Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.77 kDa 
• Atom Count: 1284 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

4J0R

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

• DOI: 10.2210/pdb4J0R/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-31 Released: 2013-02-13 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Qi, J., Felletar, I., Hewings, D.S., von Delft, F., Conway, S.J., Bountra, C., Arrowsmith, C.H., Edwards, A., Knapp, S., Structural Genomics Consortium (SGC)

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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 

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

• PubMed: 23517011 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1H2 (Subject of Investigation/LOI)	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
IOD	G [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 38.595	α = 90
b = 42.856	β = 90
c = 79.435	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2013-01-31 
• Released Date: 2013-02-13 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Qi, J., Felletar, I., Hewings, D.S., von Delft, F., Conway, S.J., Bountra, C., Arrowsmith, C.H., Edwards, A., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Database references