5DGS

Crystal structure of human FPPS in complex with the monophosphonate compound 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A General Strategy for Targeting Drugs to Bone.

Jahnke, W.Bold, G.Marzinzik, A.L.Ofner, S.Pelle, X.Cotesta, S.Bourgier, E.Lehmann, S.Henry, C.Hemmig, R.Stauffer, F.Hartwieg, J.C.Green, J.R.Rondeau, J.M.

(2015) Angew.Chem.Int.Ed.Engl. 54: 14575-14579

  • DOI: 10.1002/anie.201507064
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Targeting drugs to their desired site of action can increase their safety and efficacy. Bisphosphonates are prototypical examples of drugs targeted to bone. However, bisphosphonate bone affinity is often considered too strong and cannot be significan ...

    Targeting drugs to their desired site of action can increase their safety and efficacy. Bisphosphonates are prototypical examples of drugs targeted to bone. However, bisphosphonate bone affinity is often considered too strong and cannot be significantly modulated without losing activity on the enzymatic target, farnesyl pyrophosphate synthase (FPPS). Furthermore, bisphosphonate bone affinity comes at the expense of very low and variable oral bioavailability. FPPS inhibitors were developed with a monophosphonate as a bone-affinity tag that confers moderate affinity to bone, which can furthermore be tuned to the desired level, and the relationship between structure and bone affinity was evaluated by using an NMR-based bone-binding assay. The concept of targeting drugs to bone with moderate affinity, while retaining oral bioavailability, has broad application to a variety of other bone-targeted drugs.


    Related Citations: 
    • Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery.
      Jahnke, W.,Rondeau, J.M.,Cotesta, S.,Marzinzik, A.,Pelle, X.,Geiser, M.,Strauss, A.,Gotte, M.,Bitsch, F.,Hemmig, R.,Henry, C.,Lehmann, S.,Glickman, J.F.,Roddy, T.P.,Stout, S.J.,Green, J.R.
      (2010) Nat.Chem.Biol. 6: 660
    • Discovery of Novel Allosteric Non-Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthase by Integrated Lead Finding.
      Marzinzik, A.L.,Amstutz, R.,Bold, G.,Bourgier, E.,Cotesta, S.,Glickman, J.F.,Gotte, M.,Henry, C.,Lehmann, S.,Hartwieg, J.C.,Ofner, S.,Pelle, X.,Roddy, T.P.,Rondeau, J.M.,Stauffer, F.,Stout, S.J.,Widmer, A.,Zimmermann, J.,Zoller, T.,Jahnke, W.
      (2015) Chemmedchem 10: 1884


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland).,Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland). wolfgang.jahnke@novartis.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
F
350Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5A7
Query on 5A7

Download SDF File 
Download CCD File 
F
{(E)-2-[6-(acetylamino)-8-(naphthalen-1-yl)quinolin-2-yl]ethenyl}phosphonic acid
C23 H19 N2 O4 P
YXNCZDLAUQFYPO-VAWYXSNFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.187 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.962α = 90.00
b = 110.962β = 90.00
c = 74.772γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-07-27
    Type: Database references
  • Version 1.2: 2017-11-29
    Type: Database references