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 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1002/anie.201507064
  • Primary Citation of Related Structures:  
    5DGM, 5DGS

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthaseA [auth F]350Homo sapiensMutation(s): 0 
Gene Names: FDPSFPSKIAA1293
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
GTEx:  ENSG00000160752 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14324
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5A7
Query on 5A7

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.193 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.962α = 90
b = 110.962β = 90
c = 74.772γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling
CNXphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2017-11-29
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references