4BJK

CYP51 of Trypanosoma brucei bound to (S)-N-(3-(1H-indol-3-yl)-1-oxo-1- (pyridin-4-ylamino)propan-2-yl)-3,3'-difluoro-(1,1'-biphenyl)-4- carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Rational Development of 4-Aminopyridyl-Based Inhibitors Targeting Trypanosoma Cruzi Cyp51 as Anti-Chagas Agents.

Choi, J.Y.Calvet, C.M.Gunatilleke, S.S.Ruiz, C.Cameron, M.D.Mckerrow, J.H.Podust, L.M.Roush, W.R.

(2013) J Med Chem 56: 7651

  • DOI: https://doi.org/10.1021/jm401067s
  • Primary Citation of Related Structures:  
    4BJK

  • PubMed Abstract: 

    A new series of 4-aminopyridyl-based lead inhibitors targeting Trypanosoma cruzi CYP51 (TcCYP51) has been developed using structure-based drug design as well as structure-property relationship (SPR) analyses. The screening hit starting point, LP10 (KD ≤ 42 nM; EC50 = 0.65 μM), has been optimized to give the potential leads 14t, 27i, 27q, 27r, and 27t, which have low-nanomolar binding affinity to TcCYP51 and significant activity against T. cruzi amastigotes cultured in human myoblasts (EC50 = 14-18 nM for 27i and 27r). Many of the optimized compounds have improved microsome stability, and most are selective against human CYPs 1A2, 2D6, and 3A4 (<50% inhibition at 1 μM). A rationale for the improvement in microsome stability and selectivity of inhibitors against human metabolic CYP enzymes is presented. In addition, the binding mode of 14t with the Trypanosoma brucei CYP51 (TbCYP51) orthologue has been characterized by X-ray structure analysis.


  • Organizational Affiliation

    Department of Chemistry and ∥Department of Molecular Therapeutics, Scripps Florida , Jupiter, Florida 33458, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LANOSTEROL 14-ALPHA-DEMETHYLASE
A, B, C, D
469Trypanosoma bruceiMutation(s): 4 
EC: 1.14.13.70
UniProt
Find proteins for Q385E8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q385E8 
Go to UniProtKB:  Q385E8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ385E8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
18I
Query on 18I

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
3,3'-difluoro-N-[(2S)-3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl]biphenyl-4-carboxamide
C29 H22 F2 N4 O2
QLYGOABRPGBQNG-MHZLTWQESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.291α = 90
b = 114.671β = 132.47
c = 136.221γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2013-09-04 
  • Deposition Author(s): Podust, L.M.

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2013-10-30
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description