4NUD

Crystal structure of the first bromodomain of human BRD4 in complex with MS436 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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

  • 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, 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.


    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NUD (Subject of Investigation/LOI)
Query on NUD

Download Ideal Coordinates CCD File 
B [auth A]4-[(E)-(2-amino-4-hydroxy-5-methylphenyl)diazenyl]-N-(pyridin-2-yl)benzenesulfonamide
C18 H17 N5 O3 S
DZTGIRNXWSZBIM-QURGRASLSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NUD BindingDB:  4NUD Ki: min: 85, max: 340 (nM) from 3 assay(s)
IC50: min: 3800, max: 4900 (nM) from 2 assay(s)
Binding MOAD:  4NUD Ki: 84.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.985α = 90
b = 49.029β = 90
c = 57.903γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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