1YQY

Structure of B. Anthrax Lethal factor in complex with a hydroxamate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Anthrax lethal factor inhibition.

Shoop, W.L.Xiong, Y.Wiltsie, J.Woods, A.Guo, J.Pivnichny, J.V.Felcetto, T.Michael, B.F.Bansal, A.Cummings, R.T.Cunningham, B.R.Friedlander, A.M.Douglas, C.M.Patel, S.B.Wisniewski, D.Scapin, G.Salowe, S.P.Zaller, D.M.Chapman, K.T.Scolnick, E.M.Schmatz, D.M.Bartizal, K.MacCoss, M.Hermes, J.D.

(2005) Proc.Natl.Acad.Sci.Usa 102: 7958-7963

  • DOI: 10.1073/pnas.0502159102

  • PubMed Abstract: 
  • The primary virulence factor of Bacillus anthracis is a secreted zinc-dependent metalloprotease toxin known as lethal factor (LF) that is lethal to the host through disruption of signaling pathways, cell destruction, and circulatory shock. Inhibition ...

    The primary virulence factor of Bacillus anthracis is a secreted zinc-dependent metalloprotease toxin known as lethal factor (LF) that is lethal to the host through disruption of signaling pathways, cell destruction, and circulatory shock. Inhibition of this proteolytic-based LF toxemia could be expected to provide therapeutic value in combination with an antibiotic during and immediately after an active anthrax infection. Herein is shown the crystal structure of an intimate complex between a hydroxamate, (2R)-2-[(4-fluoro-3-methylphenyl)sulfonylamino]-N-hydroxy-2-(tetrahydro-2H-pyran-4-yl)acetamide, and LF at the LF-active site. Most importantly, this molecular interaction between the hydroxamate and the LF active site resulted in (i) inhibited LF protease activity in an enzyme assay and protected macrophages against recombinant LF and protective antigen in a cell-based assay, (ii) 100% protection in a lethal mouse toxemia model against recombinant LF and protective antigen, (iii) approximately 50% survival advantage to mice given a lethal challenge of B. anthracis Sterne vegetative cells and to rabbits given a lethal challenge of B. anthracis Ames spores and doubled the mean time to death in those that died in both species, and (iv) 100% protection against B. anthracis spore challenge when used in combination therapy with ciprofloxacin in a rabbit "point of no return" model for which ciprofloxacin alone provided 50% protection. These results indicate that a small molecule, hydroxamate LF inhibitor, as revealed herein, can ameliorate the toxemia characteristic of an active B. anthracis infection and could be a vital adjunct to our ability to combat anthrax.


    Organizational Affiliation

    Merck Research Laboratories, Rahway, NJ 07065, USA. weseley_shoop@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lethal factor
A
523Bacillus anthracisMutation(s): 0 
Gene Names: lef
EC: 3.4.24.83
Find proteins for P15917 (Bacillus anthracis)
Go to UniProtKB:  P15917
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
915
Query on 915

Download SDF File 
Download CCD File 
A
(2R)-2-{[(4-FLUORO-3-METHYLPHENYL)SULFONYL]AMINO}-N-HYDROXY-2-TETRAHYDRO-2H-PYRAN-4-YLACETAMIDE
C14 H19 F N2 O5 S
LUCFRFDOOYLALP-CYBMUJFWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
915Ki: 24 nM (99) BINDINGDB
915IC50: 54 nM (99) BINDINGDB
915Ki: 24 nM BINDINGMOAD
915Ki: 24 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.332α = 90.00
b = 75.957β = 90.00
c = 139.006γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction
autoBUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance