6PSL

Structure of a N-Me-D-Gln4,D-aza-Thr8,Arg10-teixobactin analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.117 
  • R-Value Work: 0.092 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Design, Synthesis, and Study of Lactam and Ring-Expanded Analogues of Teixobactin.

Yang, H.Pishenko, A.V.Li, X.Nowick, J.S.

(2020) J Org Chem 85: 1331-1339

  • DOI: https://doi.org/10.1021/acs.joc.9b02631
  • Primary Citation of Related Structures:  
    6PSL

  • PubMed Abstract: 

    This paper describes the chemical synthesis, X-ray crystallographic structure, and antibiotic activity assay of lactam analogues of teixobactin and explores ring-expanded analogues of teixobactin with β 3 -homo amino acids. Lactam analogues of teixobactin containing all four stereoisomers of aza-threonine at position 8 were synthesized on a solid support from commercially available stereoisomeric threonine derivatives. The threonine stereoisomers are converted to the diastereomeric aza-threonines by mesylation, azide displacement, and reduction during the synthesis. d-Aza-Thr 8 ,Arg 10 -teixobactin exhibits 2-8-fold greater antibiotic activity than the corresponding macrolactone Arg 10 -teixobactin. Azateixobactin analogues containing other stereoisomers of aza-threonine are inactive. A dramatic 16-128-fold increase in the activity of teixobactin and teixobactin analogues is observed with the inclusion of 0.002% of the mild detergent polysorbate 80 in the MIC assay. The X-ray crystallographic structure of N -Me-d-Gln 4 ,d-aza-Thr 8 ,Arg 10 -teixobactin reveals an amphipathic hydrogen-bonded antiparallel β-sheet dimer that binds chloride anions. In the binding site, the macrolactam amide NH groups of residues 8, 10, and 11, as well as the extra amide NH group of the lactam ring, hydrogen bond to the chloride anion. The teixobactin pharmacophore tolerates ring expansion of the 13-membered ring to 14-,15-, and 16-membered rings containing β 3 -homo amino acids with retention of partial or full antibiotic activity.


  • Organizational Affiliation

    Department of Chemistry and Department of Pharmaceutical Sciences , University of California , Irvine , California 92697-2025 , United States.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
teixobactin analogue11synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.117 
  • R-Value Work: 0.092 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 20.024α = 90
b = 20.024β = 90
c = 32.328γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R21AI121548-01
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56AI137258

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2021-09-15
    Changes: Advisory, Database references, Derived calculations
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection