3DYG

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 

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.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:  

  • 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 age ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FARNESYL PYROPHOSPHATE SYNTHASE
A, B
390Trypanosoma bruceiMutation(s): 0 
Find proteins for Q86C09 (Trypanosoma brucei)
Go to UniProtKB:  Q86C09
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
BME
Query on BME

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Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
NI9
Query on NI9

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Download CCD File 
A, B
3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM
C7 H11 F N O7 P2
LSEAIOLITUIQJU-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.565α = 90.00
b = 118.520β = 112.36
c = 63.186γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance