6ZB2

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH GSK549


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.139 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The Optimization of a Novel, Weak Bromo and Extra Terminal Domain (BET) Bromodomain Fragment Ligand to a Potent and Selective Second Bromodomain (BD2) Inhibitor.

Seal, J.T.Atkinson, S.J.Aylott, H.Bamborough, P.Chung, C.W.Copley, R.C.B.Gordon, L.Grandi, P.Gray, J.R.J.Harrison, L.A.Hayhow, T.G.Lindon, M.Messenger, C.Michon, A.M.Mitchell, D.Preston, A.Prinjha, R.K.Rioja, I.Taylor, S.Wall, I.D.Watson, R.J.Woolven, J.M.Demont, E.H.

(2020) J Med Chem 63: 9093-9126

  • DOI: 10.1021/acs.jmedchem.0c00796
  • Primary Citation of Related Structures:  
    6ZB1, 6ZB0, 6ZB3, 6ZB2

  • PubMed Abstract: 
  • The profound efficacy, yet associated toxicity of pan-BET inhibitors is well documented. The possibility of an ameliorated safety profile driven by significantly selective (>100-fold) inhibition of a subset of the eight bromodomains is enticing, but challenging given the close homology ...

    The profound efficacy, yet associated toxicity of pan-BET inhibitors is well documented. The possibility of an ameliorated safety profile driven by significantly selective (>100-fold) inhibition of a subset of the eight bromodomains is enticing, but challenging given the close homology. Herein, we describe the X-ray crystal structure-directed optimization of a novel weak fragment ligand with a pan-second bromodomain (BD2) bias, to potent and highly BD2 selective inhibitors. A template hopping approach, enabled by our parallel research into an orthogonal template ( 15 , GSK046), was the basis for the high selectivity observed. This culminated in two tool molecules, 20 (GSK620) and 56 (GSK549), which showed an anti-inflammatory phenotype in human whole blood, confirming their cellular target engagement. Excellent broad selectivity, developability, and in vivo oral pharmacokinetics characterize these tools, which we hope will be of broad utility to the field of epigenetics research.


    Organizational Affiliation

    IVIVT Cellzome, Platform Technology and Science, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 2A [auth AAA]115Homo sapiensMutation(s): 0 
Gene Names: BRD2KIAA9001RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QD5 (Subject of Investigation/LOI)
Query on QD5

Download Ideal Coordinates CCD File 
E [auth AAA]~{N}5-cyclopropyl-1-(1~{H}-indol-4-ylmethyl)-~{N}3-methyl-2-oxidanylidene-pyridine-3,5-dicarboxamide
C20 H20 N4 O3
PDCBJZVPIGAEBL-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth AAA]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.139 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.017α = 90
b = 52.327β = 90
c = 32.033γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2020-06-06 
  • Released Date: 2020-08-05 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references