5JI8

Crystal structure of the BRD9 bromodomain and hit 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

NMR Fragment Screening Hit Induces Plasticity of BRD7/9 Bromodomains

Wang, N.Li, F.Bao, H.Li, J.Wu, J.Ruan, K.

(2016) Chembiochem 17: 1456-1463

  • DOI: 10.1002/cbic.201600184

  • PubMed Abstract: 
  • The complex biology associated with inhibition of bromodomain and extra-terminal (BET) domains by chemical probes has attracted increasing attention, and there is a need to identify non-BET bromodomain (BD) inhibitors. Several potent inhibitors of th ...

    The complex biology associated with inhibition of bromodomain and extra-terminal (BET) domains by chemical probes has attracted increasing attention, and there is a need to identify non-BET bromodomain (BD) inhibitors. Several potent inhibitors of the BRD9 BD have recently been discovered, with anticancer and anti-inflammation activity. However, its paralogue, BRD7 BD, remains unexploited. Here, we identified new chemotypes targeting BRD7 BD by using NMR fragment-based screening. BRD7/9 BDs exhibit similar patterns of chemical-shift perturbation upon the titration of hit compound 1. The crystal structure revealed that 1 repels the Y222 group of BRD9 BD in a similar way to that for butyryllysine, but not acetyllysine and known inhibitors. Hit 1 induced less rearrangement of residue F161 of BRD9 BD than acetyllysine, butyryllysine, and crotonyllysine. Our study provides structural insight into a new generation of butyryllysine mimics for probing the function of BRD7/9 BD.


    Organizational Affiliation

    Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 9
A
111Homo sapiensMutation(s): 0 
Gene Names: BRD9
Find proteins for Q9H8M2 (Homo sapiens)
Go to Gene View: BRD9
Go to UniProtKB:  Q9H8M2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6KT
Query on 6KT

Download SDF File 
Download CCD File 
A
2-amino-1,3-benzothiazole-6-carboxamide
C8 H7 N3 O S
HPRLVAQRFQEQPF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.150 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 24.498α = 70.09
b = 34.090β = 75.28
c = 39.519γ = 73.24
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references