3KSQ | pdb_00003ksq

Discovery of C-Imidazole Azaheptapyridine FPT Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3KSQ/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-23 Released: 2010-01-26 
• Deposition Author(s): Zhu, H.Y., Cooper, A.B., Njoroge, G., Kirschmeier, P., Strickland, C., Hruza, A., Girijavallabhan, V.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Discovery of C-imidazole azaheptapyridine FPT inhibitors.

Zhu, H.Y., Cooper, A.B., Desai, J., Njoroge, G., Kirschmeier, P., Bishop, W.R., Strickland, C., Hruza, A., Doll, R.J., Girijavallabhan, V.M.

(2010) Bioorg Med Chem Lett 20: 1134-1136

• PubMed: 20056542 
• DOI: https://doi.org/10.1016/j.bmcl.2009.12.013
• Primary Citation of Related Structures:  
  3KSQ


• PubMed Abstract: 
  

  The discovery of C-linked imidazole azaheptapyridine bridgehead FPT inhibitors is described. This novel class of compounds are sub nM FPT enzyme inhibitors with potent cellular inhibitory activities. This series also has reduced hERG activity versus previous N-linked imidazole series. X-ray of compound 10a bound to FTase revealed strong interaction between bridgehead imidazole 3N with catalytic zinc atom.

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Organizational Affiliation: 
• Schering Plough Research Institute, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, 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: 93.8 kDa 
• Atom Count: 6,211 
• Modeled Residue Count: 718 
• Deposited Residue Count: 814 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyltransferase, CAAX box, alpha	A	377	Rattus norvegicus	Mutation(s): 0  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	437	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
Z96	F [auth B]	tert-butyl 4-{(11S)-8-chloro-6-[(R)-hydroxy(1-methyl-1H-imidazol-5-yl)methyl]-11H-benzo[5,6]cyclohepta[1,2-b]pyridin-11-yl}piperazine-1-carboxylate C28 H32 Cl N5 O3 YZFYPECRJZGSGJ-IZZNHLLZSA-N
FPP	E [auth B]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Z96	BindingDB:  3KSQ	IC50: 0.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.122	α = 90
b = 171.122	β = 90
c = 69.269	γ = 120

Software Package:

Software Name	Purpose
StructureStudio	data collection
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Zhu, H.Y., Cooper, A.B., Njoroge, G., Kirschmeier, P., Strickland, C., Hruza, A., Girijavallabhan, V.M.

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description