1N46

CRYSTAL STRUCTURE OF HUMAN TR BETA LIGAND-BINDING DOMAIN COMPLEXED WITH A POTENT SUBTYPE-SELECTIVE THYROMIMETIC

• PDB DOI:  https://doi.org/10.2210/pdb1N46/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-10-30 Released: 2003-04-22 
• Deposition Author(s): Dow, R.L., Schneider, S.R., Paight, E.S., Hank, R.F., Chiang, P., Cornelius, P., Lee, E., Newsome, W.P., Swick, A.G., Spitzer, J., Hargrove, D.M., Patterson, T.A., Pandit, J., Chrunyk, B.A., LeMotte, P.K., Danley, D.E., Rosner, M.H., Ammirati, M.J., Simons, S.P., Schulte, G.K., Tate, B.F., DaSilva-Jardine, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.256 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Discovery of a Novel Series of 6-Azauracil-Based Thyroid Hormone Receptor Ligands: Potent, TRbeta Subtype-Selective Thyromimetics

Dow, R.L., Schneider, S.R., Paight, E.S., Hank, R.F., Chiang, P., Cornelius, P., Lee, E., Newsome, W.P., Swick, A.G., Spitzer, J., Hargrove, D.M., Patterson, T.A., Pandit, J., Chrunyk, B.A., LeMotte, P.K., Danley, D.E., Rosner, M.H., Ammirati, M.J., Simons, S.P., Schulte, G.K., Tate, B.F., DaSilva-Jardine, P.

(2003) Bioorg Med Chem Lett 13: 379-382

• PubMed: 12565933 
• DOI: https://doi.org/10.1016/s0960-894x(02)00947-2
• Primary Citation of Related Structures:  
  1N46


• PubMed Abstract: 
  

In this communication, we wish to describe the discovery of a novel series of 6-azauracil-based thyromimetics that possess up to 100-fold selectivities for binding and functional activation of the beta(1)-isoform of the thyroid receptor family. Structure-activity relationship studies on the 3,5- and 3'-positions provided compounds with enhanced TR beta affinity and selectivity. Key binding interactions between the 6-azauracil moiety and the receptor have been determined through of X-ray crystallographic analysis.

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Organizational Affiliation: 

Cardiovascular and Metabolic Diseases, Pfizer Global Research and Development, Groton, CT 06340, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.04 kDa 
• Atom Count: 4,040 
• Modelled Residue Count: 487 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thyroid hormone receptor Beta-1	A, B	258	Homo sapiens	Mutation(s): 0  Gene Names: THRB, ERBA2, NR1A2, THR1
UniProt & NIH Common Fund Data Resources
Find proteins for P10828 (Homo sapiens) Explore P10828  Go to UniProtKB:  P10828
PHAROS:  P10828

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PFA	C [auth A], D [auth B]	[4-(4-HYDROXY-3-ISOPROPYL-PHENOXY)-3,5-DIMETHYL-PHENYL]-6-AZAURACIL C20 H21 N3 O4 RXQAVKWRCZYGMV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PFA	PDBBind:  1N46	Ki: 0.03 (nM) from 1 assay(s)
	Binding MOAD:  1N46	Ki: 0.03 (nM) from 1 assay(s)
	BindingDB:  1N46	Ki: 0.03 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.256 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.918	α = 90
b = 105.315	β = 98.19
c = 55.988	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-22 
Deposition Author(s): Dow, R.L., Schneider, S.R., Paight, E.S., Hank, R.F., Chiang, P., Cornelius, P., Lee, E., Newsome, W.P., Swick, A.G., Spitzer, J., Hargrove, D.M., Patterson, T.A., Pandit, J., Chrunyk, B.A., LeMotte, P.K., Danley, D.E., Rosner, M.H., Ammirati, M.J., Simons, S.P., Schulte, G.K., Tate, B.F., DaSilva-Jardine, P.

Revision History  

• Version 1.0: 2003-04-22
  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: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2018-04-04
  Changes: Data collection