5HKB | pdb_00005hkb

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 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.6b00173
  • Primary Citation Related Structures: 
    5HK9, 5HKA, 5HKB

  • 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-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.

Macromolecule Content 

  • Total Structure Weight: 138.84 kDa 
  • Atom Count: 11,135 
  • Modeled Residue Count: 1,188 
  • Deposited Residue Count: 1,204 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CFTR Inhibitory Factor (Cif)
A, B, C, D
301Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: PA14_26090
UniProt
Find proteins for A0A0H2ZD27 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZD27 
Go to UniProtKB:  A0A0H2ZD27
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZD27
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
64L

Query on 64L



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
KB2115
C18 H17 Br2 N O5
VPCSYAVXDAUHLT-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
64L BindingDB:  5HKB IC50: 2700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.215 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.168α = 90
b = 169.494β = 90
c = 175.568γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary