4LR6

Structure of BRD4 bromodomain 1 with a 3-methyl-4-phenylisoxazol-5-amine fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

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:  
    4LR6, 4LRG

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A128Homo sapiensMutation(s): 0 
Gene Names: BRD4BRD4_HUMANHUNK1
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1XA
Query on 1XA

Download CCD File 
A
3-methyl-4-phenyl-1,2-oxazol-5-amine
C10 H10 N2 O
ZCTBUBMRXYVEHX-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1XAIC50:  33000   nM  Binding MOAD
1XAIC50:  33000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.682α = 90
b = 47.131β = 90
c = 77.794γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

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