4J3I

X-ray crystal structure of bromodomain complex to 1.24 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 
    0.145 (Depositor), 0.150 (DCC) 
  • R-Value Work: 
    0.113 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 
    0.115 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1K0Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

RVX-208, an Inducer of ApoA-I in Humans, Is a BET Bromodomain Antagonist.

McLure, K.G.Gesner, E.M.Tsujikawa, L.Kharenko, O.A.Attwell, S.Campeau, E.Wasiak, S.Stein, A.White, A.Fontano, E.Suto, R.K.Wong, N.C.Wagner, G.S.Hansen, H.C.Young, P.R.

(2013) PLoS One 8: e83190-e83190

  • DOI: https://doi.org/10.1371/journal.pone.0083190
  • Primary Citation of Related Structures:  
    4J1P, 4J3I

  • PubMed Abstract: 

    Increased synthesis of Apolipoprotein A-I (ApoA-I) and HDL is believed to provide a new approach to treating atherosclerosis through the stimulation of reverse cholesterol transport. RVX-208 increases the production of ApoA-I in hepatocytes in vitro, and in vivo in monkeys and humans, which results in increased HDL-C, but the molecular target was not previously reported. Using binding assays and X-ray crystallography, we now show that RVX-208 selectively binds to bromodomains of the BET (Bromodomain and Extra Terminal) family, competing for a site bound by the endogenous ligand, acetylated lysine, and that this accounts for its pharmacological activity. siRNA experiments further suggest that induction of ApoA-I mRNA is mediated by BET family member BRD4. These data indicate that RVX-208 increases ApoA-I production through an epigenetic mechanism and suggests that BET inhibition may be a promising new approach to the treatment of atherosclerosis.


  • Organizational Affiliation

    Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America.


Macromolecules
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
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
1K0 BindingDB:  4J3I Ki: min: 135, max: 1142 (nM) from 2 assay(s)
Kd: min: 130, max: 8930 (nM) from 9 assay(s)
IC50: min: 2.5, max: 1.27e+4 (nM) from 28 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free:  0.145 (Depositor), 0.150 (DCC) 
  • R-Value Work:  0.113 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 0.115 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.278α = 90
b = 44.623β = 90
c = 78.064γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1K0Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description