4L1S

Covalent modification of transthyretin K15 by yielding the fluorescent conjugate (E)-3-(dimethylamino)-5-(4-hydroxy-3,5-dimethylstyryl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging-what we know and what we need to learn.

Baranczak, A.Connelly, S.Liu, Y.Choi, S.Grimster, N.P.Powers, E.T.Wilson, I.A.Kelly, J.W.

(2014) Biopolymers 101: 484-495

  • DOI: 10.1002/bip.22407
  • Primary Citation of Related Structures:  4L1T

  • PubMed Abstract: 
  • We seek fluorogenic small molecules that generate a fluorescent conjugate signal if and only if they react with a given protein-of-interest (i.e., small molecules for which noncovalent binding to the protein-of-interest is insufficient to generate fl ...

    We seek fluorogenic small molecules that generate a fluorescent conjugate signal if and only if they react with a given protein-of-interest (i.e., small molecules for which noncovalent binding to the protein-of-interest is insufficient to generate fluorescence). Consequently, it is the new chemical entity afforded by the generally irreversible reaction between the small molecule and the protein-of-interest that enables the energy of an electron occupying the lowest unoccupied molecular orbital (LUMO) of the chromophore to be given off as a photon instead of being dissipated by nonradiative mechanisms in complex biological environments. This category of fluorogenic small molecules is created by starting with environmentally sensitive fluorophores that are modified by an essential functional group that efficiently quenches the fluorescence until a chemoselective reaction between that functional group and the protein-of-interest occurs, yielding the fluorescent conjugate. Fluorogenic small molecules are envisioned to be useful for a wide variety of applications, including live cell imaging without the requirement for washing steps and pulse-chase kinetic analyses of protein synthesis, trafficking, degradation, etc.


    Organizational Affiliation

    Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, 92037.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
127Homo sapiensGene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1W4
Query on 1W4

Download SDF File 
Download CCD File 
A, B
S-(4-fluorophenyl) 3-(dimethylamino)-5-[(E)-2-(4-hydroxy-3,5-dimethylphenyl)ethenyl]benzenecarbothioate
C25 H24 F N O2 S
HDIQCNNYMZBHKA-AATRIKPKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 41.632α = 90.00
b = 86.059β = 90.00
c = 62.802γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
Blu-Icedata collection
REFMACrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references
  • Version 1.2: 2014-08-20
    Type: Database references