5L4M

Crystal Structure of Human Transthyretin in Complex with 3,5,6-Trichloro-2-pyridinyloxyacetic acid (Triclopyr)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.581 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin.

Zhang, J.Begum, A.Brannstrom, K.Grundstrom, C.Iakovleva, I.Olofsson, A.Sauer-Eriksson, A.E.Andersson, P.L.

(2016) Environ. Sci. Technol. 50: 11984-11993

  • DOI: 10.1021/acs.est.6b02771
  • Primary Citation of Related Structures:  
  • Also Cited By: 6GRP, 6GR7, 6GOO, 6GON, 6GNW, 6GNR, 6GNP, 6GNO, 6GNM

  • PubMed Abstract: 
  • Thyroid disruption by xenobiotics is associated with a broad spectrum of severe adverse outcomes. One possible molecular target of thyroid hormone disrupting chemicals (THDCs) is transthyretin (TTR), a thyroid hormone transporter in vertebrates. To b ...

    Thyroid disruption by xenobiotics is associated with a broad spectrum of severe adverse outcomes. One possible molecular target of thyroid hormone disrupting chemicals (THDCs) is transthyretin (TTR), a thyroid hormone transporter in vertebrates. To better understand the interactions between TTR and THDCs, we determined the crystallographic structures of human TTR in complex with perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), and 2,2',4,4'-tetrahydroxybenzophenone (BP2). The molecular interactions between the ligands and TTR were further characterized using molecular dynamics simulations. A structure-based virtual screening (VS) protocol was developed with the intention of providing an efficient tool for the discovery of novel TTR-binders from the Tox21 inventory. Among the 192 predicted binders, 12 representatives were selected, and their TTR binding affinities were studied with isothermal titration calorimetry, of which seven compounds had binding affinities between 0.26 and 100 μM. To elucidate structural details in their binding to TTR, crystal structures were determined of TTR in complex with four of the identified compounds including 2,6-dinitro-p-cresol, bisphenol S, clonixin, and triclopyr. The compounds were found to bind in the TTR hormone binding sites as predicted. Our results show that the developed VS protocol is able to successfully identify potential THDCs, and we suggest that it can be used to propose THDCs for future toxicological evaluations.


    Organizational Affiliation

    Department of Chemistry and ‡Department of Medical Biochemistry and Biophysics, Umeå University , SE-901 87 Umeå, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
127Homo sapiensMutation(s): 0 
Gene 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
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SBK
Query on SBK

Download SDF File 
Download CCD File 
A, B
Triclopyr
C7 H4 Cl3 N O3
REEQLXCGVXDJSQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.581 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.543α = 90.00
b = 85.520β = 90.00
c = 64.012γ = 90.00
Software Package:
Software NamePurpose
SADABSdata scaling
PHENIXrefinement
PHASERphasing
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-11-09
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence