1N9A | pdb_00001n9a

Farnesyltransferase complex with tetrahydropyridine inhibitors

PDB DOI: https://doi.org/10.2210/pdb1N9A/pdb

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

Deposited: 2002-11-22 Released: 2003-01-07
Deposition Author(s): Gwaltney II, S.L., O'Conner, S.J., Nelson, L.T., Sullivan, G.M., Imade, H., Wang, W., Hasvold, L., Li, Q., Cohen, J., Gu, W.Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.375 (Depositor), 0.343 (DCC)
R-Value Work:
0.329 (Depositor), 0.291 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Aryl tetrahydropyridine inhibitors of farnesyltransferase: bioavailable analogues with improved cellular potency.

Gwaltney II, S.L., O'Connor, S.J., Nelson, L.T., Sullivan, G.M., Imade, H., Wang, W., Hasvold, L., Li, Q., Cohen, J., Gu, W.Z., Tahir, S.K., Bauch, J., Marsh, K., Ng, S.C., Frost, D.J., Zhang, H., Muchmore, S., Jakob, C.G., Stoll, V., Hutchins, C., Rosenberg, S.H., Sham, H.L.

(2003) Bioorg Med Chem Lett 13: 1363-1366

PubMed: 12657283 Search on PubMed
DOI: https://doi.org/10.1016/s0960-894x(03)00094-5
Primary Citation Related Structures:
1N9A

PubMed Abstract:
Inhibitors of farnesyltransferase are effective against a variety of tumors in mouse models of cancer. Clinical trials to evaluate these agents in humans are ongoing. In our effort to develop new farnesyltransferase inhibitors, we have discovered bioavailable aryl tetrahydropyridines that are potent in cell culture. The design, synthesis, SAR and biological properties of these compounds will be discussed.

Organizational Affiliation

Pharmaceutical Discovery, R47B, Building AP-10, Abbott Laboratories, Abbott Park, IL 60064-6101, USA. stephen.gwaltney@syrrx.com

Macromolecule Content

Total Structure Weight: 83.82 kDa
Atom Count: 5,870
Modeled Residue Count: 713
Deposited Residue Count: 717
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase alpha subunit	A	315	Rattus norvegicus	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04631
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase beta subunit	B	402	Rattus norvegicus	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02293
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FTI Query on FTI 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]	1-{2-[3-(4-CYANO-BENZYL)-3H-IMIDAZOL-4-YL]-ACETYL}-5-NAPHTHALEN-1-YL-1,2,3,6-TETRAHYDRO-PYRIDINE-4-CARBONITRILE C₂₉ H₂₃ N₅ O KXPIURLUHSBSHE-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density 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] Interactions & Density 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] Interactions & Density Focus chain C [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
FTI	BindingDB: 1N9A	IC50: min: 2.2, max: 4500 (nM) from 2 assay(s)
FTI	BindingDB: 1N9A	EC50: 3.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.375 (Depositor), 0.343 (DCC)
R-Value Work: 0.329 (Depositor), 0.291 (DCC)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.503	α = 90
b = 170.503	β = 90
c = 69.272	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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-01-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-01-07
Type: Initial release
Version 1.1: 2008-04-28
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