4DEM

Crystal structure of human FPPS in complex with YS_04_70


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design and Synthesis of Active Site Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Apoptosis and Inhibition of ERK Phosphorylation in Multiple Myeloma Cells.

Lin, Y.S.Park, J.De Schutter, J.W.Huang, X.F.Berghuis, A.M.Sebag, M.Tsantrizos, Y.S.

(2012) J Med Chem 55: 3201-3215

  • DOI: 10.1021/jm201657x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human farnesyl pyrophosphate synthase (hFPPS) controls intracellular levels of FPP and post-translational prenylation of small GTPase proteins, which are essential for cell signaling and cell proliferation. Clinical investigations provide evidence th ...

    Human farnesyl pyrophosphate synthase (hFPPS) controls intracellular levels of FPP and post-translational prenylation of small GTPase proteins, which are essential for cell signaling and cell proliferation. Clinical investigations provide evidence that N-BP inhibitors of hFPPS are disease modifying agents that improve survival of multiple myeloma (MM) patients via mechanisms unrelated to their skeletal effects. A new series of N-BPs was designed that interact with a larger portion of the GPP subpocket, as compared to the current therapeutic drugs, and rigidify the (364)KRRK(367) tail of hFPPS in the closed conformation in the absence of IPP. An analogue of this series was used to demonstrate inhibition of the intended biological target, resulting in apoptosis and down-regulation of ERK phosphorylation in human MM cell lines.


    Organizational Affiliation

    Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
F
375Homo sapiensMutation(s): 0 
Gene Names: FDPSFPSKIAA1293
EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (PDB Primary Data)
Find proteins for P14324 (Homo sapiens)
Go to UniProtKB:  P14324
NIH Common Fund Data Resources
PHAROS  P14324
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YS4
Query on YS4

Download CCD File 
F
[({4-[4-(propan-2-yloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)
C15 H20 N2 O7 P2
DTXBFSJBRGLOHO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YS4IC50 :  28   nM  PDBBind
YS4IC50:  1390   nM  BindingDB
YS4IC50:  28   nM  BindingDB
YS4IC50:  28   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.23α = 90
b = 111.23β = 90
c = 67.724γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references