4RXD | pdb_00004rxd

T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.251 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.211 (Depositor) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4RXD

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 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.

Macromolecule Content 

  • Total Structure Weight: 134.5 kDa 
  • Atom Count: 9,091 
  • Modeled Residue Count: 1,069 
  • Deposited Residue Count: 1,170 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 ΔG: min: -4.06e+1, max: 7.26 (kJ/mol) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.251 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.211 (Depositor) 
  • R-Value Observed: 0.213 (Depositor) 
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

View Full Validation Report



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