1ZW5

X-ray structure of Farnesyl diphosphate synthase protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs.

Kavanagh, K.L.Guo, K.Dunford, J.E.Wu, X.Knapp, S.Ebetino, F.H.Rogers, M.J.Russell, R.G.Oppermann, U.

(2006) Proc Natl Acad Sci U S A 103: 7829-7834

  • DOI: 10.1073/pnas.0601643103
  • Primary Citation of Related Structures:  
    1YV5, 1ZW5

  • PubMed Abstract: 
  • Osteoporosis and low bone mass are currently estimated to be a major public health risk affecting >50% of the female population over the age of 50. Because of their bone-selective pharmacokinetics, nitrogen-containing bisphosphonates (N-BPs), current ...

    Osteoporosis and low bone mass are currently estimated to be a major public health risk affecting >50% of the female population over the age of 50. Because of their bone-selective pharmacokinetics, nitrogen-containing bisphosphonates (N-BPs), currently used as clinical inhibitors of bone-resorption diseases, target osteoclast farnesyl pyrophosphate synthase (FPPS) and inhibit protein prenylation. FPPS, a key branchpoint of the mevalonate pathway, catalyzes the successive condensation of isopentenyl pyrophosphate with dimethylallyl pyrophosphate and geranyl pyrophosphate. To understand the molecular events involved in inhibition of FPPS by N-BPs, we used protein crystallography, enzyme kinetics, and isothermal titration calorimetry. We report here high-resolution x-ray structures of the human enzyme in complexes with risedronate and zoledronate, two of the leading N-BPs in clinical use. These agents bind to the dimethylallyl/geranyl pyrophosphate ligand pocket and induce a conformational change. The interactions of the N-BP cyclic nitrogen with Thr-201 and Lys-200 suggest that these inhibitors achieve potency by positioning their nitrogen in the proposed carbocation-binding site. Kinetic analyses reveal that inhibition is competitive with geranyl pyrophosphate and is of a slow, tight binding character, indicating that isomerization of an initial enzyme-inhibitor complex occurs with inhibitor binding. Isothermal titration calorimetry indicates that binding of N-BPs to the apoenzyme is entropy-driven, presumably through desolvation entropy effects. These experiments reveal the molecular binding characteristics of an important pharmacological target and provide a route for further optimization of these important drugs.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, United Kingdom. kate.kavanagh@sgc.ox.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
farnesyl diphosphate synthaseA355Homo sapiensMutation(s): 0 
Gene Names: FDPSFPSKIAA1293
EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (UniProt)
Find proteins for P14324 (Homo sapiens)
Explore P14324 
Go to UniProtKB:  P14324
NIH Common Fund Data Resources
PHAROS  P14324
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZOL
Query on ZOL

Download CCD File 
A
ZOLEDRONIC ACID
C5 H10 N2 O7 P2
XRASPMIURGNCCH-UHFFFAOYSA-N
 Ligand Interaction
IPE
Query on IPE

Download CCD File 
A
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZOLIC50:  110   nM  BindingDB
ZOLKi:  10   nM  BindingDB
ZOLIC50:  0.23999999463558197   nM  BindingDB
ZOLIC50:  100   nM  BindingDB
ZOLIC50:  130   nM  BindingDB
ZOLIC50:  475   nM  BindingDB
ZOLIC50:  4.099999904632568   nM  BindingDB
ZOLIC50:  200   nM  BindingDB
ZOLIC50:  3   nM  BindingDB
ZOLKi:  0.07000000029802322   nM  BindingDB
ZOLKi:  85.9000015258789   nM  BindingDB
ZOLIC50:  475.29998779296875   nM  BindingDB
ZOLIC50:  4   nM  BindingDB
ZOLIC50:  60   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.255α = 90
b = 112.255β = 90
c = 63.245γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2013-05-22
    Changes: Non-polymer description
  • Version 1.4: 2017-10-11
    Changes: Refinement description
  • Version 1.5: 2018-01-31
    Changes: Structure summary