5DIQ

Crystal structure of human FPPS in complex with salicylic acid derivative 3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1884-1891

  • DOI: 10.1002/cmdc.201500338
  • Primary Citation of Related Structures:  
  • Also Cited By: 5DGS, 5DGM

  • PubMed Abstract: 
  • Farnesyl pyrophosphate synthase (FPPS) is an established target for the treatment of bone diseases, but also shows promise as an anticancer and anti-infective drug target. Currently available anti-FPPS drugs are active-site-directed bisphosphonate in ...

    Farnesyl pyrophosphate synthase (FPPS) is an established target for the treatment of bone diseases, but also shows promise as an anticancer and anti-infective drug target. Currently available anti-FPPS drugs are active-site-directed bisphosphonate inhibitors, the peculiar pharmacological profile of which is inadequate for therapeutic indications beyond bone diseases. The recent discovery of an allosteric binding site has paved the way toward the development of novel non-bisphosphonate FPPS inhibitors with broader therapeutic potential, notably as immunomodulators in oncology. Herein we report the discovery, by an integrated lead finding approach, of two new chemical classes of allosteric FPPS inhibitors that belong to the salicylic acid and quinoline chemotypes. We present their synthesis, biochemical and cellular activities, structure-activity relationships, and provide X-ray structures of several representative FPPS complexes. These novel allosteric FPPS inhibitors are devoid of any affinity for bone mineral and could serve as leads to evaluate their potential in none-bone diseases.


    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
    • Tuning bone affinity into non-bisphosphonate FPPS inhibitors: a general strategy for targeting drugs acting on bone
      Jahnke, W.,Bold, G.,Marzinzik, A.,Ofner, S.,Pelle, X.,Cotesta, S.,Bourgier, E.,Lehmann, S.,Henry, C.,Hemmig, R.,Stauffer, F.,Mueller-Hartwieg, C.,Green, J.R.,Rondeau, J.M.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Basel, 4002, 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 4 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

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

Download SDF File 
Download CCD File 
F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
5B9
Query on 5B9

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Download CCD File 
F
2-(naphthalen-1-ylmethoxy)benzoic acid
C18 H14 O3
MDMYMMOPBHNQFV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.629α = 90.00
b = 111.629β = 90.00
c = 76.835γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
CNXphasing
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-11-04
    Type: Database references
  • Version 1.2: 2016-07-27
    Type: Database references