1NL4

Crystal Structure of Rat Farnesyl Transferase in Complex With A Potent Biphenyl Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Novel and Selective Imidazole-containing Biphenyl Inhibitors of Protein Farnesyltransferase

Curtin, M.L., Florjancic, A.S., Cohen, J., Gu, W.-J., Frost, D.J., Muchmore, S.W., Sham, H.L.

(2003) Bioorg Med Chem Lett 13: 1367-1371

  • DOI: https://doi.org/10.1016/s0960-894x(03)00096-9
  • Primary Citation of Related Structures:  
    1NL4

  • PubMed Abstract: 

    A series of imidazole-containing biphenyls was prepared and evaluated in vitro for inhibition of FTase and cellular Ras processing. Several of these analogues, such as 21, are potent inhibitors of FTase (<1nM), FTase/GGTase selective (>300-fold) and cellularly active (

    • Organizational Affiliation: 

    Department of Cancer Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA. mike.curtin@abbott.com


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase alpha subunit312Rattus norvegicusMutation(s): 0 
Gene Names: FNTA
EC: 2.5.1
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04631
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase beta subunit401Rattus norvegicusMutation(s): 0 
Gene Names: FNTB
EC: 2.5.1
UniProt
Find proteins for Q02293 (Rattus norvegicus)
Explore Q02293 
Go to UniProtKB:  Q02293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02293
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FTL
Query on FTL
Download Ideal Coordinates CCD File 
E [auth B]4-[(3-CYANO-BENZYL)-(3-METHYL-3H-IMIDAZOL-4-YLMETHYL)-AMINO]-2-NAPHTHALEN-1-YL-BENZONITRILE
C30 H23 N5
IQZCODLAPFPVNS-UHFFFAOYSA-N
HFP
Query on HFP
Download Ideal Coordinates CCD File 
D [auth B]ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID
C15 H33 O4 P
IJNCEETVCWDDQB-KFWWJZLASA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FTL BindingDB:  1NL4 IC50: min: 0.39, max: 150 (nM) from 3 assay(s)
PDBBind:  1NL4 IC50: 0.39 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.62α = 90
b = 168.62β = 90
c = 69.123γ = 120
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-11
    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: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations