4N86

Crystal structure of human transthyretin complexed with glabridin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 

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This is version 1.1 of the entry. See complete history

Literature

Crystal structures of human transthyretin complexed with glabridin

Yokoyama, T.Kosaka, Y.Mizuguchi, M.

(2014) J.Med.Chem. 57: 1090-1096

  • DOI: 10.1021/jm401832j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transthyretin (TTR) is a plasma protein implicated in human amyloid diseases. Several small molecules that bind to the thyroxine-binding site of TTR have been shown to stabilize the TTR tetramer and to inhibit amyloid fibril formation of TTR. Herein, ...

    Transthyretin (TTR) is a plasma protein implicated in human amyloid diseases. Several small molecules that bind to the thyroxine-binding site of TTR have been shown to stabilize the TTR tetramer and to inhibit amyloid fibril formation of TTR. Herein, we demonstrated that glabridin (Glab), a prenylated isoflavan isolated from Glycyrrhiza glabra L., inhibited aggregation of TTR in a thioflavin assay. The TTR-Glab complex structure revealed a novel binding mode including a CH-π interaction with A108 and a hydrogen bond with K15. A structural comparison with the wild type-apo structure revealed that the CH-π interaction with A108 was strengthened by the induced-fit conformational change upon Glab binding. Furthermore, the binding of Glab induced a rotation of the T119 side chain, and the inclusion of a water molecule, leading to stabilization of the dimer-dimer interface. These results demonstrate that Glab is a novel inhibitor of TTR fibrillization and suggest the molecular mechanism by which Glab binding stabilizes the tetramer.


    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
159Homo sapiensGene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GBJ
Query on GBJ

Download SDF File 
Download CCD File 
A, B
4-[(3R)-8,8-dimethyl-3,4-dihydro-2H,8H-pyrano[2,3-f]chromen-3-yl]benzene-1,3-diol
glabridin
C20 H20 O4
LBQIJVLKGVZRIW-ZDUSSCGKSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.829α = 90.00
b = 84.582β = 90.00
c = 65.265γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Database references