6XV3

CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 

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 4ABCD127Homo 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
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O2B
Query on O2B

Download CCD File 
A, B, C, D
3-methyl-6-[6-[(3~{S})-3-methylmorpholin-4-yl]-1-[(1~{S})-1-phenylethyl]imidazo[4,5-c]pyridin-2-yl]-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine
C28 H33 N9 O
PPMNCASBGOVBMV-OALUTQOASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.184α = 105.25
b = 58.955β = 90.7
c = 59.639γ = 97.94
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
STARANISOdata reduction
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