4J1P

X-ray crystal structure of bromodomain 2 of human brd2 in complex with rvx208 to 1.08 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 2, isoform CRA_a114Homo sapiensMutation(s): 0 
Gene Names: BRD2DKFZp313H139hCG_17503
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
GTEx:  ENSG00000204256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1K0
Query on 1K0

Download Ideal Coordinates CCD File 
B [auth A]2-[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]-5,7-dimethoxyquinazolin-4(3H)-one
C20 H22 N2 O5
NETXMUIMUZJUTB-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1K0 Binding MOAD:  4J1P Kd: 206 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.1α = 90
b = 66.35β = 90
c = 75.854γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata 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: 2014-01-15
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description