4C27

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-fluoro-4-(4-(4-(trifluoromethyl)phenyl)piperazin-1-yl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Binding Mode and Potency of N-Indolyl-Oxopyridinyl-4-Amino-Propanyl-Based Inhibitors Targeting Trypanosoma Cruzi Cyp51

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

(2014) J.Med.Chem. 57: 10162

  • DOI: 10.1021/jm501568b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chagas disease is a chronic infection in humans caused by Trypanosoma cruzi and manifested in progressive cardiomyopathy and/or gastrointestinal dysfunction. Limited therapeutic options to prevent and treat Chagas disease put 8 million people infecte ...

    Chagas disease is a chronic infection in humans caused by Trypanosoma cruzi and manifested in progressive cardiomyopathy and/or gastrointestinal dysfunction. Limited therapeutic options to prevent and treat Chagas disease put 8 million people infected with T. cruzi worldwide at risk. CYP51, involved in the biosynthesis of the membrane sterol component in eukaryotes, is a promising drug target in T. cruzi. We report the structure-activity relationships (SAR) of an N-arylpiperazine series of N-indolyloxopyridinyl-4-aminopropanyl-based inhibitors designed to probe the impact of substituents in the terminal N-phenyl ring on binding mode, selectivity and potency. Depending on the substituents at C-4, two distinct ring binding modes, buried and solvent-exposed, have been observed by X-ray structure analysis (resolution of 1.95-2.48 Å). The 5-chloro-substituted analogs 9 and 10 with no substituent at C-4 demonstrated improved selectivity and potency, suppressing ≥ 99.8% parasitemia in mice when administered orally at 25 mg/kg, b.i.d., for 4 days.


    Organizational Affiliation

    Center for Discovery and Innovation in Parasitic Diseases, ‡Department of Pathology, and §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
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
26N
Query on 26N

Download SDF File 
Download CCD File 
A, B
Nalpha-(2-fluoro-4-{4-[4-(trifluoromethyl)phenyl]piperazin-1-yl}benzoyl)-N-pyridin-4-yl-D-tryptophanamide
C34 H30 F4 N6 O2
CYPNHMRAJORLFS-WJOKGBTCSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.104α = 90.00
b = 79.158β = 90.00
c = 176.945γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references
  • Version 1.2: 2015-01-14
    Type: Database references
  • Version 1.3: 2017-03-29
    Type: Structure summary