2XG5

E. coli P pilus chaperone-subunit complex PapD-PapH bound to pilus biogenesis inhibitor, pilicide 5d

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.2 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHAPERONE PROTEIN PAPD218Escherichia coliMutation(s): 0 
Gene Names: papD
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
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PAP FIMBRIAL MINOR PILIN PROTEIN173Escherichia coliMutation(s): 0 
Gene Names: papH
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EC5
Query on EC5
Download Ideal Coordinates CCD File 
E [auth A](2R)-2-[5-CYCLOPROPYL-6-(HYDROXYSULFANYL)-4-(NAPHTHALEN-1-YLMETHYL)-2-OXOPYRIDIN-1(2H)-YL]-3-PHENYLPROPANOIC ACID
C28 H25 N O4 S
RDAFPBNHIKAVPQ-DEOSSOPVSA-N		 Ligand Interaction
EC2
Query on EC2
Download Ideal Coordinates CCD File 
D [auth A](2R,3R)-8-CYCLOPROPYL-7-(NAPHTHALEN-1-YLMETHYL)-5-OXO-2-PHENYL-2,3-DIHYDRO-5H-[1,3]THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID
C28 H23 N O3 S
QSGWJHVTILGJTA-IZZNHLLZSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
PGO
Query on PGO
Download Ideal Coordinates CCD File 
F [auth B]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N		 Ligand Interaction
CO
Query on CO
Download Ideal Coordinates CCD File 
G [auth B]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EC2 Binding MOAD:  2XG5 IC50: 2.20e+4 (nM) from 1 assay(s)
PDBBind:  2XG5 IC50: 2.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.61α = 90
b = 149.83β = 90
c = 82.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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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