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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/jm500448u
  • Primary Citation of Related Structures:  

  • 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 causa ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STEROL 14-ALPHA DEMETHYLASE
A, B, C, D
467Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Gene Names: CYP51
EC: 1.14.14.154
Find proteins for Q7Z1V1 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q7Z1V1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
TU1
Query on TU1

Download SDF File 
Download CCD File 
A, B, C, D
4-[2,5-bis(fluoranyl)phenyl]-2-fluoranyl-N-[(2R)-3-(1H-indol-3-yl)-1-oxidanylidene-1-(pyridin-4-ylamino)propan-2-yl]benzamide
C29 H21 F3 N4 O2
AHABCZVHHYTXPC-HHHXNRCGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 272.469α = 90.00
b = 66.452β = 110.65
c = 122.219γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references, Other
  • Version 1.2: 2014-09-10
    Type: Database references