4UVR

Binding mode, selectivity and potency of N-indolyl-oxopyridinyl-4- amino-propanyl-based inhibitors targeting Trypanosoma cruzi CYP51


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm501568b
  • Primary Citation of Related Structures:  
    4C27, 4C28, 4UVR

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STEROL 14-DEMETHYLASE, CYP51467Trypanosoma cruziMutation(s): 0 
EC: 1.14.13.70 (PDB Primary Data), 1.14.14.154 (UniProt)
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
J5Y
Query on J5Y

Download Ideal Coordinates CCD File 
C [auth A]Nalpha-{4-[4-(5-chloro-2-methylphenyl)piperazin-1-yl]-2-fluorobenzoyl}-N-pyridin-4-yl-D-tryptophanamide
C34 H32 Cl F N6 O2
JYSKTRNZALHBHU-WJOKGBTCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.115α = 90
b = 128.115β = 90
c = 117.781γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description