1PWP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nsmb711

  • 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 mitog ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lethal factor
A, B
776Bacillus anthracisGene 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, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NSC
Query on NSC

Download SDF File 
Download CCD File 
A, B
N,N'-BIS(4-AMINO-2-METHYLQUINOLIN-6-YL)UREA
C21 H20 N6 O
HOUSDILKOJMENG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NSCKi: 500 nM (99) BINDINGDB
NSCIC50: 3200 nM (99) BINDINGDB
NSCKi: 500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 96.700α = 90.00
b = 137.400β = 98.00
c = 98.300γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance