1PWP

Crystal Structure of the Anthrax Lethal Factor complexed with Small Molecule Inhibitor NSC 12155


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Identification of small molecule inhibitors of anthrax lethal factor.

Panchal, R.G.Hermone, A.R.Nguyen, T.L.Wong, T.Y.Schwarzenbacher, R.Schmidt, J.Lane, D.McGrath, C.Turk, B.E.Burnett, J.Aman, M.J.Little, S.Sausville, E.A.Zaharevitz, D.W.Cantley, L.C.Liddington, R.C.Gussio, R.Bavari, S.

(2004) Nat Struct Mol Biol 11: 67-72

  • DOI: https://doi.org/10.1038/nsmb711
  • Primary Citation of Related Structures:  
    1PWP

  • PubMed Abstract: 

    The virulent spore-forming bacterium Bacillus anthracis secretes anthrax toxin composed of protective antigen (PA), lethal factor (LF) and edema factor (EF). LF is a Zn-dependent metalloprotease that inactivates key signaling molecules, such as mitogen-activated protein kinase kinases (MAPKK), to ultimately cause cell death. We report here the identification of small molecule (nonpeptidic) inhibitors of LF. Using a two-stage screening assay, we determined the LF inhibitory properties of 19 compounds. Here, we describe six inhibitors on the basis of a pharmacophoric relationship determined using X-ray crystallographic data, molecular docking studies and three-dimensional (3D) database mining from the US National Cancer Institute (NCI) chemical repository. Three of these compounds have K(i) values in the 0.5-5 microM range and show competitive inhibition. These molecular scaffolds may be used to develop therapeutically viable inhibitors of LF.


  • Organizational Affiliation

    Developmental Therapeutics Program, NCI Frederick, Frederick, Maryland 21702-1201, USA. panchal@dtpax2.ncifcrf.gov


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lethal factor
A, B
776Bacillus anthracisMutation(s): 0 
Gene Names: LEF
EC: 3.4.24.83
UniProt
Find proteins for P15917 (Bacillus anthracis)
Explore P15917 
Go to UniProtKB:  P15917
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15917
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
NSC PDBBind:  1PWP Ki: 500 (nM) from 1 assay(s)
BindingDB:  1PWP Ki: 500 (nM) from 1 assay(s)
IC50: 3200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.7α = 90
b = 137.4β = 98
c = 98.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description