1X81

Farnesyl transferase structure of Jansen compound

• PDB DOI: https://doi.org/10.2210/pdb1X81/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2004-08-16 Released: 2004-12-21 
• Deposition Author(s): Li, Q., Claiborne, A., Li, T., Hasvold, L., Stoll, V.S., Muchmore, S., Jakob, C.G., Gu, W., Cohen, J., Hutchins, C., Frost, D., Rosenberg, S.H., Sham, H.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.292 
• R-Value Work: 0.223 

Literature

Design, synthesis, and activity of 4-quinolone and pyridone compounds as nonthiol-containing farnesyltransferase inhibitors.

Li, Q., Claiborne, A., Li, T., Hasvold, L., Stoll, V.S., Muchmore, S., Jakob, C.G., Gu, W., Cohen, J., Hutchins, C., Frost, D., Rosenberg, S.H., Sham, H.L.

(2004) Bioorg Med Chem Lett 14: 5367-5370

• PubMed: 15454228 
• DOI: https://doi.org/10.1016/j.bmcl.2004.08.012
• Primary Citation of Related Structures:  
  1X81


• PubMed Abstract: 
  

  As a part of our efforts to identify potent inhibitors of farnesyltransferase (FTase), modification of the structure of tipifarnib through structure-based design was undertaken by replacing the 2-quinolones with 4-quinolones and pyridones, and subsequent relocation of the D-ring to the N-methyl group on the imidazole ring. This study has yielded a novel series of potent and selective FTase inhibitors. The X-ray structure of tipifarnib (1) in complex with FTase was described.

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Organizational Affiliation: 

Cancer Research, GPRD, Abbott Laboratories, 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: 83.06 kDa 
• Atom Count: 5,849 
• Modelled Residue Count: 712 
• Deposited Residue Count: 712 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit	A	315	Rattus norvegicus	Mutation(s): 0  EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
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	397	Rattus norvegicus	Mutation(s): 0  EC: 2.5.1.58
UniProt
Find proteins for Q02293 (Rattus norvegicus) Explore Q02293  Go to UniProtKB:  Q02293

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JAN	D [auth B]	6-[(S)-AMINO(4-CHLOROPHENYL)(1-METHYL-1H-IMIDAZOL-5-YL)METHYL]-4-(3-CHLOROPHENYL)-1-METHYLQUINOLIN-2(1H)-ONE C27 H22 Cl2 N4 O PLHJCIYEEKOWNM-HHHXNRCGSA-N
ZN	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JAN	BindingDB:  1X81	IC50: min: 0.65, max: 1100 (nM) from 6 assay(s)
	PDBBind:  1X81	IC50: 0.65 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.292 
• R-Value Work: 0.223 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.086	α = 90
b = 170.086	β = 90
c = 69.133	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Li, Q., Claiborne, A., Li, T., Hasvold, L., Stoll, V.S., Muchmore, S., Jakob, C.G., Gu, W., Cohen, J., Hutchins, C., Frost, D., Rosenberg, S.H., Sham, H.L.

Revision History  

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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