Crystal structure of the first bromodomain of human BRD4 in complex with MS417 inhibitor

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 

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This is version 1.2 of the entry. See complete history


Down-regulation of NF-{kappa}B Transcriptional Activity in HIV-associated Kidney Disease by BRD4 Inhibition.

Zhang, G.Liu, R.Zhong, Y.Plotnikov, A.N.Zhang, W.Zeng, L.Rusinova, E.Gerona-Nevarro, G.Moshkina, N.Joshua, J.Chuang, P.Y.Ohlmeyer, M.He, J.C.Zhou, M.M.

(2012) J Biol Chem 287: 28840-28851

  • DOI: https://doi.org/10.1074/jbc.M112.359505
  • Primary Citation of Related Structures:  
    2LSP, 4F3I

  • PubMed Abstract: 

    NF-κB-mediated inflammation is the major pathology in chronic kidney diseases, including HIV-associated nephropathy (HIVAN) that ultimately progresses to end stage renal disease. HIV infection in the kidney induces NF-κB activation, leading to the production of proinflammatory chemokines, cytokines, and adhesion molecules. In this study, we explored selective inhibition of NF-κB transcriptional activity by small molecule blocking NF-κB binding to the transcriptional cofactor BRD4, which is required for the assembly of the productive transcriptional complex comprising positive transcription elongation factor b and RNA polymerase II. We showed that our BET (Bromodomain and Extra-Terminal domain)-specific bromodomain inhibitor MS417, designed to block BRD4 binding to the acetylated NF-κB, effectively attenuates NF-κB transcriptional activation of proinflammatory genes in kidney cells treated with TNFα or infected by HIV. MS417 ameliorates inflammation and kidney injury in HIV-1 transgenic mice, an animal model for HIVAN. Our study suggests that BET bromodomain inhibition, targeting at the proinflammatory activity of NF-κB, represents a new therapeutic approach for treating NF-κB-mediated inflammation and kidney injury in HIVAN.

  • Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York 10029, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4127Homo 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
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0S6

Download Ideal Coordinates CCD File 
D [auth A]methyl [(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate
C20 H19 Cl N4 O2 S
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
0S6 BindingDB:  4F3I Ki: 17 (nM) from 1 assay(s)
IC50: 18.2 (nM) from 1 assay(s)
PDBBind:  4F3I Kd: 36.1 (nM) from 1 assay(s)
Binding MOAD:  4F3I Kd: 36.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.843α = 90
b = 44.659β = 90
c = 78.237γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Experimental preparation
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description