1NL4

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

PDB DOI: https://doi.org/10.2210/pdb1NL4/pdb

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

Deposited: 2003-01-06 Released: 2003-02-11
Deposition Author(s): Curtin, M.L., Florjancic, A.S., Cohen, J., Gu, W.-J., Frost, D.J., Muchmore, S.W., Sham, H.L.

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

PubMed: 12657284 Search on PubMed
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

Macromolecule Content

Total Structure Weight: 83.34 kDa
Atom Count: 5,871
Modelled Residue Count: 713
Deposited Residue Count: 713
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase alpha subunit	A	312	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04631
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase beta subunit	B	401	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02293
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FTL Query on FTL Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	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		Interactions Focus chain E [auth B]
HFP Query on HFP Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID C₁₅ H₃₃ O₄ P IJNCEETVCWDDQB-KFWWJZLASA-N		Interactions Focus chain D [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
FTL	BindingDB: 1NL4	IC50: min: 0.39, max: 150 (nM) from 3 assay(s)
FTL	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 = 168.62	α = 90
b = 168.62	β = 90
c = 69.123	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-02-11

Deposition Author(s):

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