1PZJ

Cholera Toxin B-Pentamer Complexed With Nitrophenyl Galactoside 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    1PZK, 1PZJ, 1PZI

  • 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 structure-based inhibitor design efforts ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cholera Toxin B SubunitA [auth D], B [auth E], C [auth F], D [auth G], E [auth H]103Vibrio choleraeMutation(s): 0 
Gene Names: CAA41591ctxBC9J66_18955ERS013165_03981ERS013197_06217ERS013202_03762ERS013206_03003
Find proteins for Q57193 (Vibrio cholerae)
Explore Q57193 
Go to UniProtKB:  Q57193
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
15B
Query on 15B

Download Ideal Coordinates CCD File 
F [auth D], I [auth G], J [auth H]N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-NITRO-5-(GALACTOPYRANOSYL)-BETA-BENZAMIDE
C23 H37 N5 O9
UEIGEWJJVQHIAX-DLBZZEGUSA-N
 Ligand Interaction
J15
Query on J15

Download Ideal Coordinates CCD File 
G [auth E], H [auth F]N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-NITRO-5-(GALACTOPYRANOSYL)-ALPHA-BENZAMIDE
C23 H37 N5 O9
UEIGEWJJVQHIAX-MKQKURRLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
15BIC50 :  320000   nM  PDBBind
J15IC50:  320000   nM  Binding MOAD
15BIC50:  320000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.117 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.754α = 90
b = 65.998β = 105.44
c = 77.362γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
TRUNCATEdata reduction
XTALVIEWrefinement
HKL-2000data collection
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description