4LRG

Structure of BRD4 bromodomain 1 with a dimethyl thiophene isoxazole azepine carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery, Design, and Optimization of Isoxazole Azepine BET Inhibitors.

Gehling, V.S.Hewitt, M.C.Vaswani, R.G.Leblanc, Y.Cote, A.Nasveschuk, C.G.Taylor, A.M.Harmange, J.C.Audia, J.E.Pardo, E.Joshi, S.Sandy, P.Mertz, J.A.Sims, R.J.Bergeron, L.Bryant, B.M.Bellon, S.Poy, F.Jayaram, H.Sankaranarayanan, R.Yellapantula, S.Bangalore Srinivasamurthy, N.Birudukota, S.Albrecht, B.K.

(2013) ACS Med Chem Lett 4: 835-840

  • DOI: 10.1021/ml4001485
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The identification of a novel series of small molecule BET inhibitors is described. Using crystallographic binding modes of an amino-isoxazole fragment and known BET inhibitors, a structure-based drug design effort lead to a novel isoxazole azepine s ...

    The identification of a novel series of small molecule BET inhibitors is described. Using crystallographic binding modes of an amino-isoxazole fragment and known BET inhibitors, a structure-based drug design effort lead to a novel isoxazole azepine scaffold. This scaffold showed good potency in biochemical and cellular assays and oral activity in an in vivo model of BET inhibition.


    Organizational Affiliation

    Constellation Pharmaceuticals , 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A
128Homo sapiensMutation(s): 0 
Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens)
Go to Gene View: BRD4
Go to UniProtKB:  O60885
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1XB
Query on 1XB

Download SDF File 
Download CCD File 
A
2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-[1,2]oxazolo[5,4-c]thieno[2,3-e]azepin-6-yl]acetamide
C20 H18 Cl N3 O2 S
DRSQZZRFHBWKKZ-AWEZNQCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1XBIC50: 26 - 140 nM (99) BINDINGDB
1XBIC50: 26 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.044α = 90.00
b = 45.604β = 90.00
c = 78.581γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-08-14
    Type: Other, Structure summary
  • Version 1.2: 2014-10-08
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description