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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.42 kDa 
• Atom Count: 1203 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

6FT4

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

• DOI: 10.2210/pdb6FT4/pdb

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


• Deposited: 2018-02-20 Released: 2018-04-18 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Pike, A.C.W., Krojer, T., Conway, S.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.217 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 

Literature

BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stability.

Jennings, L.E., Schiedel, M., Hewings, D.S., Picaud, S., Laurin, C.M.C., Bruno, P.A., Bluck, J.P., Scorah, A.R., See, L., Reynolds, J.K., Moroglu, M., Mistry, I.N., Hicks, A., Guzanov, P., Clayton, J., Evans, C.N.G., Stazi, G., Biggin, P.C., Mapp, A.K., Hammond, E.M., Humphreys, P.G., Filippakopoulos, P., Conway, S.J.

(2018) Bioorg Med Chem 26: 2937-2957

• PubMed: 29776834 
• DOI: 10.1016/j.bmc.2018.05.003
• Primary Citation of Related Structures:  
  6FSY, 6FT3, 6FT4


• PubMed Abstract: 
  

Ligands for the bromodomain and extra-terminal domain (BET) family of bromodomains have shown promise as useful therapeutic agents for treating a range of cancers and inflammation. Here we report that our previously developed 3,5-dimethylisoxazole-based BET bromodomain ligand (OXFBD02) inhibits interactions of BRD4(1) with the RelA subunit of NF-κB, in addition to histone H4. This ligand shows a promising profile in a screen of the NCI-60 panel but was rapidly metabolised (t _½  = 39.8 min). Structure-guided optimisation of compound properties led to the development of the 3-pyridyl-derived OXFBD04. Molecular dynamics simulations assisted our understanding of the role played by an internal hydrogen bond in altering the affinity of this series of molecules for BRD4(1). OXFBD04 shows improved BRD4(1) affinity (IC ₅₀  = 166 nM), optimised physicochemical properties (LE = 0.43; LLE = 5.74; SFI = 5.96), and greater metabolic stability (t _½  = 388 min).

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Organizational Affiliation: 

Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom. Electronic address: [e-mail].

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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E5W (Subject of Investigation/LOI)	B [auth A]	3-[[4,4-bis(fluoranyl)piperidin-1-yl]methyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)phenol C17 H20 F2 N2 O2 ASWANVCVFDVNLN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E5W	BindingDB:  6FT4	IC50: min: 234, max: 235 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.217 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.665	α = 90
b = 48.982	β = 90
c = 60.494	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-02-20 
• Released Date: 2018-04-18 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Pike, A.C.W., Krojer, T., Conway, S.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	095751/Z/11/Z

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2019-04-24
  Changes: Data collection, Database references