6EUT

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (KSK67)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Design of Inhibitors Targeting PrfA, the Master Virulence Regulator of Listeria monocytogenes.

Kulen, M.Lindgren, M.Hansen, S.Cairns, A.G.Grundstrom, C.Begum, A.van der Lingen, I.Brannstrom, K.Hall, M.Sauer, U.H.Johansson, J.Sauer-Eriksson, A.E.Almqvist, F.

(2018) J Med Chem 61: 4165-4175

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00289
  • Primary Citation of Related Structures:  
    6EUT, 6EUU, 6EUZ, 6EV0, 6EXK, 6EXL, 6EXM

  • PubMed Abstract: 

    Listeria monocytogenes is a bacterial pathogen that controls much of its virulence through the transcriptional regulator PrfA. In this study, we describe structure-guided design and synthesis of a set of PrfA inhibitors based on ring-fused 2-pyridone heterocycles. Our most effective compound decreased virulence factor expression, reduced bacterial uptake into eukaryotic cells, and improved survival of chicken embryos infected with L. monocytogenes compared to previously identified compounds. Crystal structures identified an intraprotein "tunnel" as the main inhibitor binding site (A I ), where the compounds participate in an extensive hydrophobic network that restricts the protein's ability to form functional DNA-binding helix-turn-helix (HTH) motifs. Our studies also revealed a hitherto unsuspected structural plasticity of the HTH motif. In conclusion, we have designed 2-pyridone analogues that function as site-A I selective PrfA inhibitors with potent antivirulence properties.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Listeriolysin regulatory protein
A, B
239Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: prfAlmo0200
UniProt
Find proteins for P22262 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore P22262 
Go to UniProtKB:  P22262
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22262
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BY8
Query on BY8

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
(3~{R})-8-cyclopropyl-7-[(4-methylnaphthalen-1-yl)methyl]-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid
C23 H21 N O3 S
XQPUCYFOBBJYCO-IBGZPJMESA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
E [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.934α = 90
b = 88.71β = 90
c = 116.788γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description