2ZIR

Crystal Structure of rat protein farnesyltransferase complexed with a benzofuran inhibitor and FPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis and structure-activity relationships of novel benzofuran farnesyltransferase inhibitors

Asoh, K.Kohchi, M.Hyoudoh, I.Ohtsuka, T.Masubuchi, M.Kawasaki, K.Ebiike, H.Shiratori, Y.Fukami, T.A.Kondoh, O.Tsukaguchi, T.Ishii, N.Aoki, Y.Shimma, N.Sakaitani, M.

(2009) Bioorg.Med.Chem.Lett. 19: 1753-1757

  • DOI: 10.1016/j.bmcl.2009.01.074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of benzofuran-based farnesyltransferase inhibitors have been designed and synthesized as antitumor agents. Among them, 11f showed the most potent enzyme inhibitory activity (IC(50)=1.1nM) and antitumor activity in human cancer xenografts in ...

    A series of benzofuran-based farnesyltransferase inhibitors have been designed and synthesized as antitumor agents. Among them, 11f showed the most potent enzyme inhibitory activity (IC(50)=1.1nM) and antitumor activity in human cancer xenografts in mice.


    Organizational Affiliation

    Kamakura Research Laboratories, Chugai Pharmaceutical Co. Ltd., 200-Kajiwara, Kamakura, Kanagawa 247-8530, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase subunit alpha
A
377Rattus norvegicusMutation(s): 1 
Gene Names: Fnta
EC: 2.5.1.58, 2.5.1.59
Find proteins for Q04631 (Rattus norvegicus)
Go to UniProtKB:  Q04631
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase subunit beta
B
440Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.58
Find proteins for Q02293 (Rattus norvegicus)
Go to UniProtKB:  Q02293
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FPP
Query on FPP

Download SDF File 
Download CCD File 
B
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
NH7
Query on NH7

Download SDF File 
Download CCD File 
B
2-[(S)-(4-chlorophenyl)(hydroxy)(1-methyl-1H-imidazol-5-yl)methyl]-N-morpholin-4-yl-7-phenyl-1-benzofuran-5-carboxamide
C30 H27 Cl N4 O4
DEXSDZQNSUQUAY-PMERELPUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NH7IC50: 6.4 nM BINDINGMOAD
NH7IC50: 6.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 171.996α = 90.00
b = 171.996β = 90.00
c = 69.179γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
CNXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance