2J7L

E. coli P Pilus chaperone PapD in complex with a pilus biogenesis inhibitor, pilicide 2c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Rationally Designed Small Compounds Inhibit Pilus Biogenesis in Uropathogenic Bacteria.

Pinkner, J.S.Remaut, H.Buelens, F.Miller, E.Aberg, V.Pemberton, N.Hedenstrom, M.Larsson, A.Seed, P.Waksman, G.Hultgren, S.J.Almqvist, F.

(2006) Proc Natl Acad Sci U S A 103: 17897

  • DOI: https://doi.org/10.1073/pnas.0606795103
  • Primary Citation of Related Structures:  
    2J7L

  • PubMed Abstract: 

    A chemical synthesis platform with broad applications and flexibility was rationally designed to inhibit biogenesis of adhesive pili assembled by the chaperone-usher pathway in Gram-negative pathogens. The activity of a family of bicyclic 2-pyridones, termed pilicides, was evaluated in two different pilus biogenesis systems in uropathogenic Escherichia coli. Hemagglutination mediated by either type 1 or P pili, adherence to bladder cells, and biofilm formation mediated by type 1 pili were all reduced by approximately 90% in laboratory and clinical E. coli strains. The structure of the pilicide bound to the P pilus chaperone PapD revealed that the pilicide bound to the surface of the chaperone known to interact with the usher, the outer-membrane assembly platform where pili are assembled. Point mutations in the pilicide-binding site dramatically reduced pilus formation but did not block the ability of PapD to bind subunits and mediate their folding. Surface plasmon resonance experiments confirmed that the pilicide interfered with the binding of chaperone-subunit complexes to the usher. These pilicides thus target key virulence factors in pathogenic bacteria and represent a promising proof of concept for developing drugs that function by targeting virulence factors.


  • Organizational Affiliation

    Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHAPERONE PROTEIN PAPD218Escherichia coliMutation(s): 0 
UniProt
Find proteins for P15319 (Escherichia coli)
Explore P15319 
Go to UniProtKB:  P15319
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15319
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XC2
Query on XC2

Download Ideal Coordinates CCD File 
B [auth A](3R)-8-CYCLOPROPYL-6-(MORPHOLIN-4-YLMETHYL)-7-(1-NAPHTHYLMETHYL)-5-OXO-2,3-DIHYDRO-5H-[1,3]THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID
C27 H28 N2 O4 S
QFNHKTSOHATKEL-QHCPKHFHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.315α = 90
b = 94.315β = 90
c = 121.992γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description