6EV0 | pdb_00006ev0

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (AC129)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.263 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 56.18 kDa 
  • Atom Count: 3,961 
  • Modeled Residue Count: 466 
  • Deposited Residue Count: 478 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8N

Query on C8N



Download:Ideal Coordinates CCD File
F [auth B][(3~{S})-3-carboxy-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium
C21 H21 N2 O3 S
BCEJXMPUFHXHBT-QGZVFWFLSA-O
BYK

Query on BYK



Download:Ideal Coordinates CCD File
C [auth A],
E [auth B]
[(3~{R})-3-carboxy-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium
C21 H21 N2 O3 S
BCEJXMPUFHXHBT-KRWDZBQOSA-O
IPA

Query on IPA



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.263 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.734α = 90
b = 80.514β = 113.93
c = 62.578γ = 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, Refinement description