Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.37 kDa 
• Atom Count: 1989 
• Modelled Residue Count: 231 
• Deposited Residue Count: 256 
• Unique protein chains: 1

5U4D

Wild-type Transthyretin in complex with 3-[(1E)-2-(2-Chloro-4-hydroxyphenyl)ethenyl]benzoic Acid

• DOI: 10.2210/pdb5U4D/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-03 Released: 2017-09-27 
• Deposition Author(s): Windsor, I.W., Smith, T.P., Raines, R.T., Forest, K.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.243 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 

Literature

Stilbene Boronic Acids Form a Covalent Bond with Human Transthyretin and Inhibit Its Aggregation.

Smith, T.P., Windsor, I.W., Forest, K.T., Raines, R.T.

(2017) J Med Chem 60: 7820-7834

• PubMed: 28920684 
• DOI: 10.1021/acs.jmedchem.7b00952
• Primary Citation of Related Structures:  
  5U48, 5U49, 5U4A, 5U4B, 5U4C, 5U4D, 5U4E, 5U4F, 5U4G


• PubMed Abstract: 
  

Transthyretin (TTR) is a homotetrameric protein. Its dissociation into monomers leads to the formation of fibrils that underlie human amyloidogenic diseases. The binding of small molecules to the thyroxin-binding sites in TTR stabilizes the homotetramer and attenuates TTR amyloidosis. Herein, we report on boronic acid-substituted stilbenes that limit TTR amyloidosis in vitro. Assays of affinity for TTR and inhibition of its tendency to form fibrils were coupled with X-ray crystallographic analysis of nine TTR·ligand complexes. The ensuing structure-function data led to a symmetrical diboronic acid that forms a boronic ester reversibly with serine 117. This diboronic acid inhibits fibril formation by both wild-type TTR and a common disease-related variant, V30M TTR, as effectively as does tafamidis, a small-molecule drug used to treat TTR-related amyloidosis in the clinic. These findings establish a new modality for covalent inhibition of fibril formation and illuminate a path for future optimization.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transthyretin	A, B	128	Homo sapiens	Mutation(s): 0  Gene Names: TTR, PALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens) Explore P02766  Go to UniProtKB:  P02766
PHAROS:  P02766 GTEx:  ENSG00000118271

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XLO (Subject of Investigation/LOI)	C [auth A], D [auth B]	3-[(E)-2-(2-chloro-4-hydroxyphenyl)ethenyl]benzoic acid C15 H11 Cl O3 FFFUYAAIQHIBGO-SNAWJCMRSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XLO	BindingDB:  5U4D	Kd: 470 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.243 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.207	α = 90
b = 84.814	β = 90
c = 64.618	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
HKL	data reduction

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-12-03 
• Released Date: 2017-09-27 
Deposition Author(s): Windsor, I.W., Smith, T.P., Raines, R.T., Forest, K.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008349
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM044783
National Science Foundation (NSF, United States)	United States	MCB 1518160

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Database references
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence, Derived calculations