4DWG

Crystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(n-heptylamino)ethane-1,1-diyl]bisphosphonic acid and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


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Literature

Design, synthesis, calorimetry, and crystallographic analysis of 2-alkylaminoethyl-1,1-bisphosphonates as inhibitors of Trypanosoma cruzi farnesyl diphosphate synthase.

Aripirala, S.Szajnman, S.H.Jakoncic, J.Rodriguez, J.B.Docampo, R.Gabelli, S.B.Amzel, L.M.

(2012) J.Med.Chem. 55: 6445-6454

  • DOI: 10.1021/jm300425y
  • Primary Citation of Related Structures:  4DWB, 4DXJ, 4DZW, 4E1E

  • PubMed Abstract: 
  • Linear 2-alkylaminoethyl-1,1-bisphosphonates are effective agents against proliferation of Trypanosoma cruzi , the etiologic agent of American trypanosomiasis (Chagas disease), exhibiting IC(50) values in the nanomolar range against the parasites. Th ...

    Linear 2-alkylaminoethyl-1,1-bisphosphonates are effective agents against proliferation of Trypanosoma cruzi , the etiologic agent of American trypanosomiasis (Chagas disease), exhibiting IC(50) values in the nanomolar range against the parasites. This activity is associated with inhibition at the low nanomolar level of the T. cruzi farnesyl diphosphate synthase (TcFPPS). X-ray structures and thermodynamic data of the complexes TcFPPS with five compounds of this family show that the inhibitors bind to the allylic site of the enzyme, with their alkyl chain occupying the cavity that binds the isoprenoid chain of the substrate. The compounds bind to TcFPPS with unfavorable enthalpy compensated by a favorable entropy that results from a delicate balance between two opposing effects: the loss of conformational entropy due to freezing of single bond rotations and the favorable burial of the hydrophobic alkyl chains. The data suggest that introduction of strategically placed double bonds and methyl branches should increase affinity substantially.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
A
362Trypanosoma cruziN/A
Find proteins for Q95WL3 (Trypanosoma cruzi)
Go to UniProtKB:  Q95WL3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
0M8
Query on 0M8

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A
[2-(heptylamino)ethane-1,1-diyl]bis(phosphonic acid)
C9 H23 N O6 P2
WRMHTOUCTOHPIY-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0M8IC50: 58 nM (99) BINDINGDB
0M8IC50: 58 nM BINDINGMOAD
0M8IC50: 58 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.202 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.173α = 90.00
b = 58.173β = 90.00
c = 391.822γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
REFMACphasing
ADSCdata collection
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release