4P0V

Crystal structure of human farnesyl diphosphoate synthase in complex with zoledronate and taxodione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site.

Liu, Y.L.Lindert, S.Zhu, W.Wang, K.McCammon, J.A.Oldfield, E.

(2014) Proc.Natl.Acad.Sci.USA 111: E2530-E2539

  • DOI: 10.1073/pnas.1409061111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We used in silico methods to screen a library of 1,013 compounds for possible binding to the allosteric site in farnesyl diphosphate synthase (FPPS). Two of the 50 predicted hits had activity against either human FPPS (HsFPPS) or Trypanosoma brucei F ...

    We used in silico methods to screen a library of 1,013 compounds for possible binding to the allosteric site in farnesyl diphosphate synthase (FPPS). Two of the 50 predicted hits had activity against either human FPPS (HsFPPS) or Trypanosoma brucei FPPS (TbFPPS), the most active being the quinone methide celastrol (IC50 versus TbFPPS ∼ 20 µM). Two rounds of similarity searching and activity testing then resulted in three leads that were active against HsFPPS with IC50 values in the range of ∼ 1-3 µM (as compared with ∼ 0.5 µM for the bisphosphonate inhibitor, zoledronate). The three leads were the quinone methides taxodone and taxodione and the quinone arenarone, compounds with known antibacterial and/or antitumor activity. We then obtained X-ray crystal structures of HsFPPS with taxodione+zoledronate, arenarone+zoledronate, and taxodione alone. In the zoledronate-containing structures, taxodione and arenarone bound solely to the homoallylic (isopentenyl diphosphate, IPP) site, not to the allosteric site, whereas zoledronate bound via Mg(2+) to the same site as seen in other bisphosphonate-containing structures. In the taxodione-alone structure, one taxodione bound to the same site as seen in the taxodione+zoledronate structure, but the second located to a more surface-exposed site. In differential scanning calorimetry experiments, taxodione and arenarone broadened the native-to-unfolded thermal transition (Tm), quite different to the large increases in ΔTm seen with biphosphonate inhibitors. The results identify new classes of FPPS inhibitors, diterpenoids and sesquiterpenoids, that bind to the IPP site and may be of interest as anticancer and antiinfective drug leads.


    Organizational Affiliation

    Departments of Pharmacology andNational Science Foundation Center for Theoretical Biological Physics, La Jolla, CA 92093Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093; andChemistry and Biochemistry and jmccammon@ucsd.edu eoldfiel@illinois.edu.,Departments of Pharmacology andNational Science Foundation Center for Theoretical Biological Physics, La Jolla, CA 92093.,Department of Chemistry and.,Department of Chemistry andCenter for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801; jmccammon@ucsd.edu eoldfiel@illinois.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
A
347Homo sapiensMutation(s): 0 
Gene Names: FDPS (FPS, KIAA1293)
EC: 2.5.1.10
Find proteins for P14324 (Homo sapiens)
Go to Gene View: FDPS
Go to UniProtKB:  P14324
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
1WO
Query on 1WO

Download SDF File 
Download CCD File 
A
(5beta)-11-hydroxyabieta-7,9(11),13-triene-6,12-dione
taxodione
C20 H26 O3
FNNZMRSRVYUVQT-AZUAARDMSA-N
 Ligand Interaction
ZOL
Query on ZOL

Download SDF File 
Download CCD File 
A
ZOLEDRONIC ACID
(1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID
C5 H10 N2 O7 P2
XRASPMIURGNCCH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZOLKi: 0.1 - 85.9 nM (100) BINDINGDB
ZOLIC50: 0.2 - 475.3 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.202 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 112.143α = 90.00
b = 112.143β = 90.00
c = 67.053γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesCA158191
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM065307

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy