4QXS

Crystal structure of human FPPS in complex with WC01088


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Probing the molecular and structural elements of ligands binding to the active site versus an allosteric pocket of the human farnesyl pyrophosphate synthase.

Gritzalis, D.Park, J.Chiu, W.Cho, H.Lin, Y.S.De Schutter, J.W.Lacbay, C.M.Zielinski, M.Berghuis, A.M.Tsantrizos, Y.S.

(2015) Bioorg.Med.Chem.Lett. 25: 1117-1123

  • DOI: 10.1016/j.bmcl.2014.12.089

  • PubMed Abstract: 
  • In order to explore the interactions of bisphosphonate ligands with the active site and an allosteric pocket of the human farnesyl pyrophosphate synthase (hFPPS), substituted indole and azabenzimidazole bisphosphonates were designed as chameleon liga ...

    In order to explore the interactions of bisphosphonate ligands with the active site and an allosteric pocket of the human farnesyl pyrophosphate synthase (hFPPS), substituted indole and azabenzimidazole bisphosphonates were designed as chameleon ligands. NMR and crystallographic studies revealed that these compounds can occupy both sub-pockets of the active site cavity, as well as the allosteric pocket of hFPPS in the presence of the enzyme's Mg(2+) ion cofactor. These results are consistent with the previously proposed hypothesis that the allosteric pocket of hFPPS, located near the active site, plays a feed-back regulatory role for this enzyme.


    Organizational Affiliation

    Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
F
375Homo 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
PO4
Query on PO4

Download SDF File 
Download CCD File 
F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
WC1
Query on WC1

Download SDF File 
Download CCD File 
F
(2-{2-[(2S)-3-methylbutan-2-yl]-5-phenyl-1H-indol-3-yl}ethane-1,1-diyl)bis(phosphonic acid)
C21 H27 N O6 P2
PCZFJEHMSDBRJQ-AWEZNQCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WC1IC50: 1100 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.650α = 90.00
b = 110.650β = 90.00
c = 77.920γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACphasing
REFMACrefinement
MxDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-04
    Type: Database references