2ZEV

S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, IPP and BPH-715


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation

Zhang, Y.Cao, R.Yin, F.Hudock, M.P.Guo, R.T.Krysiak, K.Mukherjee, S.Gao, Y.-G.Robinson, H.Song, Y.No, J.H.Bergan, K.Leon, A.Cass, L.Goddard, A.Chang, T.-K.Lin, F.-Y.Van Beek, E.Papapoulos, S.Wang, A.H.-J.Kubo, T.Ochi, M.Mukkamala, D.Oldfield, E.

(2009) J Am Chem Soc 131: 5153-5162

  • DOI: 10.1021/ja808285e
  • Primary Citation of Related Structures:  
    2OPM, 3DYF, 3DYG, 3DYH, 3EFQ, 3EGT, 2ZEU, 2ZEV

  • PubMed Abstract: 
  • Considerable effort has focused on the development of selective protein farnesyl transferase (FTase) and protein geranylgeranyl transferase (GGTase) inhibitors as cancer chemotherapeutics. Here, we report a new strategy for anticancer therapeutic agents involving inhibition of farnesyl diphosphate synthase (FPPS) and geranylgeranyl diphosphate synthase (GGPPS), the two enzymes upstream of FTase and GGTase, by lipophilic bisphosphonates ...

    Considerable effort has focused on the development of selective protein farnesyl transferase (FTase) and protein geranylgeranyl transferase (GGTase) inhibitors as cancer chemotherapeutics. Here, we report a new strategy for anticancer therapeutic agents involving inhibition of farnesyl diphosphate synthase (FPPS) and geranylgeranyl diphosphate synthase (GGPPS), the two enzymes upstream of FTase and GGTase, by lipophilic bisphosphonates. Due to dual site targeting and decreased polarity, the compounds have activities far greater than do current bisphosphonate drugs in inhibiting tumor cell growth and invasiveness, both in vitro and in vivo. We explore how these compounds inhibit cell growth and how cell activity can be predicted based on enzyme inhibition data, and using X-ray diffraction, solid state NMR, and isothermal titration calorimetry, we show how these compounds bind to FPPS and/or GGPPS.


    Organizational Affiliation

    Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranyl pyrophosphate synthetaseA, B340Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.5.1.30 (PDB Primary Data), 2.5.1 (UniProt), 2.5.1.1 (UniProt), 2.5.1.29 (UniProt), 2.5.1.10 (UniProt)
Find proteins for Q12051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12051 
Go to UniProtKB:  Q12051
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B71
Query on B71

Download Ideal Coordinates CCD File 
E [auth A], I [auth B]3-(DECYLOXY)-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM
C17 H32 N O7 P2
QYJHUOZDBUEKQC-UHFFFAOYSA-O
 Ligand Interaction
IPE
Query on IPE

Download Ideal Coordinates CCD File 
H [auth B]3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], F [auth B], G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.822α = 90
b = 115.879β = 90
c = 128.336γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance