3SGV

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1290


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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 U S A 110: 123-128

  • DOI: 10.1073/pnas.1219899110
  • Primary Citation of Related Structures:  
    3SGX, 3SH0, 3SGT, 3SGV, 4H3A, 4H3C, 4H8E, 4H38, 4H2O, 4H2J

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Undecaprenyl pyrophosphate synthaseAB253Escherichia coli K-12Mutation(s): 0 
Gene Names: b0174ispUJW0169rthuppSyaeS
EC: 2.5.1.31
Find proteins for P60472 (Escherichia coli (strain K12))
Explore P60472 
Go to UniProtKB:  P60472
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2BJ
Query on 2BJ

Download CCD File 
A, B
2-{[3-(3,4-dimethylphenoxy)phenyl]carbamoyl}-4-nitrobenzoic acid
C22 H18 N2 O6
GQGBAJUULMBPOF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2BJIC50 :  35000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.139α = 90
b = 69.004β = 90
c = 112.561γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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