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: 15.54 kDa 
• Atom Count: 1257 
• Residue Count: 126 
• Unique protein chains: 1

4NUC

Crystal structure of the first bromodomain of human BRD4 in complex with MS435 inhibitor

• DOI: 10.2210/pdb4NUC/pdb

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


• Deposited: 2013-12-03 Released: 2014-04-02 
• Deposition Author(s): Plotnikov, A.N., Joshua, J., Zhou, M.-M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.186 
• R-Value Work: 0.135 
• R-Value Observed: 0.137 

Literature

Structure-Guided Design of Potent Diazobenzene Inhibitors for the BET Bromodomains

Zhang, G., Plotnikov, A.N., Rusinova, E., Shen, T., Morohashi, K., Joshua, J., Zeng, L., Mujtaba, S., Ohlmeyer, M., Zhou, M.-M.

(2013) J Med Chem 56: 9251-9264

• PubMed: 24144283 
• DOI: 10.1021/jm401334s
• Primary Citation of Related Structures:  
  4NUC, 4NUD, 4NUE


• PubMed Abstract: 
  

BRD4, characterized by two acetyl-lysine binding bromodomains and an extra-terminal (ET) domain, is a key chromatin organizer that directs gene activation in chromatin through transcription factor recruitment, enhancer assembly, and pause release of the RNA polymerase II complex for transcription elongation. BRD4 has been recently validated as a new epigenetic drug target for cancer and inflammation. Our current knowledge of the functional differences of the two bromodomains of BRD4, however, is limited and is hindered by the lack of selective inhibitors. Here, we report our structure-guided development of diazobenzene-based small-molecule inhibitors for the BRD4 bromodomains that have over 90% sequence identity at the acetyl-lysine binding site. Our lead compound, MS436, through a set of water-mediated interactions, exhibits low nanomolar affinity (estimated Ki of 30-50 nM), with preference for the first bromodomain over the second. We demonstrated that MS436 effectively inhibits BRD4 activity in NF-κB-directed production of nitric oxide and proinflammatory cytokine interleukin-6 in murine macrophages. MS436 represents a new class of bromodomain inhibitors and will facilitate further investigation of the biological functions of the two bromodomains of BRD4 in gene expression.

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Organizational Affiliation: 

Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States.

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
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885 GTEx  ENSG00000141867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
435	A	4-[(E)-(4-hydroxy-3,5-dimethylphenyl)diazenyl]-N-(pyridin-2-yl)benzenesulfonamide C19 H18 N4 O3 S UPZISPNEBVCTRN-QURGRASLSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
435	Ki:  910   nM  BindingDB
435	Ki:  912   nM  BindingDB
435	IC50:  16000   nM  BindingDB
435	Ki:  910   nM  Binding MOAD
435	IC50:  46300   nM  BindingDB
435	Ki:  4300   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.186 
• R-Value Work: 0.135 
• R-Value Observed: 0.137 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.729	α = 90
b = 49.552	β = 90
c = 56.057	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-03 
• Released Date: 2014-04-02 
Deposition Author(s): Plotnikov, A.N., Joshua, J., Zhou, M.-M.

Revision History 

• Version 1.0: 2014-04-02
  Type: Initial release