Structure of S. aureus undecaprenyl diphosphate synthase in complex with FPP and sulfate

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1073/pnas.1219899110
  • Primary Citation of Related Structures:  
    3SGT, 3SGV, 3SGX, 3SH0, 4H2J, 4H2M, 4H2O, 4H38, 4H3A, 4H3C, 4H8E

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Undecaprenyl pyrophosphate synthase256Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: uppSSA1103
Find proteins for P60477 (Staphylococcus aureus (strain N315))
Explore P60477 
Go to UniProtKB:  P60477
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60477
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.303α = 90
b = 57.303β = 90
c = 158.824γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2013-01-16
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations