4L2X

Crystal structure of human FPPS in complex with magnesium, CL02134, and inorganic pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition.

Leung, C.Y.Park, J.De Schutter, J.W.Sebag, M.Berghuis, A.M.Tsantrizos, Y.S.

(2013) J Med Chem 56: 7939-7950

  • DOI: https://doi.org/10.1021/jm400946f
  • Primary Citation of Related Structures:  
    4JVJ, 4L2X

  • PubMed Abstract: 

    Human farnesyl pyrophosphate synthase (hFPPS) controls the post-translational prenylation of small GTPase proteins that are essential for cell signaling, cell proliferation, and osteoclast-mediated bone resorption. Inhibition of hFPPS is a clinically validated mechanism for the treatment of lytic bone diseases, including osteoporosis and cancer related bone metastases. A new series of thienopyrimidine-based bisphosphonates (ThP-BPs) were identified that inhibit hFPPS with low nanomolar potency. Crystallographic evidence revealed binding of ThP-BP inhibitors in the allylic subpocket of hFPPS. Simultaneous binding of inorganic pyrophosphate in the IPP subpocket leads to conformational closing of the active site cavity. The ThP-BP analogues are significantly less hydrophilic yet exhibit higher affinity for the bone mineral hydroxyapatite than the current N-BP drug risedronic acid. The antiproliferation properties of a potent ThB-BP analogue was assessed in a multiple myeloma cell line and found to be equipotent to the best current N-BP drugs. Consequently, these compounds represent a new structural class of hFPPS inhibitors and a novel scaffold for the development of human therapeutics.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthaseA [auth F]375Homo 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
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
POP BindingDB:  4L2X Ki: min: 2.98e+4, max: 4.05e+4 (nM) from 2 assay(s)
IC50: min: 1.81e+5, max: 2.43e+5 (nM) from 2 assay(s)
YL2 BindingDB:  4L2X IC50: min: 39, max: 115 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.34α = 90
b = 111.34β = 90
c = 68.77γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-01
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description