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


This is version 1.0 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain containing 2, isoform CRA_a A114Homo sapiensMutation(s): 0 
Gene Names: BRD2, DKFZp313H139, hCG_17503, KIAA9001, RING3
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
NIH Common Fund Data Resources
PHAROS:  P25440
GTEx:  ENSG00000204256
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1K0
Query on 1K0
Download Ideal Coordinates CCD File 
A
2-[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]-5,7-dimethoxyquinazolin-4(3H)-one
C20 H22 N2 O5
NETXMUIMUZJUTB-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1K0Kd:  206   nM  Binding MOAD
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


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release