4Y9B

Crystal structure of V30M mutated transthyretin in complex with alpha-mangostin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of gamma-Mangostin as an Amyloidogenesis Inhibitor

Yokoyama, T.Ueda, M.Ando, Y.Mizuguchi, M.

(2015) Sci Rep 5: 13570-13570

  • DOI: 10.1038/srep13570
  • Primary Citation of Related Structures:  4Y9C, 4Y9E, 4Y9F, 4Y9G

  • PubMed Abstract: 
  • Transthyretin (TTR) is a homotetrameric protein involved in human hereditary amyloidoses. The discovery and development of small molecules that inhibit the amyloid fibril formation of TTR is one of the therapeutic strategies for these diseases. Herei ...

    Transthyretin (TTR) is a homotetrameric protein involved in human hereditary amyloidoses. The discovery and development of small molecules that inhibit the amyloid fibril formation of TTR is one of the therapeutic strategies for these diseases. Herein, we discovered that γ-mangostin (γ-M) is an effective inhibitor against the amyloid fibril formation of V30M amyloidogenic TTR. In-vitro binding assays revealed that γ-M was the most potent of the selected xanthone derivatives, and it bound to the thyroxine (T4)-binding sites and stabilized the TTR tetramer. X-ray crystallographic analysis revealed the diagonal binding mode of γ-M and the two binding sites of chloride ions at the T4-binding site. One of the chloride ions was replaced with a water molecule in the α-mangostin complex, which is a methylated derivative of γ-M. The stronger inhibitory potency of γ-M could be explained by the additional hydrogen bonds with the chloride ion. The present study establishes γ-M as a novel inhibitor of TTR fibrillization.


    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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MKS
Query on MKS

Download SDF File 
Download CCD File 
A, B
1,3,6-trihydroxy-7-methoxy-2,8-bis(3-methylbut-2-en-1-yl)-9H-xanthen-9-one
alpha-Mangostin
C24 H26 O6
GNRIZKKCNOBBMO-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 43.633α = 90.00
b = 85.365β = 90.00
c = 64.703γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Takeda Science FoundationJapan--
Amyloidosis Research CommitteeJapan--

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release