3N5J

Human fpps complex with NOV_311


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 660-666

  • DOI: 10.1038/nchembio.421
  • Primary Citation of Related Structures:  
  • Also Cited By: 5DJV, 5DJR, 5DJP, 5DIQ, 5DGS, 5DGN, 5DGM

  • PubMed Abstract: 
  • Bisphosphonates are potent inhibitors of farnesyl pyrophosphate synthase (FPPS) and are highly efficacious in the treatment of bone diseases such as osteoporosis, Paget's disease and tumor-induced osteolysis. In addition, the potential for direct ant ...

    Bisphosphonates are potent inhibitors of farnesyl pyrophosphate synthase (FPPS) and are highly efficacious in the treatment of bone diseases such as osteoporosis, Paget's disease and tumor-induced osteolysis. In addition, the potential for direct antitumor effects has been postulated on the basis of in vitro and in vivo studies and has recently been demonstrated clinically in early breast cancer patients treated with the potent bisphosphonate zoledronic acid. However, the high affinity of bisphosphonates for bone mineral seems suboptimal for the direct treatment of soft-tissue tumors. Here we report the discovery of the first potent non-bisphosphonate FPPS inhibitors. These new inhibitors bind to a previously unknown allosteric site on FPPS, which was identified by fragment-based approaches using NMR and X-ray crystallography. This allosteric and druggable pocket allows the development of a new generation of FPPS inhibitors that are optimized for direct antitumor effects in soft tissue.


    Related Citations: 
    • Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs
      Rondeau, J.M.,Bitsch, F.,Bourgier, E.,Geiser, M.,Hemmig, R.,Kroemer, M.,Lehmann, S.,Ramage, P.,Rieffel, S.,Strauss, A.
      (2006) ChemMedChem 1: 267


    Organizational Affiliation

    Center for Proteomic Chemistry and Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GO1
Query on GO1

Download SDF File 
Download CCD File 
F
3-(carboxymethyl)-5,7-dichloro-1H-indole-2-carboxylic acid
C11 H7 Cl2 N O4
UDTYSEWCICAFSB-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GO1IC50: 6000 nM (100) BINDINGDB
GO1IC50: 8000 nM BINDINGMOAD
GO1IC50: 6000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.112α = 90.00
b = 111.112β = 90.00
c = 78.245γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
XSCALEdata scaling
XDSdata reduction
APRVmodel building
APRVphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-05-25 
  • Released Date: 2010-08-18 
  • Deposition Author(s): Rondeau, J.-M.

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance