Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.54 kDa 
• Atom Count: 6,325 
• Modelled Residue Count: 716 
• Deposited Residue Count: 817 
• Unique protein chains: 2

 2ZIR

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

• PDB DOI:  https://doi.org/10.2210/pdb2ZIR/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-02-22 Released: 2009-02-24 
• Deposition Author(s): Fukami, T.A., Sogabe, S., Nagata, Y., Kondoh, O., Ishii, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.230 
• R-Value Work: 0.195 

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

• PubMed: 19217288 
• DOI: https://doi.org/10.1016/j.bmcl.2009.01.074
• Primary Citation of Related Structures:  
  2ZIR, 2ZIS


• 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 mice.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase subunit alpha	A	377	Rattus norvegicus	Mutation(s): 1  Gene Names: Fnta EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (UniProt)
UniProt
Find proteins for Q04631 (Rattus norvegicus) Explore Q04631  Go to UniProtKB:  Q04631

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase subunit beta	B	440	Rattus norvegicus	Mutation(s): 0  Gene Names: Fntb EC: 2.5.1.58
UniProt
Find proteins for Q02293 (Rattus norvegicus) Explore Q02293  Go to UniProtKB:  Q02293

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NH7	G [auth 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
FPP	F [auth B]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
GOL	C [auth A], D [auth A], H [auth B], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FPP	BindingDB:  2ZIR	Kd: 2 (nM) from 1 assay(s)
NH7	PDBBind:  2ZIR	IC50: 6.4 (nM) from 1 assay(s)
	BindingDB:  2ZIR	IC50: 6.4 (nM) from 1 assay(s)
	Binding MOAD:  2ZIR	IC50: 6.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.230 
• R-Value Work: 0.195 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.996	α = 90
b = 171.996	β = 90
c = 69.179	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-24 
Deposition Author(s): Fukami, T.A., Sogabe, S., Nagata, Y., Kondoh, O., Ishii, N.

Revision History  

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