2XG4

E. coli P pilus chaperone-subunit complex PapD-PapH bound to pilus biogenesis inhibitor, pilicide 2c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Design and Synthesis of C-2 Substituted Thiazolo and Dihydrothiazolo Ring-Fused 2-Pyridones: Pilicides with Increased Antivirulence Activity.

Chorell, E.Pinkner, J.S.Phan, G.Edvinsson, S.Buelens, F.Remaut, H.Waksman, G.Hultgren, S.J.Almqvist, F.

(2010) J Med Chem 53: 5690

  • DOI: https://doi.org/10.1021/jm100470t
  • Primary Citation of Related Structures:  
    2XG4, 2XG5

  • PubMed Abstract: 

    Pilicides block pili formation by binding to pilus chaperones and blocking their function in the chaperone/usher pathway in E. coli. Various C-2 substituents were introduced on the pilicide scaffold by design and synthetic method developments. Experimental evaluation showed that proper substitution of this position affected the biological activity of the compound. Aryl substituents resulted in pilicides with significantly increased potencies as measured in pili-dependent biofilm and hemagglutination assays. The structural basis of the PapD chaperone-pilicide interactions was determined by X-ray crystallography.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden.


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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PAP FIMBRIAL MINOR PILIN PROTEIN173Escherichia coliMutation(s): 0 
UniProt
Find proteins for P07111 (Escherichia coli)
Explore P07111 
Go to UniProtKB:  P07111
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07111
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XC2
Query on XC2

Download Ideal Coordinates CCD File 
C [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
GOL
Query on GOL

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

Download Ideal Coordinates CCD File 
D [auth B]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.1α = 90
b = 148.73β = 90
c = 82.639γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    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: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description