4J0R

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: 1.72 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 1.1 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: 10.1021/jm301588r
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A127Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1H2 (Subject of Investigation/LOI)
Query on 1H2

Download Ideal Coordinates CCD File 
F [auth A]3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(R)-hydroxy(phenyl)methyl]phenol
C18 H17 N O3
FEQUIPXIENTMJN-GOSISDBHSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
G [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1H2 BindingDB:  4J0R Kd: 360 (nM) from 1 assay(s)
IC50: 386 (nM) from 1 assay(s)
PDBBind:  4J0R IC50: 386 (nM) from 1 assay(s)
Binding MOAD:  4J0R IC50: 386 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.595α = 90
b = 42.856β = 90
c = 79.435γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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