5F1L

Crystal structure of the bromodomain of BRD9 in complex with compound 9.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor.

Martin, L.J.Koegl, M.Bader, G.Cockcroft, X.L.Fedorov, O.Fiegen, D.Gerstberger, T.Hofmann, M.H.Hohmann, A.F.Kessler, D.Knapp, S.Knesl, P.Kornigg, S.Muller, S.Nar, H.Rogers, C.Rumpel, K.Schaaf, O.Steurer, S.Tallant, C.Vakoc, C.R.Zeeb, M.Zoephel, A.Pearson, M.Boehmelt, G.McConnell, D.

(2016) J.Med.Chem. 59: 4462-4475

  • DOI: 10.1021/acs.jmedchem.5b01865
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Components of the chromatin remodelling switch/sucrose nonfermentable (SWI/SNF) complex are recurrently mutated in tumors, suggesting that altering the activity of the complex plays a role in oncogenesis. However, the role that the individual subunit ...

    Components of the chromatin remodelling switch/sucrose nonfermentable (SWI/SNF) complex are recurrently mutated in tumors, suggesting that altering the activity of the complex plays a role in oncogenesis. However, the role that the individual subunits play in this process is not clear. We set out to develop an inhibitor compound targeting the bromodomain of BRD9 in order to evaluate its function within the SWI/SNF complex. Here, we present the discovery and development of a potent and selective BRD9 bromodomain inhibitor series based on a new pyridinone-like scaffold. Crystallographic information on the inhibitors bound to BRD9 guided their development with respect to potency for BRD9 and selectivity against BRD4. These compounds modulate BRD9 bromodomain cellular function and display antitumor activity in an AML xenograft model. Two chemical probes, BI-7273 (1) and BI-9564 (2), were identified that should prove to be useful in further exploring BRD9 bromodomain biology in both in vitro and in vivo settings.


    Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 9
A, B
123Homo 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
5U2
Query on 5U2

Download SDF File 
Download CCD File 
A, B
5-[3,5-dimethoxy-4-[(3-oxidanylazetidin-1-yl)methyl]phenyl]-1,3-dimethyl-pyridin-2-one
C19 H24 N2 O4
YZIWDEXMYWHXDR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5U2IC50: 21 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.308α = 90.00
b = 125.165β = 90.00
c = 30.016γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references