Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.97 kDa 
• Atom Count: 5,034 
• Modelled Residue Count: 512 
• Deposited Residue Count: 526 
• Unique protein chains: 1

 4DV8

Anthrax Lethal Factor metalloproteinase in complex with the Hydroxamic acid based small molecule PT8421

• PDB DOI: 10.2210/pdb4DV8/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-22 Released: 2012-03-14 
• Deposition Author(s): Margosiak, S.A., Sankaran, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Literature

Antidotes to anthrax lethal factor intoxication. Part 3: Evaluation of core structures and further modifications to the C2-side chain.

Jiao, G.S., Kim, S., Moayeri, M., Crown, D., Thai, A., Cregar-Hernandez, L., McKasson, L., Sankaran, B., Lehrer, A., Wong, T., Johns, L., Margosiak, S.A., Leppla, S.H., Johnson, A.T.

(2012) Bioorg Med Chem Lett 22: 2242

• PubMed: 22342144 
• DOI: 10.1016/j.bmcl.2012.01.095
• Primary Citation of Related Structures:  
  4DV8


• PubMed Abstract: 
  

Four core structures capable of providing sub-nanomolar inhibitors of anthrax lethal factor (LF) were evaluated by comparing the potential for toxicity, physicochemical properties, in vitro ADME profiles, and relative efficacy in a rat lethal toxin (LT) model of LF intoxication. Poor efficacy in the rat LT model exhibited by the phenoxyacetic acid series (3) correlated with low rat microsome and plasma stability. Specific molecular interactions contributing to the high affinity of inhibitors with a secondary amine in the C2-side chain were revealed by X-ray crystallography.

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Organizational Affiliation: 

PanThera Biopharma, LLC, Aiea, HI 96701, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lethal factor	A	526	Bacillus anthracis	Mutation(s): 0  Gene Names: lef, pXO1-107, BXA0172, GBAA_pXO1_0172 EC: 3.4.24.83
UniProt
Find proteins for P15917 (Bacillus anthracis) Explore P15917  Go to UniProtKB:  P15917

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0LX	C [auth A]	(2S)-6-[(4-fluorobenzyl)amino]-2-[(2R)-2-(4-fluorophenyl)-2-methoxyethyl]-N-hydroxyhexanamide C22 H28 F2 N2 O3 SZPWYHRMRFNOHH-GHTZIAJQSA-N
MLI	D [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0LX	PDBBind:  4DV8	Ki: 0.58 (nM) from 1 assay(s)
	BindingDB:  4DV8	Ki: 0.58 (nM) from 1 assay(s)
	Binding MOAD:  4DV8	Ki: 0.58 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.09	α = 90
b = 74.253	β = 90
c = 139.53	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Margosiak, S.A., Sankaran, B.

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Advisory, Refinement description