2Z78

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with BPH-806


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 

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, 2Z4X, 2Z4Y, 2Z4Z, 2Z50, 2Z52, 2Z7I, 2Z78

  • 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, 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranyl pyrophosphate synthetaseA, B340Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.5.1.30 (PDB Primary Data), 2.5.1.1 (PDB Primary Data), 2.5.1.10 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1 (UniProt)
Find proteins for Q12051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12051 
Go to UniProtKB:  Q12051
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H86
Query on H86

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]3-(decyloxy)-5-(3,5-difluorophenyl)-1-(2,2-diphosphonoethyl)pyridinium
C23 H34 F2 N O7 P2
JONDYIHZOFRLBH-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
H86IC50 :  760   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.33α = 90
b = 116.639β = 90
c = 129.78γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
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: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance