4RXA

Crystal structure of human farnesyl diphosphate synthase in complex with BPH-1358


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1021/ml500528x
  • Primary Citation of Related Structures:  

  • 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 hu ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
A
348Homo sapiensMutation(s): 0 
Gene Names: FDPS (FPS, KIAA1293)
EC: 2.5.1.10
Find proteins for P14324 (Homo sapiens)
Go to Gene View: FDPS
Go to UniProtKB:  P14324
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
3F2
Query on 3F2

Download SDF File 
Download CCD File 
A
N,N'-bis[3-(4,5-dihydro-1H-imidazol-2-yl)phenyl]biphenyl-4,4'-dicarboxamide
BPH-1358
C32 H28 N6 O2
HOYOJUMMRGKESB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3F2IC50: 1800 nM (100) BINDINGDB
3F2IC50: 1800 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.221 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.757α = 90.00
b = 110.757β = 90.00
c = 77.960γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-3000data reduction
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release