1PZK

Cholera Toxin B-Pentamer Complexed With N-Acyl Phenyl Galactoside 9h


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

3,5-Substituted phenyl galactosides as leads in designing effective cholera toxin antagonists; synthesis and crystallographic studies

Mitchell, D.D.Pickens, J.C.Korotkov, K.Fan, E.Hol, W.G.J.

(2004) Bioorg.Med.Chem. 12: 907-920

  • DOI: 10.1016/j.bmc.2003.12.019
  • Primary Citation of Related Structures:  1PZI, 1PZJ

  • PubMed Abstract: 
  • With the aim of developing high-affinity mono and multivalent antagonists of cholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT) we are using the galactose portion of the natural receptor ganglioside GM1 as an anchoring fragment in s ...

    With the aim of developing high-affinity mono and multivalent antagonists of cholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT) we are using the galactose portion of the natural receptor ganglioside GM1 as an anchoring fragment in structure-based inhibitor design efforts. In order to establish a better structure-activity relationship for guiding these studies, we designed and prepared a small focused library of twenty 3,5-substituted phenylgalactosides based on two previous leads. The compounds were tested for their ability to block CTB(5) binding to immobilized ganglioside receptor and compared to the two previous leads. The crystal structures of the most promising compounds bound to either CTB(5) or LTB(5) were then determined in order to understand the basis for affinity differences. The most potent new compound yielded a six-fold improvement over our benchmark lead m-nitrophenyl-alpha-d-galactopyranoside (MNPG), and a two-fold improvement in IC(50) over a newer MNPG derivative. These results support the notion that the m-nitrophenyl moiety of MNPG and its derivatives is an important element to retain in future optimization efforts. Additionally, a consensus binding-pocket for the alkylmorpholine or piperazine moiety present in all of the designed antagonists was established as an important area of the GM1 binding site to target in future work.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cholera Toxin B Subunit
D, E, F, G, H
103Vibrio choleraeGene Names: ctxB
Find proteins for Q57193 (Vibrio cholerae)
Go to UniProtKB:  Q57193
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J12
Query on J12

Download SDF File 
Download CCD File 
D, E, F, G, H
N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-(2-THIOPHEN-2-YL-ACETYLAMINO)-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-BENZAMIDE
C29 H43 N5 O8 S
ZIXIINLBMSXOQV-ADWZMSLQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
J12IC50: 200000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.132 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.048α = 90.00
b = 66.137β = 105.78
c = 78.185γ = 90.00
Software Package:
Software NamePurpose
XTALVIEWrefinement
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
CCP4data scaling
TRUNCATEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance