4ABU

CRYSTAL STRUCTURE OF TRANSTHYRETIN IN COMPLEX WITH LIGAND C-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystallographic Study of Novel Transthyretin Ligands Exhibiting Negative-Cooperativity between Two Thyroxine Binding Sites.

Tomar, D.Khan, T.Singh, R.R.Mishra, S.Gupta, S.Surolia, A.Salunke, D.M.

(2012) PLoS One 7: 43522

  • DOI: https://doi.org/10.1371/journal.pone.0043522
  • Primary Citation of Related Structures:  
    4ABQ, 4ABU, 4ABV, 4ABW, 4AC2, 4AC4, 4ANK

  • PubMed Abstract: 

    Transthyretin (TTR) is a homotetrameric serum and cerebrospinal fluid protein that transports thyroxine (T4) and retinol by binding to retinol binding protein. Rate-limiting tetramer dissociation and rapid monomer misfolding and disassembly of TTR lead to amyloid fibril formation in different tissues causing various amyloid diseases. Based on the current understanding of the pathogenesis of TTR amyloidosis, it is considered that the inhibition of amyloid fibril formation by stabilization of TTR in native tetrameric form is a viable approach for the treatment of TTR amyloidosis.


  • Organizational Affiliation

    Structural Biology Unit, National Institute of Immunology, New Delhi, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRANSTHYRETIN
A, B
124Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  P02766
GTEx:  ENSG00000118271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02766
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FT1
Query on FT1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-(2,4-dichlorophenoxy)-3-hydroxybenzaldehyde
C13 H8 Cl2 O3
GKHZEXMYTPRFKV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FT1 BindingDB:  4ABU Kd: 13.9 (nM) from 1 assay(s)
IC50: 520 (nM) from 1 assay(s)
PDBBind:  4ABU IC50: 520 (nM) from 1 assay(s)
Binding MOAD:  4ABU IC50: 520 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.6α = 90
b = 42.47β = 90
c = 63.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description