5HKB

Crystal structure of the CFTR inhibitory factor Cif bound to the inhibitor KB2115


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rational Design of Potent and Selective Inhibitors of an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa.

Kitamura, S.Hvorecny, K.L.Niu, J.Hammock, B.D.Madden, D.R.Morisseau, C.

(2016) J.Med.Chem. 59: 4790-4799

  • DOI: 10.1021/acs.jmedchem.6b00173
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The virulence factor cystic fibrosis transmembrane conductance regulator (CFTR) inhibitory factor (Cif) is secreted by Pseudomonas aeruginosa and is the founding member of a distinct class of epoxide hydrolases (EHs) that triggers the catalysis-depen ...

    The virulence factor cystic fibrosis transmembrane conductance regulator (CFTR) inhibitory factor (Cif) is secreted by Pseudomonas aeruginosa and is the founding member of a distinct class of epoxide hydrolases (EHs) that triggers the catalysis-dependent degradation of the CFTR. We describe here the development of a series of potent and selective Cif inhibitors by structure-based drug design. Initial screening revealed 1a (KB2115), a thyroid hormone analog, as a lead compound with low micromolar potency. Structural requirements for potency were systematically probed, and interactions between Cif and 1a were characterized by X-ray crystallography. On the basis of these data, new compounds were designed to yield additional hydrogen bonding with residues of the Cif active site. From this effort, three compounds were identified that are 10-fold more potent toward Cif than our first-generation inhibitors and have no detectable thyroid hormone-like activity. These inhibitors will be useful tools to study the pathological role of Cif and have the potential for clinical application.


    Organizational Affiliation

    Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California, Davis , One Shields Avenue, Davis, California 95616, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CFTR Inhibitory Factor (Cif)
A, B, C, D
301Pseudomonas aeruginosa (strain UCBPP-PA14)Mutation(s): 0 
Find proteins for A0A0H2ZD27 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Go to UniProtKB:  A0A0H2ZD27
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
64L
Query on 64L

Download SDF File 
Download CCD File 
A, B, C, D
KB2115
3-({3,5-dibromo-4-[4-hydroxy-3-(propan-2-yl)phenoxy]phenyl}amino)-3-oxopropanoic acid
C18 H17 Br2 N O5
VPCSYAVXDAUHLT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
64LIC50: 2600 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 84.168α = 90.00
b = 169.494β = 90.00
c = 175.568γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references