3O6O

Crystal Structure of the N-terminal domain of an HSP90 from Trypanosoma Brucei, Tb10.26.1080 in the presence of an the inhibitor BIIB021


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Exploring the Trypanosoma brucei Hsp83 potential as a target for structure guided drug design.

Pizarro, J.C.Hills, T.Senisterra, G.Wernimont, A.K.Mackenzie, C.Norcross, N.R.Ferguson, M.A.Wyatt, P.G.Gilbert, I.H.Hui, R.

(2013) PLoS Negl Trop Dis 7: e2492-e2492

  • DOI: https://doi.org/10.1371/journal.pntd.0002492
  • Primary Citation of Related Structures:  
    3O6O, 3OMU, 3OPD, 3U67

  • PubMed Abstract: 

    Human African trypanosomiasis is a neglected parasitic disease that is fatal if untreated. The current drugs available to eliminate the causative agent Trypanosoma brucei have multiple liabilities, including toxicity, increasing problems due to treatment failure and limited efficacy. There are two approaches to discover novel antimicrobial drugs--whole-cell screening and target-based discovery. In the latter case, there is a need to identify and validate novel drug targets in Trypanosoma parasites. The heat shock proteins (Hsp), while best known as cancer targets with a number of drug candidates in clinical development, are a family of emerging targets for infectious diseases. In this paper, we report the exploration of T. brucei Hsp83--a homolog of human Hsp90--as a drug target using multiple biophysical and biochemical techniques. Our approach included the characterization of the chemical sensitivity of the parasitic chaperone against a library of known Hsp90 inhibitors by means of differential scanning fluorimetry (DSF). Several compounds identified by this screening procedure were further studied using isothermal titration calorimetry (ITC) and X-ray crystallography, as well as tested in parasite growth inhibitions assays. These experiments led us to the identification of a benzamide derivative compound capable of interacting with TbHsp83 more strongly than with its human homologs and structural rationalization of this selectivity. The results highlight the opportunities created by subtle structural differences to develop new series of compounds to selectively target the Trypanosoma brucei chaperone and effectively kill the sleeping sickness parasite.


  • Organizational Affiliation

    The Structural Genomics Consortium (SGC), University of Toronto, Toronto, Ontario, Canada ; Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein 83
A, B
214Trypanosoma bruceiMutation(s): 0 
Gene Names: Tb10.26.1080
UniProt
Find proteins for Q389P1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q389P1 
Go to UniProtKB:  Q389P1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ389P1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
94M
Query on 94M

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-chloro-9-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-9H-purin-2-amine
C14 H15 Cl N6 O
QULDDKSCVCJTPV-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
E [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.65α = 90
b = 65.812β = 92.28
c = 62.745γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Database references, Refinement description, Structure summary
  • Version 1.3: 2017-11-29
    Changes: Database references
  • Version 1.4: 2022-10-05
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2024-05-22
    Changes: Data collection