9DRH | pdb_00009drh

Crystal structure of Tet(X7) bound to anhydrotetracycline C10-benzoate ester


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.291 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

C10-Benzoate Esters of Anhydrotetracycline Inhibit Tetracycline Destructases and Recover Tetracycline Antibacterial Activity.

Williford, E.E.Xue, Y.P.Tang, W.K.Li, R.Jones, K.V.Blake, K.S.Blaine, H.C.Lian, X.Stallings, C.L.Tolia, N.H.Dantas, G.Wencewicz, T.A.

(2025) ACS Infect Dis 11: 738-749

  • DOI: https://doi.org/10.1021/acsinfecdis.4c00912
  • Primary Citation of Related Structures:  
    9DRH

  • PubMed Abstract: 

    Tetracyclines (TCs) are an important class of antibiotics threatened by enzymatic inactivation. These tetracycline-inactivating enzymes, also known as tetracycline destructases (TDases), are a subfamily of class A flavin monooxygenases (FMOs) that catalyze hydroxyl group transfer and oxygen insertion (Baeyer-Villiger type) reactions on TC substrate scaffolds. Semisynthetic modification of TCs (e.g., tigecycline, omadacycline, eravacycline, and sarecycline) has proven effective in evading certain resistance mechanisms, such as ribosomal protection and efflux, but does not protect against TDase-mediated resistance. Here, we report the design, synthesis, and evaluation of a new series of 22 semisynthetic TDase inhibitors that explore D-ring substitution of anhydrotetracycline (aTC) including 14 C10-benzoate ester and eight C9-benzamides. Overall, the C10-benzoate esters displayed enhanced bioactivity and water solubility compared to the corresponding C9-benzamides featuring the same heterocyclic aryl side chains. The C10-benzoate ester derivatives of aTC were prepared in a high-yield one-step synthesis without the need for protecting groups. The C10-esters are water-soluble, stable toward hydrolysis, and display dose-dependent rescue of tetracycline antibiotic activity in E. coli expressing two types of tetracycline destructases, represented by TetX7 (Type 1) and Tet50 (Type 2). The best inhibitors recovered tetracycline antibiotic activity at concentrations as low as 2 μM, producing synergistic scores <0.5 in the fractional inhibitory concentration index (FICI) against TDase-expressing strains of E. coli and clinical P. aeruginosa . The C10-benzoate ester derivatives of aTC reported here are promising new leads for the development of tetracycline drug combination therapies to overcome TDase-mediated antibiotic resistance.


  • Organizational Affiliation
    • Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tet(X7)398Pseudomonas aeruginosaMutation(s): 0 
EC: 1.14.13
UniProt
Find proteins for Q7X2A0 (Pseudomonas aeruginosa)
Explore Q7X2A0 
Go to UniProtKB:  Q7X2A0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7X2A0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
A1BDP (Subject of Investigation/LOI)
Query on A1BDP

Download Ideal Coordinates CCD File 
B [auth A](6aS,7S,10aS)-9-carbamoyl-7-(dimethylamino)-8,10a,12-trihydroxy-5-methyl-10,11-dioxo-6,6a,7,10,10a,11-hexahydrotetracen-1-yl pyrimidine-2-carboxylate
C27 H24 N4 O8
DFIDZPZXUCCNPB-DCOBRAFBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.291 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.73α = 90
b = 132.73β = 90
c = 57.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references