Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.88 kDa 
• Atom Count: 2,866 
• Modelled Residue Count: 341 
• Deposited Residue Count: 375 
• Unique protein chains: 1

 4QXS

Crystal structure of human FPPS in complex with WC01088

• PDB DOI:  https://doi.org/10.2210/pdb4QXS/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-21 Released: 2015-02-25 
• Deposition Author(s): Park, J., Zielinski, M., Weiling, C., Tsantrizos, Y.S., Berghuis, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

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

• PubMed: 25630225 
• DOI: https://doi.org/10.1016/j.bmcl.2014.12.089
• Primary Citation of Related Structures:  
  4QXS


• 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 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.

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Organizational Affiliation: 

Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada; Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montréal, QC H3G 0B1, Canada. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A [auth F]	375	Homo sapiens	Mutation(s): 0  Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14324 (Homo sapiens) Explore P14324  Go to UniProtKB:  P14324
PHAROS:  P14324

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WC1	D [auth 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
PO4	B [auth F], C [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
WC1	Binding MOAD:  4QXS	IC50: 1100 (nM) from 1 assay(s)
	BindingDB:  4QXS	IC50: 1100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.65	α = 90
b = 110.65	β = 90
c = 77.92	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Park, J., Zielinski, M., Weiling, C., Tsantrizos, Y.S., Berghuis, A.M.

Revision History  

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