6C56

Crystal structure of mutant human geranylgeranyl pyrophosphate synthase (Y246D) in its Apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report



Literature

Unraveling the Prenylation-Cancer Paradox in Multiple Myeloma with Novel Geranylgeranyl Pyrophosphate Synthase (GGPPS) Inhibitors.

Lacbay, C.M.Waller, D.D.Park, J.Gomez Palou, M.Vincent, F.Huang, X.F.Ta, V.Berghuis, A.M.Sebag, M.Tsantrizos, Y.S.

(2018) J Med Chem 61: 6904-6917

  • DOI: 10.1021/acs.jmedchem.8b00886
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Post-translational prenylation of the small GTP-binding proteins (GTPases) is vital to a plethora of biological processes, including cellular proliferation. We have identified a new class of thienopyrimidine-based bisphosphonate (ThP-BP) inhibitors o ...

    Post-translational prenylation of the small GTP-binding proteins (GTPases) is vital to a plethora of biological processes, including cellular proliferation. We have identified a new class of thienopyrimidine-based bisphosphonate (ThP-BP) inhibitors of the human geranylgeranyl pyrophosphate synthase (hGGPPS) that block protein prenylation in multiple myeloma (MM) cells leading to cellular apoptosis. These inhibitors are also effective in blocking the proliferation of other types of cancer cells. We confirmed intracellular target engagement, demonstrated the mechanism of action leading to apoptosis, and determined a direct correlation between apoptosis and intracellular inhibition of hGGPPS. Administration of a ThP-BP inhibitor to a MM mouse model confirmed in vivo downregulation of Rap1A geranylgeranylation and reduction of monoclonal immunoglobulins (M-protein, a biomarker of disease burden) in the serum. These results provide the first proof-of-principle that hGGPPS is a valuable therapeutic target in oncology and more specifically for the treatment of multiple myeloma.


    Organizational Affiliation

    Department of Biochemistry , McGill University , Montreal , QC H3G 1Y6 , Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranyl pyrophosphate synthase
A, B
322Homo sapiensMutation(s): 1 
Gene Names: GGPS1
EC: 2.5.1 (PDB Primary Data), 2.5.1.1 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1.10 (PDB Primary Data)
Find proteins for O95749 (Homo sapiens)
Go to UniProtKB:  O95749
NIH Common Fund Data Resources
PHAROS  O95749
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VT0
Query on VT0

Download CCD File 
B
{[(2-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)
C13 H13 N3 O6 P2 S
OVNNLIKSDUSVRR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.1α = 90
b = 185.1β = 90
c = 115.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release