5AYT | pdb_00005ayt

Crystal structure of transthyretin in complex with L6

• PDB DOI: https://doi.org/10.2210/pdb5AYT/pdb

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


• Deposited: 2015-09-03 Released: 2016-01-20 
• Deposition Author(s): Yokoyama, T., Mizuguchi, M., Kai, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Structural stabilization of transthyretin by a new compound, 6-benzoyl-2-hydroxy-1H-benzo[de]isoquinoline-1,3(2H)-dione

Yokoyama, T., Takaki, S., Chosa, K., Sato, T., Suico, M.A., Teranishi, Y., Shuto, T., Mizuguchi, M., Kai, H.

(2015) J Pharmacol Sci 129: 240-243

• PubMed: 26639444 
• DOI: https://doi.org/10.1016/j.jphs.2015.09.006
• Primary Citation Related Structures: 
  5AYT


• PubMed Abstract: 
  

  Familial amyloid polyneuropathy (FAP) is a genetic, adult-onset, neurodegenerative disorder caused by amyloid formation of transthyretin (TTR), a thyroxine-binding protein. Mutation in TTR causes a propensity of TTR tetramer to dissociate to monomer, which is the first step to amyloidosis. Thus, a drug that can stabilize the tetramer structure will have therapeutic benefit. Here, by virtual screening and biochemical assays, we identified small molecule 6-benzoyl-2-hydroxy-1H-benzo[de]isoquinoline-1,3(2H)-dione (L6) that can prevent the dissociation of TTR to monomer. X-ray crystallography reveals that L6 binds to the T4 binding pocket of TTR. These findings show that L6 is a candidate TTR stabilizer.

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Organizational Affiliation: 
• Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan.
Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.
Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.
Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan. Electronic address: [e-mail].
Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.26 kDa 
• Atom Count: 2,102 
• Modeled Residue Count: 230 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transthyretin	A, B	159	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
L6Y	C [auth A], D [auth B]	2-oxidanyl-6-(phenylcarbonyl)benzo[de]isoquinoline-1,3-dione C19 H11 N O4 AFGMHSZWGJYWFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.578	α = 90
b = 84.814	β = 90
c = 65.291	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Yokoyama, T., Mizuguchi, M., Kai, H.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references