T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-597

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


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: https://doi.org/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 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 Interdisciplinary Programs of Functional Genomics, Yonsei University, Seoul, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
367Trypanosoma bruceiMutation(s): 0 
Find proteins for Q86C09 (Trypanosoma brucei)
Explore Q86C09 
Go to UniProtKB:  Q86C09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86C09
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.835α = 90
b = 118.25β = 112.39
c = 62.424γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description