5AFX

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-1238


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inhibition of Trypanosoma Brucei Cell Growth by Lipophilic Bisphosphonates: An in Vitro and in Vivo Investigation.

Yang, G.Zhu, W.Kim, K.Byun, S.Y.Choi, G.Wang, K.Cha, J.S.Cho, H.Oldfield, E.No, J.H.

(2015) Antimicrob Agents Chemother 59: 7530

  • DOI: 10.1128/AAC.01873-15
  • Primary Citation of Related Structures:  
    5AEL, 5AFX, 5AHU

  • PubMed Abstract: 
  • We report the results of a screen of a library of 925 potential prenyl synthase inhibitors against Trypanosoma brucei farnesyl diphosphate synthase (TbFPPS) and against T. brucei, the causative agent of human African trypanosomiasis. The most potent ...

    We report the results of a screen of a library of 925 potential prenyl synthase inhibitors against Trypanosoma brucei farnesyl diphosphate synthase (TbFPPS) and against T. brucei, the causative agent of human African trypanosomiasis. The most potent compounds were lipophilic analogs of the bone resorption drug zoledronate, some of which had submicromolar to low micromolar activity against bloodstream form T. brucei and selectivity indices of up to ∼ 300. We evaluated the effects of two such inhibitors on survival and parasitemia in a T. brucei mouse model of infection and found that survival increased by up to 16 days. We also investigated the binding of three lipophilic bisphosphonates to an expressed TbFPPS using crystallography and investigated the thermodynamics of binding using isothermal titration calorimetry.


    Organizational Affiliation

    Leishmania Research Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, Republic of Korea eoldfiel@illinois.edu joohwan.no@ip-korea.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FARNESYL PYROPHOSPHATE SYNTHASEAB367Trypanosoma bruceiMutation(s): 0 
Find proteins for Q86C09 (Trypanosoma brucei)
Explore Q86C09 
Go to UniProtKB:  Q86C09
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PVZ
Query on PVZ

Download CCD File 
A, B
[1-hydroxy-2-(1-nonyl-1H-3lambda~5~-imidazol-3-yl)ethane-1,1-diyl]bis(phosphonic acid)
C14 H29 N2 O7 P2
ANVJZSKZYXLDSP-UHFFFAOYSA-O
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PVZIC50:  1200   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.263 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.471α = 90
b = 119.026β = 112.47
c = 63.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-02-06
    Changes: Data collection, Experimental preparation