8C0S | pdb_00008c0s

Crystal structure of S. aureus BlaR1 sensor domain in complex with an imidazole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.232 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.195 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Restoring susceptibility to beta-lactam antibiotics in methicillin-resistant Staphylococcus aureus.

Nguyen, V.T.Birhanu, B.T.Miguel-Ruano, V.Kim, C.Batuecas, M.Yang, J.El-Araby, A.M.Jimenez-Faraco, E.Schroeder, V.A.Alba, A.Rana, N.Sader, S.Thomas, C.A.Feltzer, R.Lee, M.Fisher, J.F.Hermoso, J.A.Chang, M.Mobashery, S.

(2024) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-024-01688-0
  • Primary Citation Related Structures: 
    8C0P, 8C0S, 8CF3

  • PubMed Abstract: 

    Infections by Staphylococcus aureus have been treated historically with β-lactam antibiotics. However, these antibiotics have become obsolete in methicillin-resistant S. aureus by acquisition of the bla and mec operons. The presence of the β-lactam antibiotic is detected by the sensor domains of BlaR and/or MecR, and the information is transmitted to the cytoplasm, resulting in derepression of the antibiotic-resistance genes. We hypothesized that inhibition of the sensor domain would shut down this response system, and β-lactam susceptibility would be restored. An in silico search of 11 million compounds led to a benzimidazole-based hit and, ultimately, to the boronate 4. The X-ray structure of 4 is covalently engaged with the active-site serine of BlaR. Compound 4 potentiates by 16- to 4,096-fold the activities of oxacillin and of meropenem against methicillin-resistant S. aureus strains. The combination of 4 with oxacillin or meropenem shows efficacy in infected mice, validating the strategy.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.

Macromolecule Content 

  • Total Structure Weight: 60.25 kDa 
  • Atom Count: 4,293 
  • Modeled Residue Count: 503 
  • Deposited Residue Count: 508 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Regulatory protein BlaR1
A, B
254Staphylococcus aureusMutation(s): 3 
Gene Names: blaR1
UniProt
Find proteins for P18357 (Staphylococcus aureus)
Explore P18357 
Go to UniProtKB:  P18357
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18357
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SYU
(Subject of Investigation/LOI)

Query on SYU



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
3-[[2,4-bis(trifluoromethyl)phenyl]methyl]-5-(hydroxymethyl)-1~{H}-imidazole-2-thione
C13 H10 F6 N2 O S
WXKONROFPLKHOA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.232 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.195 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.027α = 90
b = 107.943β = 109.454
c = 56.39γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2017-90030-P

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references