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 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


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: 10.1021/jm100470t
  • Primary Citation of Related Structures:  

  • 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. Experi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHAPERONE PROTEIN PAPD
A
218Escherichia coliMutation(s): 0 
Gene Names: papD
Find proteins for P15319 (Escherichia coli)
Go to UniProtKB:  P15319
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PAP FIMBRIAL MINOR PILIN PROTEIN
B
173Escherichia coliMutation(s): 0 
Gene Names: papH
Find proteins for P07111 (Escherichia coli)
Go to UniProtKB:  P07111
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EC2
Query on EC2

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Download CCD File 
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

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EC5
Query on EC5

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Download CCD File 
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
CO
Query on CO

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Download CCD File 
B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

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Download CCD File 
B
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EC2IC50: 22000 nM BINDINGMOAD
EC2IC50: 22000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 103.610α = 90.00
b = 149.830β = 90.00
c = 82.900γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance