4BMM

Crystal structure of Trypanosoma cruzi CYP51 bound to the inhibitor (R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-2',3, 5'-trifluoro-(1,1'-biphenyl)-4-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.194 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

4-Aminopyridyl-Based Cyp51 Inhibitors as Anti-Trypanosoma Cruzi Drug Leads with Improved Pharmacokinetic Profile and in Vivo Potency.

Calvet, C.M.Vieira, D.F.Choi, J.Y.Kellar, D.Cameron, M.D.Siqueira-Neto, J.L.Gut, J.Johnston, J.B.Lin, L.Khan, S.Mckerrow, J.H.Roush, W.R.Podust, L.M.

(2014) J Med Chem 57: 6989

  • DOI: https://doi.org/10.1021/jm500448u
  • Primary Citation of Related Structures:  
    4BMM, 4C0C, 4UQH

  • PubMed Abstract: 

    CYP51 is a P450 enzyme involved in the biosynthesis of the sterol components of eukaryotic cell membranes. CYP51 inhibitors have been developed to treat infections caused by fungi, and more recently the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease. To specifically optimize drug candidates for T. cruzi CYP51 (TcCYP51), we explored the structure-activity relationship (SAR) of a N-indolyl-oxopyridinyl-4-aminopropanyl-based scaffold originally identified in a target-based screen. This scaffold evolved via medicinal chemistry to yield orally bioavailable leads with potent anti-T. cruzi activity in vivo. Using an animal model of infection with a transgenic T. cruzi Y luc strain expressing firefly luciferase, we prioritized the biaryl and N-arylpiperazine analogues by oral bioavailability and potency. The drug-target complexes for both scaffold variants were characterized by X-ray structure analysis. Optimization of both binding mode and pharmacokinetic properties of these compounds led to potent inhibitors against experimental T. cruzi infection.


  • Organizational Affiliation

    Center for Discovery and Innovation in Parasitic Diseases, ‡Department of Pathology and §Department of Medicine, ∥Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STEROL 14-ALPHA DEMETHYLASE
A, B, C, D
467Trypanosoma cruzi strain CL BrenerMutation(s): 0 
EC: 1.14.13.70 (PDB Primary Data), 1.14.14.154 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q7Z1V1 (Trypanosoma cruzi (strain CL Brener))
Explore Q7Z1V1 
Go to UniProtKB:  Q7Z1V1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z1V1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 272.469α = 90
b = 66.452β = 110.65
c = 122.219γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references, Other
  • Version 1.2: 2014-09-10
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description