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: 15.47 kDa 
• Atom Count: 1266 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

4HBW

Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazoline ligand

• DOI: 10.2210/pdb4HBW/pdb

• Classification: PROTEIN BINDING/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-28 Released: 2012-10-31 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Qi, J., Felletar, I., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A., Fish, P.V., Bunnage, M.E., Cook, A.S., Owen, D.R., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.228 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Literature

Identification of a Chemical Probe for Bromo and Extra C-Terminal Bromodomain Inhibition through Optimization of a Fragment-Derived Hit.

Fish, P.V., Filippakopoulos, P., Bish, G., Brennan, P.E., Bunnage, M.E., Cook, A.S., Federov, O., Gerstenberger, B.S., Jones, H., Knapp, S., Marsden, B., Nocka, K., Owen, D.R., Philpott, M., Picaud, S., Primiano, M.J., Ralph, M.J., Sciammetta, N., Trzupek, J.D.

(2012) J Med Chem 55: 9831-9837

• PubMed: 23095041 
• DOI: 10.1021/jm3010515
• Primary Citation of Related Structures:  
  4E96, 4HBV, 4HBW, 4HBX, 4HBY


• PubMed Abstract: 
  

The posttranslational modification of chromatin through acetylation at selected histone lysine residues is governed by histone acetyltransferases (HATs) and histone deacetylases (HDACs). The significance of this subset of the epigenetic code is interrogated and interpreted by an acetyllysine-specific protein-protein interaction with bromodomain reader modules. Selective inhibition of the bromo and extra C-terminal domain (BET) family of bromodomains with a small molecule is feasible, and this may represent an opportunity for disease intervention through the recently disclosed antiproliferative and anti-inflammatory properties of such inhibitors. Herein, we describe the discovery and structure-activity relationship (SAR) of a novel, small-molecule chemical probe for BET family inhibition that was identified through the application of structure-based fragment assessment and optimization techniques. This has yielded a potent, selective compound with cell-based activity (PFI-1) that may further add to the understanding of BET family function within the bromodomains.

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Organizational Affiliation: 

Pfizer Worldwide Medicinal Chemistry, Pfizer Worldwide R&D , Ramsgate Road, Sandwich CT13 9NJ, 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 GTEx:  ENSG00000141867

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
14Z (Subject of Investigation/LOI)	C [auth A]	N-ethyl-3-methyl-2-oxo-1,2,3,4-tetrahydroquinazoline-6-sulfonamide C11 H15 N3 O3 S AUPWODYXIHOKFV-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
14Z	PDBBind:  4HBW	IC50: 4800 (nM) from 1 assay(s)
	BindingDB:  4HBW	IC50: 1900 (nM) from 1 assay(s)
	Binding MOAD:  4HBW	IC50: 4800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.228 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.65	α = 90
b = 46.02	β = 90
c = 77.31	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

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2012-09-28 
• Released Date: 2012-10-31 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Qi, J., Felletar, I., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A., Fish, P.V., Bunnage, M.E., Cook, A.S., Owen, D.R., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references
• Version 1.2: 2012-12-12
  Changes: Database references