8B5J

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 7,8-dimethoxy-1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.146 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification and Optimization of a Ligand-Efficient Benzoazepinone Bromodomain and Extra Terminal (BET) Family Acetyl-Lysine Mimetic into the Oral Candidate Quality Molecule I-BET432.

Humphreys, P.G.Anderson, N.A.Bamborough, P.Baxter, A.Chung, C.W.Cookson, R.Craggs, P.D.Dalton, T.Fournier, J.C.L.Gordon, L.J.Gray, H.F.Gray, M.W.Gregory, R.Hirst, D.J.Jamieson, C.Jones, K.L.Kessedjian, H.Lugo, D.McGonagle, G.Patel, V.K.Patten, C.Poole, D.L.Prinjha, R.K.Ramirez-Molina, C.Rioja, I.Seal, G.Stafford, K.A.J.Shah, R.R.Tape, D.Theodoulou, N.H.Tomlinson, L.Ukuser, S.Wall, I.D.Wellaway, N.White, G.

(2022) J Med Chem 65: 15174-15207

  • DOI: 10.1021/acs.jmedchem.2c01102
  • Primary Citation of Related Structures:  
    8B5G, 8B5H, 8B5I, 8B5J

  • PubMed Abstract: 
  • The bromodomain and extra terminal (BET) family of proteins are an integral part of human epigenome regulation, the dysregulation of which is implicated in multiple oncology and inflammatory diseases. Disrupting the BET family bromodomain acetyl-lysine (KAc) histone protein-protein interaction with small-molecule KAc mimetics has proven to be a disease-relevant mechanism of action, and multiple molecules are currently undergoing oncology clinical trials ...

    The bromodomain and extra terminal (BET) family of proteins are an integral part of human epigenome regulation, the dysregulation of which is implicated in multiple oncology and inflammatory diseases. Disrupting the BET family bromodomain acetyl-lysine (KAc) histone protein-protein interaction with small-molecule KAc mimetics has proven to be a disease-relevant mechanism of action, and multiple molecules are currently undergoing oncology clinical trials. This work describes an efficiency analysis of published GSK pan-BET bromodomain inhibitors, which drove a strategic choice to focus on the identification of a ligand-efficient KAc mimetic with the hypothesis that lipophilic efficiency could be drastically improved during optimization. This focus drove the discovery of the highly ligand-efficient and structurally distinct benzoazepinone KAc mimetic. Following crystallography to identify suitable growth vectors, the benzoazepinone core was optimized through an explore-exploit structure-activity relationship (SAR) approach while carefully monitoring lipophilic efficiency to deliver I-BET432 ( 41 ) as an oral candidate quality molecule.


    Organizational Affiliation

    GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
P3R (Subject of Investigation/LOI)
Query on P3R

Download Ideal Coordinates CCD File 
F [auth AAA](5~{R})-7,8-dimethoxy-3,5-dimethyl-2,5-dihydro-1~{H}-3-benzazepin-4-one
C14 H19 N O3
PREGEFBQCOFCDI-SECBINFHSA-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: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.802α = 90
b = 52.416β = 90
c = 31.983γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-11-30 
  • Deposition Author(s): Chung, C.

Funding OrganizationLocationGrant Number
Not fundedUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references