Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with BPH-1260

Experimental Data Snapshot

  • Resolution: 2.39 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 

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Chemo-Immunotherapeutic Anti-Malarials Targeting Isoprenoid Biosynthesis.

Zhang, Y.Zhu, W.Liu, Y.L.Wang, H.Wang, K.Li, K.No, J.H.Ayong, L.Gulati, A.Pang, R.Freitas-Junior, L.Morita, C.T.Old-Field, E.

(2013) ACS Med Chem Lett 4: 423-427

  • DOI: https://doi.org/10.1021/ml4000436
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We synthesized 30 lipophilic bisphosphonates and tested them in malaria parasite killing (targeting parasite geranylgeranyl diphosphate synthase, GGPPS) as well in human γδ T cell activation (targeting human farnesyl diphosphate synthase, FPPS). Similar patterns of activity were seen in inhibiting human FPPS and Plasmodium GGPPS, with short to medium chain-length species having most activity. In cells, shorter chain-length species had low activity, due to poor membrane permeability, and longer chain length species were poor enzyme inhibitors. Optimal activity was thus seen with ~C 10 side-chains, which have the best combination of enzyme inhibition and cell penetration. We also solved the crystal structure of one potent inhibitor, bound to FPPS. The results are of interest since they suggest the possibility of a combined chemo/immuno-therapeutic approach to anti-malarial development in which both direct parasite killing as well as γδ T cell activation can be achieved with a single compound.

  • Organizational Affiliation

    PrenylX Research Institute, Zhangjiagang, 215600, People's Republic of China ; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthase348Homo sapiensMutation(s): 0 
Gene Names: FDPSFPSKIAA1293
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14324 (Homo sapiens)
Explore P14324 
Go to UniProtKB:  P14324
PHAROS:  P14324
GTEx:  ENSG00000160752 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14324
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.39 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.29α = 90
b = 112.29β = 90
c = 68.553γ = 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: 2013-05-08
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description