T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-14

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries.

Liu, Y.L.Cao, R.Wang, Y.Oldfield, E.

(2015) ACS Med Chem Lett 6: 349-354

  • DOI: https://doi.org/10.1021/ml500528x
  • Primary Citation of Related Structures:  
    4RXA, 4RXC, 4RXD, 4RXE, 4RYP

  • PubMed Abstract: 

    Farnesyl diphosphate synthase (FPPS) is an important drug target for bone resorption, cancer, and some infectious diseases. Here, we report five new structures including two having unique bound ligand geometries. The diamidine inhibitor 7 binds to human FPPS close to the homoallylic (S2) and allosteric (S3) sites and extends into a new site, here called S4. With the bisphosphonate inhibitor 8, two molecules bind to Trypanosoma brucei FPPS, one molecule in the allylic site (S1) and the other close to S2, the first observation of two bisphosphonate molecules bound to FPPS. We also report the structures of apo-FPPS from T. brucei, together with two more bisphosphonate-bound structures (2,9), for purposes of comparison. The diamidine structure is of particular interest because 7 could represent a new lead for lipophilic FPPS inhibitors, while 8 has low micromolar activity against T. brucei, the causative agent of human African trypanosomiasis.

  • Organizational Affiliation

    Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthase
A, B
390Trypanosoma 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: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.149α = 90
b = 119.149β = 112.24
c = 62.824γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description