S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with BPH-715

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl pyrophosphate synthetase
A, B
340Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12051 
Go to UniProtKB:  Q12051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12051
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B71

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C17 H32 N O7 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.256α = 90
b = 116.207β = 90
c = 129.385γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

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
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description