diketo, and phosphonic acids, as well as a ...

    With the rise in resistance to antibiotics such as methicillin, there is a need for new drugs. We report here the discovery and X-ray crystallographic structures of 10 chemically diverse compounds (benzoic, diketo, and phosphonic acids, as well as a bisamidine and a bisamine) that inhibit bacterial undecaprenyl diphosphate synthase, an essential enzyme involved in cell wall biosynthesis. The inhibitors bind to one or more of the four undecaprenyl diphosphate synthase inhibitor binding sites identified previously, with the most active leads binding to site 4, outside the catalytic center. The most potent leads are active against Staphylococcus aureus [minimal inhibitory concentration (MIC)(90) ∼0.25 µg/mL], and one potently synergizes with methicillin (fractional inhibitory concentration index = 0.25) and is protective in a mouse infection model. These results provide numerous leads for antibacterial development and open up the possibility of restoring sensitivity to drugs such as methicillin, using combination therapies.


    Organizational Affiliation

    Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Undecaprenyl pyrophosphate synthase
B, A
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
SAX
Query on SAX

Download SDF File 
Download CCD File 
A, B
2-(dodecyloxy)-6-hydroxybenzoic acid
C19 H30 O4
HMYWVVRALHTQJQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAXIC50: 2200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.765α = 90.00
b = 68.724β = 90.00
c = 112.056γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data scaling
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-01-16
    Type: Database references