7NQ5

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 3-(2-(benzyloxy)phenyl)-5-methyl-1H-1,2,4-triazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Template-Hopping Approach Leads to Potent, Selective, and Highly Soluble Bromo and Extraterminal Domain (BET) Second Bromodomain (BD2) Inhibitors.

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

(2021) J Med Chem 64: 3249-3281

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02156
  • Primary Citation of Related Structures:  
    7NQ5, 7NQ7, 7NQ8, 7NQ9, 7NQI, 7NQJ

  • PubMed Abstract: 

    A number of reports have recently been published describing the discovery and optimization of bromo and extraterminal inhibitors which are selective for the second bromodomain (BD2); these include our own work toward GSK046 ( 3 ) and GSK620 ( 5 ). This paper describes our approach to mitigating the genotoxicity risk of GSK046 by replacement of the acetamide functionality with a heterocyclic ring. This was followed by a template-hopping and hybridization approach, guided by structure-based drug design, to incorporate learnings from other BD2-selective series, optimize the vector for the amide region, and explore the ZA cleft, leading to the identification of potent, selective, and bioavailable compounds 28 (GSK452), 39 (GSK737), and 36 (GSK217).


  • Organizational Affiliation

    Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
GTEx:  ENSG00000204256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download Ideal Coordinates CCD File 
E [auth AAA]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
ULB (Subject of Investigation/LOI)
Query on ULB

Download Ideal Coordinates CCD File 
F [auth AAA]3-methyl-5-(2-phenylmethoxyphenyl)-4~{H}-1,2,4-triazole
C16 H15 N3 O
NPTNHLPXAAOUPO-UHFFFAOYSA-N
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.311α = 90
b = 52.646β = 90
c = 31.89γ = 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: 2021-03-24 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection, Database references, Derived calculations