4RXD

T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries.

Liu, Y.L.Cao, R.Wang, Y.Oldfield, E.

(2015) ACS Med Chem Lett 6: 349-354

  • DOI: https://doi.org/10.1021/ml500528x
  • Primary Citation of Related Structures:  
    4RXA, 4RXC, 4RXD, 4RXE, 4RYP

  • PubMed Abstract: 

    Farnesyl diphosphate synthase (FPPS) is an important drug target for bone resorption, cancer, and some infectious diseases. Here, we report five new structures including two having unique bound ligand geometries. The diamidine inhibitor 7 binds to human FPPS close to the homoallylic (S2) and allosteric (S3) sites and extends into a new site, here called S4. With the bisphosphonate inhibitor 8, two molecules bind to Trypanosoma brucei FPPS, one molecule in the allylic site (S1) and the other close to S2, the first observation of two bisphosphonate molecules bound to FPPS. We also report the structures of apo-FPPS from T. brucei, together with two more bisphosphonate-bound structures (2,9), for purposes of comparison. The diamidine structure is of particular interest because 7 could represent a new lead for lipophilic FPPS inhibitors, while 8 has low micromolar activity against T. brucei, the causative agent of human African trypanosomiasis.


  • Organizational Affiliation

    Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthase
A, B, C
390Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q86C09 (Trypanosoma brucei)
Explore Q86C09 
Go to UniProtKB:  Q86C09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86C09
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RIS
Query on RIS

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
L [auth C]
1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID
C7 H11 N O7 P2
IIDJRNMFWXDHID-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
M [auth C],
N [auth C],
O [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RIS BindingDB:  4RXD -TΔS: min: -3.54e+0, max: 7.26 (kJ/mol) from 2 assay(s)
ΔG: min: -4.06e+1, max: -3.63e+1 (kJ/mol) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.34α = 90
b = 90.305β = 89.91
c = 88.709γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Structure summary
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description