6XUZ

CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

PI by NMR: Probing CH-pi Interactions in Protein-Ligand Complexes by NMR Spectroscopy.

Platzer, G.Mayer, M.Beier, A.Bruschweiler, S.Fuchs, J.E.Engelhardt, H.Geist, L.Bader, G.Schorghuber, J.Lichtenecker, R.Wolkerstorfer, B.Kessler, D.McConnell, D.B.Konrat, R.

(2020) Angew Chem Int Ed Engl 

  • DOI: 10.1002/anie.202003732
  • Primary Citation of Related Structures:  
    6XV3, 6XVC, 6XV7, 6XUZ

  • PubMed Abstract: 
  • While CH-π-interactions with target proteins are crucial determinants for the affinity of arguably every drug molecule, no method exists to directly measure the strength of individual CH-π interactions in drug-protein complexes. Here we present a fas ...

    While CH-π-interactions with target proteins are crucial determinants for the affinity of arguably every drug molecule, no method exists to directly measure the strength of individual CH-π interactions in drug-protein complexes. Here we present a fast and reliable methodology called PI (π interactions) by NMR, which can differentiate the strength of protein-ligand CH-π interactions in solution. By combining selective amino-acid side-chain labeling with 1 H- 13 C NMR, we are able to identify specific protein protons of side-chains engaged in CH-π interactions with aromatic ring-systems of a ligand, based solely on 1 H chemical shift values of the interacting protein aromatic ring protons. The information encoded in the chemical shifts induced by such interactions serves as a proxy for the strength of each individual CH-π interaction. PI by NMR changes the paradigm by which chemists can optimize the potency of drug candidates: direct determination of individual π-interactions rather than averaged measures of all interactions.


    Organizational Affiliation

    Universitat Wien, Department of Structural and Computational Biology, AUSTRIA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O1W
Query on O1W

Download CCD File 
A
6-[1-[(2~{S})-1-methoxypropan-2-yl]-6-[(3~{S})-3-methylmorpholin-4-yl]imidazo[4,5-c]pyridin-2-yl]-3-methyl-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine
C24 H33 N9 O2
JZCZJRBLMNHFSU-HOTGVXAUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.857α = 90
b = 48.287β = 90
c = 57.885γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references, Refinement description