2Z4X

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-252 (P21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation

Chen, C.K.-M.Hudock, M.P.Zhang, Y.Guo, R.-T.Cao, R.No, J.H.Liang, P.-H.Ko, T.-P.Chang, T.-H.Chang, S.-C.Song, Y.Axelson, J.Kumar, A.Wang, A.H.-J.Oldfield, E.

(2008) J.Med.Chem. 51: 5594-5607

  • DOI: 10.1021/jm800325y
  • Primary Citation of Related Structures:  2Z4V, 2Z4W, 2Z4Y, 2Z4Z, 2Z50, 2Z52, 2Z78, 2Z7I

  • PubMed Abstract: 
  • We report the X-ray structures of several bisphosphonate inhibitors of geranylgeranyl diphosphate synthase, a target for anticancer drugs. Bisphosphonates containing unbranched side chains bind to either the farnesyl diphosphate (FPP) substrate site, ...

    We report the X-ray structures of several bisphosphonate inhibitors of geranylgeranyl diphosphate synthase, a target for anticancer drugs. Bisphosphonates containing unbranched side chains bind to either the farnesyl diphosphate (FPP) substrate site, the geranylgeranyl diphosphate (GGPP) product site, and in one case, both sites, with the bisphosphonate moiety interacting with 3 Mg (2+) that occupy the same position as found in FPP synthase. However, each of three "V-shaped" bisphosphonates bind to both the FPP and GGPP sites. Using the Glide program, we reproduced the binding modes of 10 bisphosphonates with an rms error of 1.3 A. Activities of the bisphosphonates in GGPPS inhibition were predicted with an overall error of 2x by using a comparative molecular similarity analysis based on a docked-structure alignment. These results show that some GGPPS inhibitors can occupy both substrate and product site and that binding modes as well as activity can be accurately predicted, facilitating the further development of GGPPS inhibitors as anticancer agents.


    Organizational Affiliation

    Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranyl pyrophosphate synthetase
A, B
340Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: BTS1
EC: 2.5.1.10, 2.5.1.29, 2.5.1.1, 2.5.1.-
Find proteins for Q12051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12051
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
252
Query on 252

Download SDF File 
Download CCD File 
A, B
(1-HYDROXYNONANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
C9 H22 O7 P2
COHUUYPEYRMWTH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
252IC50: 710 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.405α = 90.00
b = 47.874β = 110.86
c = 91.799γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data collection
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance