3RBM | pdb_00003rbm

Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH -703


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.253 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity.

No, J.H.de Macedo Dossin, F.Zhang, Y.Liu, Y.L.Zhu, W.Feng, X.Yoo, J.A.Lee, E.Wang, K.Hui, R.Freitas-Junior, L.H.Oldfield, E.

(2012) Proc Natl Acad Sci U S A 109: 4058-4063

  • DOI: https://doi.org/10.1073/pnas.1118215109
  • Primary Citation Related Structures: 
    3RBM, 3RYW

  • PubMed Abstract: 

    We report the results of an in vitro screening assay targeting the intraerythrocytic form of the malaria parasite Plasmodium falciparum using a library of 560 prenyl-synthase inhibitors. Based on "growth-rescue" and enzyme-inhibition experiments, geranylgeranyl diphosphate synthase (GGPPS) is shown to be a major target for the most potent leads, BPH-703 and BPH-811, lipophilic analogs of the bone-resorption drugs zoledronate and risedronate. We determined the crystal structures of these inhibitors bound to a Plasmodium GGPPS finding that their head groups bind to the [Mg(2+)](3) cluster in the active site in a similar manner to that found with their more hydrophilic parents, whereas their hydrophobic tails occupy a long-hydrophobic tunnel spanning both molecules in the dimer. The results of isothermal-titration-calorimetric experiments show that both lipophilic bisphosphonates bind to GGPPS with, on average, a ΔG of -9 kcal mol(-1), only 0.5 kcal mol(-1) worse than the parent bisphosphonates, consistent with the observation that conversion to the lipophilic species has only a minor effect on enzyme activity. However, only the lipophilic species are active in cells. We also tested both compounds in mice, finding major decreases in parasitemia and 100% survival. These results are of broad general interest because they indicate that it may be possible to overcome barriers to cell penetration of existing bisphosphonate drugs in this and other systems by simple covalent modification to form lipophilic analogs that retain their enzyme-inhibition activity and are also effective in vitro and in vivo.


  • Organizational Affiliation
    • Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Macromolecule Content 

  • Total Structure Weight: 187.24 kDa 
  • Atom Count: 12,025 
  • Modeled Residue Count: 1,430 
  • Deposited Residue Count: 1,584 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthase
A, B, C, D
396Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVX_092040
UniProt
Find proteins for A5K4U6 (Plasmodium vivax (strain Salvador I))
Explore A5K4U6 
Go to UniProtKB:  A5K4U6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K4U6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B73

Query on B73



Download:Ideal Coordinates CCD File
H [auth A],
M [auth B],
R [auth C],
W [auth D]
3-(2,2-diphosphonoethyl)-1-dodecyl-1H-imidazol-3-ium
C17 H35 N2 O6 P2
LPGGFVFFIYFOME-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A],
N [auth B],
S [auth C],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
Q [auth C],
T [auth D],
U [auth D],
V [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.253 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.682α = 90
b = 107.952β = 90
c = 140.703γ = 90
Software Package:
Software NamePurpose
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description