1NI1

Imidazole and cyanophenyl farnesyl transferase inhibitors

• PDB DOI: https://doi.org/10.2210/pdb1NI1/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2002-12-20 Released: 2004-04-06 
• Deposition Author(s): Tong, Y., Lin, N.H., Wang, L., Hasvold, L., Wang, W., Leonard, N., Li, T., Li, Q., Cohen, J., Gu, W.Z., Zhang, H., Stoll, V., Bauch, J., Marsh, K., Rosenberg, S.H., Sham, H.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.327 
• R-Value Work: 0.264 

Literature

Discovery of potent imidazole and cyanophenyl containing farnesyltransferase inhibitors with improved oral bioavailability.

Tong, Y., Lin, N.H., Wang, L., Hasvold, L., Wang, W., Leonard, N., Li, T., Li, Q., Cohen, J., Gu, W.Z., Zhang, H., Stoll, V., Bauch, J., Marsh, K., Rosenberg, S.H., Sham, H.L.

(2003) Bioorg Med Chem Lett 13: 1571-1574

• PubMed: 12699757 
• DOI: https://doi.org/10.1016/s0960-894x(03)00195-1
• Primary Citation of Related Structures:  
  1NI1


• PubMed Abstract: 
  

  A pyridyl moiety was introduced into a previously developed series of farnesyltransferase inhibitors containing imidazole and cyanophenyl (such as 4), resulting in potent inhibitors with improved pharmacokinetics.

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Organizational Affiliation: 

R47B, AP10, Global Pharmaceutical R&D, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6101, USA. [e-mail]

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: 83.84 kDa 
• Atom Count: 5,868 
• Modelled Residue Count: 713 
• Deposited Residue Count: 717 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase alpha subunit	A	315	Rattus norvegicus	Mutation(s): 0  Gene Names: FNTA EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt), 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 beta subunit	B	402	Rattus norvegicus	Mutation(s): 0  Gene Names: FNTB EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt)
UniProt
Find proteins for Q02293 (Rattus norvegicus) Explore Q02293  Go to UniProtKB:  Q02293

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2C5	E [auth B]	2-CHLORO-5-(3-CHLORO-PHENYL)-6-[(4-CYANO-PHENYL)-(3-METHYL-3H-IMIDAZOL-4-YL)- METHOXYMETHYL]-NICOTINONITRILE C25 H17 Cl2 N5 O JVWHVGIRXILXMU-XMMPIXPASA-N
HFP	D [auth B]	ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID C15 H33 O4 P IJNCEETVCWDDQB-KFWWJZLASA-N
ZN	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2C5	PDBBind:  1NI1	IC50: 0.9 (nM) from 1 assay(s)
	BindingDB:  1NI1	IC50: 0.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.327 
• R-Value Work: 0.264 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.096	α = 90
b = 170.096	β = 90
c = 69.286	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
HKL-2000	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-06 
Deposition Author(s): Tong, Y., Lin, N.H., Wang, L., Hasvold, L., Wang, W., Leonard, N., Li, T., Li, Q., Cohen, J., Gu, W.Z., Zhang, H., Stoll, V., Bauch, J., Marsh, K., Rosenberg, S.H., Sham, H.L.

Revision History  

• Version 1.0: 2004-04-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations