4BY0 | pdb_00004by0

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)-3,3'- difluoro-(1,1'-biphenyl)-4-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb4BY0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2013-07-16 Released: 2014-01-22 
• Deposition Author(s): Choi, J.Y., Calvet, C.M., Vierira, D.F., Gunatilleke, S.S., Cameron, M.D., McKerrow, J.H., Podust, L.M., Roush, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.297 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

R-Configuration of 4-Aminopyridyl-Based Inhibitors of Cyp51 Confers Superior Efficacy Against Trypanosoma Cruzi

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

(2014) ACS Med Chem Lett 5: 434

• PubMed: 24900854 
• DOI: https://doi.org/10.1021/ml500010m
• Primary Citation Related Structures: 
  4BY0


• PubMed Abstract: 
  

  Sterol 14α-demethylase (CYP51) is an important therapeutic target for fungal and parasitic infections due to its key role in the biosynthesis of ergosterol, an essential component of the cell membranes of these pathogenic organisms. We report the development of potent and selective d-tryptophan-derived inhibitors of T. cruzi CYP51. Structural information obtained from the cocrystal structure of CYP51 and (R)-2, which is >1000-fold more potent than its enantiomer (S)-1, was used to guide design of additional analogues. The in vitro efficacy data presented here for (R)-2-(R)-8, together with preliminary in vitro pharmacokinetic data suggest that this new CYP51 inhibitor scaffold series has potential to deliver drug candidates for treatment of T. cruzi infections.

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Organizational Affiliation: 
• Department of Chemistry, Scripps Florida , Jupiter, Florida 33458, United States.
Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, University of California San Francisco , San Francisco, California 94158, United States ; Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, University of California San Francisco , San Francisco, California 94158, United States ; Cellular Ultra-Structure Laboratory, Oswaldo Cruz Institute (IOC), FIOCRUZ , Rio de Janeiro, RJ 21040-362, Brazil.
Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, University of California San Francisco , San Francisco, California 94158, United States ; Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, University of California San Francisco , San Francisco, California 94158, United States.
Department of Molecular Therapeutics, Scripps Florida , Jupiter, Florida 33458, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 108.8 kDa 
• Atom Count: 6,834 
• Modeled Residue Count: 883 
• Deposited Residue Count: 934 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STEROL 14-ALPHA DEMETHYLASE	A, B	467	Trypanosoma cruzi	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
5PS	D [auth A], F [auth B]	(R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-3,3'-difluoro-(1,1'-biphenyl)-4-carboxamide C29 H22 F2 N4 O2 QLYGOABRPGBQNG-HHHXNRCGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.297 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.167	α = 90
b = 124.167	β = 90
c = 119.839	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-22 
Deposition Author(s): Choi, J.Y., Calvet, C.M., Vierira, D.F., Gunatilleke, S.S., Cameron, M.D., McKerrow, J.H., Podust, L.M., Roush, W.R.

Revision History  

• Version 1.0: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2014-04-02
  Changes: Database references
• Version 1.2: 2014-06-18
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description