6SWN

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH iBET-BD1 (GSK778)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammation.

Gilan, O.Rioja, I.Knezevic, K.Bell, M.J.Yeung, M.M.Harker, N.R.Lam, E.Y.N.Chung, C.W.Bamborough, P.Petretich, M.Urh, M.Atkinson, S.J.Bassil, A.K.Roberts, E.J.Vassiliadis, D.Burr, M.L.Preston, A.G.S.Wellaway, C.Werner, T.Gray, J.R.Michon, A.M.Gobbetti, T.Kumar, V.Soden, P.E.Haynes, A.Vappiani, J.Tough, D.F.Taylor, S.Dawson, S.J.Bantscheff, M.Lindon, M.Drewes, G.Demont, E.H.Daniels, D.L.Grandi, P.Prinjha, R.K.Dawson, M.A.

(2020) Science 368: 387-394

  • DOI: https://doi.org/10.1126/science.aaz8455
  • Primary Citation of Related Structures:  
    6SWN, 6SWO, 6SWP, 6SWQ

  • PubMed Abstract: 

    The two tandem bromodomains of the BET (bromodomain and extraterminal domain) proteins enable chromatin binding to facilitate transcription. Drugs that inhibit both bromodomains equally have shown efficacy in certain malignant and inflammatory conditions. To explore the individual functional contributions of the first (BD1) and second (BD2) bromodomains in biology and therapy, we developed selective BD1 and BD2 inhibitors. We found that steady-state gene expression primarily requires BD1, whereas the rapid increase of gene expression induced by inflammatory stimuli requires both BD1 and BD2 of all BET proteins. BD1 inhibitors phenocopied the effects of pan-BET inhibitors in cancer models, whereas BD2 inhibitors were predominantly effective in models of inflammatory and autoimmune disease. These insights into the differential requirement of BD1 and BD2 for the maintenance and induction of gene expression may guide future BET-targeted therapies.


  • Organizational Affiliation

    Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A [auth AAA]127Homo 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
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LWB (Subject of Investigation/LOI)
Query on LWB

Download Ideal Coordinates CCD File 
C [auth AAA]4-[2-(methoxymethyl)-1-[(1~{R})-1-phenylethyl]-8-[[(3~{S})-pyrrolidin-3-yl]methoxy]imidazo[4,5-c]quinolin-7-yl]-3,5-dimethyl-1,2-oxazole
C30 H33 N5 O3
ZORLJXWXFABTPZ-CTNGQTDRSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
B [auth AAA]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth AAA]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.28α = 90
b = 42.32β = 90
c = 90.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-04-01 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references