4J0S | pdb_00004j0s

Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Optimization of 3,5-dimethylisoxazole derivatives as potent bromodomain ligands.

Hewings, D.S.Fedorov, O.Filippakopoulos, P.Martin, S.Picaud, S.Tumber, A.Wells, C.Olcina, M.M.Freeman, K.Gill, A.Ritchie, A.J.Sheppard, D.W.Russell, A.J.Hammond, E.M.Knapp, S.Brennan, P.E.Conway, S.J.

(2013) J Med Chem 56: 3217-3227

  • DOI: https://doi.org/10.1021/jm301588r
  • Primary Citation Related Structures: 
    4J0R, 4J0S

  • PubMed Abstract: 

    The bromodomain protein module, which binds to acetylated lysine, is emerging as an important epigenetic therapeutic target. We report the structure-guided optimization of 3,5-dimethylisoxazole derivatives to develop potent inhibitors of the BET (bromodomain and extra terminal domain) bromodomain family with good ligand efficiency. X-ray crystal structures of the most potent compounds reveal key interactions required for high affinity at BRD4(1). Cellular studies demonstrate that the phenol and acetate derivatives of the lead compounds showed strong antiproliferative effects on MV4;11 acute myeloid leukemia cells, as shown for other BET bromodomain inhibitors and genetic BRD4 knockdown, whereas the reported compounds showed no general cytotoxicity in other cancer cell lines tested.


  • Organizational Affiliation
    • Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.

Macromolecule Content 

  • Total Structure Weight: 15.64 kDa 
  • Atom Count: 1,253 
  • Modeled Residue Count: 127 
  • Deposited Residue Count: 127 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.655α = 90
b = 42.981β = 90
c = 79.547γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description