Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.84 kDa 
• Atom Count: 4,228 
• Modelled Residue Count: 503 
• Deposited Residue Count: 519 
• Unique protein chains: 1

 4WF6

Anthrax toxin lethal factor with bound small molecule inhibitor MK-31

• PDB DOI: 10.2210/pdb4WF6/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-09-12 Released: 2015-09-09 
• Deposition Author(s): Maize, K.M., De la Mora-Rey, T., Finzel, B.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Minnesota Dept. of Employment and Economic Development

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.240 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Probing the S2' Subsite of the Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates.

Kurbanov, E.K., Chiu, T.L., Solberg, J., Francis, S., Maize, K.M., Fernandez, J., Johnson, R.L., Hawkinson, J.E., Walters, M.A., Finzel, B.C., Amin, E.A.

(2015) J Med Chem 58: 8723-8733

• PubMed: 26492514 
• DOI: 10.1021/acs.jmedchem.5b01446
• Primary Citation of Related Structures:  
  4WF6, 5D1S, 5D1T, 5D1U


• PubMed Abstract: 
  

The lethal factor (LF) enzyme secreted by Bacillus anthracis is a zinc hydrolase that is chiefly responsible for anthrax-related cell death. Although many studies of the design of small molecule LF inhibitors have been conducted, no LF inhibitor is yet available as a therapeutic agent. Inhibitors with considerable chemical diversity have been developed and investigated; however, the LF S2' subsite has not yet been systematically explored as a potential target for lead optimization. Here we present synthesis, experimental evaluation, modeling, and structural biology for a novel series of sulfonamide hydroxamate LF inhibitor analogues specifically designed to extend into, and probe chemical preferences of, this S2' subsite. We discovered that this region accommodates a wide variety of chemical functionalities and that a broad selection of ligand structural modifications directed to this area can be incorporated without significant deleterious alterations in biological activity. We also identified key residues in this subsite that can potentially be targeted to improve inhibitor binding.

---

Related Citations: 

• The discovery of a potent and selective lethal factor inhibitor for adjunct therapy of anthrax infection.
  Xiong, Y., Wiltsie, J., Woods, A., Guo, J., Pivnichny, J.V., Tang, W., Bansal, A., Cummings, R.T., Cunningham, B.R., Friedlander, A.M., Douglas, C.M., Salowe, S.P., Zaller, D.M., Scolnick, E.M., Schmatz, D.M., Bartizal, K., Hermes, J.D., MacCoss, M., Chapman, K.T.
  (2006) Bioorg Med Chem Lett 16: 964

---

Organizational Affiliation: 

Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota , Minneapolis, Minnesota 55455, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lethal factor	A	519	Bacillus anthracis	Mutation(s): 1  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
407	C [auth A]	N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide C10 H13 F N2 O4 S PGNDHTMCXOFNMS-SSDOTTSWSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
407	BindingDB:  4WF6	IC50: min: 130, max: 1600 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.240 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.4	α = 90
b = 75.2	β = 90
c = 138.8	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Maize, K.M., De la Mora-Rey, T., Finzel, B.C.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5T32-GM008700
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI091790-01
Minnesota Dept. of Employment and Economic Development	United States	SPAP-06-0014-P-FY07

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-11-11
  Changes: Database references
• Version 1.2: 2015-11-25
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence