Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 15.53 kDa 
• Atom Count: 1297 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

4MEO

Crystal Structure of the first bromodomain of human BRD4 in complex with a 2-methyl-quinoline ligand

• PDB DOI: 10.2210/pdb4MEO/pdb

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


• Deposited: 2013-08-27 Released: 2013-09-25 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Fedorov, O., Vidler, L.R., Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Hoelder, S., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.213 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 

Literature

Discovery of Novel Small-Molecule Inhibitors of BRD4 Using Structure-Based Virtual Screening.

Vidler, L.R., Filippakopoulos, P., Fedorov, O., Picaud, S., Martin, S., Tomsett, M., Woodward, H., Brown, N., Knapp, S., Hoelder, S.

(2013) J Med Chem 56: 8073-8088

• PubMed: 24090311 
• DOI: 10.1021/jm4011302
• Primary Citation of Related Structures:  
  4MEN, 4MEO, 4MEP, 4MEQ


• PubMed Abstract: 
  

Bromodomains (BRDs) are epigenetic readers that recognize acetylated-lysine (KAc) on proteins and are implicated in a number of diseases. We describe a virtual screening approach to identify BRD inhibitors. Key elements of this approach are the extensive design and use of substructure queries to compile a set of commercially available compounds featuring novel putative KAc mimetics and docking this set for final compound selection. We describe the validation of this approach by applying it to the first BRD of BRD4. The selection and testing of 143 compounds lead to the discovery of six novel hits, including four unprecedented KAc mimetics. We solved the crystal structure of four hits, determined their binding mode, and improved their potency through synthesis and the purchase of derivatives. This work provides a validated virtual screening approach that is applicable to other BRDs and describes novel KAc mimetics that can be further explored to design more potent inhibitors.

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Organizational Affiliation: 

Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , 15 Cotswold Road, Sutton, Surrey SM2 5NG, United Kingdom.

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
25V	C [auth A]	N-[3-(2-methyl-1-oxidoquinolin-4-yl)phenyl]acetamide C18 H16 N2 O2 YSGOTUAMXVUKOD-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
25V	BindingDB:  4MEO	IC50: 4.20e+4 (nM) from 1 assay(s)
	PDBBind:  4MEO	IC50: 2.50e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.213 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.5	α = 90
b = 44.18	β = 90
c = 78.01	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-27 
• Released Date: 2013-09-25 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Fedorov, O., Vidler, L.R., Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Hoelder, S., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references
• Version 1.2: 2014-02-19
  Changes: Database references