4DV8

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lethal factorA526Bacillus anthracisMutation(s): 0 
Gene Names: lefpXO1-107BXA0172GBAA_pXO1_0172
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0LX
Query on 0LX

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
MLI
Query on MLI

Download Ideal Coordinates CCD File 
D [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 57.09α = 90
b = 74.253β = 90
c = 139.53γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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