6E6J

BRD2_Bromodomain2 complex with inhibitor 744


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Selective inhibition of the BD2 bromodomain of BET proteins in prostate cancer.

Faivre, E.J.McDaniel, K.F.Albert, D.H.Mantena, S.R.Plotnik, J.P.Wilcox, D.Zhang, L.Bui, M.H.Sheppard, G.S.Wang, L.Sehgal, V.Lin, X.Huang, X.Lu, X.Uziel, T.Hessler, P.Lam, L.T.Bellin, R.J.Mehta, G.Fidanze, S.Pratt, J.K.Liu, D.Hasvold, L.A.Sun, C.Panchal, S.C.Nicolette, J.J.Fossey, S.L.Park, C.H.Longenecker, K.Bigelow, L.Torrent, M.Rosenberg, S.H.Kati, W.M.Shen, Y.

(2020) Nature 578: 306-310

  • DOI: 10.1038/s41586-020-1930-8
  • Primary Citation of Related Structures:  
    6E6J, 6ONY

  • PubMed Abstract: 
  • Proteins of the bromodomain and extra-terminal (BET) domain family are epigenetic readers that bind acetylated histones through their bromodomains to regulate gene transcription. Dual-bromodomain BET inhibitors (DbBi) that bind with similar affinities to the first (BD1) and second (BD2) bromodomains of BRD2, BRD3, BRD4 and BRDt have displayed modest clinical activity in monotherapy cancer trials ...

    Proteins of the bromodomain and extra-terminal (BET) domain family are epigenetic readers that bind acetylated histones through their bromodomains to regulate gene transcription. Dual-bromodomain BET inhibitors (DbBi) that bind with similar affinities to the first (BD1) and second (BD2) bromodomains of BRD2, BRD3, BRD4 and BRDt have displayed modest clinical activity in monotherapy cancer trials. A reduced number of thrombocytes in the blood (thrombocytopenia) as well as symptoms of gastrointestinal toxicity are dose-limiting adverse events for some types of DbBi 1-5 . Given that similar haematological and gastrointestinal defects were observed after genetic silencing of Brd4 in mice 6 , the platelet and gastrointestinal toxicities may represent on-target activities associated with BET inhibition. The two individual bromodomains in BET family proteins may have distinct functions 7-9 and different cellular phenotypes after pharmacological inhibition of one or both bromodomains have been reported 10,11 , suggesting that selectively targeting one of the bromodomains may result in a different efficacy and tolerability profile compared with DbBi. Available compounds that are selective to individual domains lack sufficient potency and the pharmacokinetics properties that are required for in vivo efficacy and tolerability assessment 10-13 . Here we carried out a medicinal chemistry campaign that led to the discovery of ABBV-744, a highly potent and selective inhibitor of the BD2 domain of BET family proteins with drug-like properties. In contrast to the broad range of cell growth inhibition induced by DbBi, the antiproliferative activity of ABBV-744 was largely, but not exclusively, restricted to cell lines of acute myeloid leukaemia and prostate cancer that expressed the full-length androgen receptor (AR). ABBV-744 retained robust activity in prostate cancer xenografts, and showed fewer platelet and gastrointestinal toxicities than the DbBi ABBV-075 14 . Analyses of RNA expression and chromatin immunoprecipitation followed by sequencing revealed that ABBV-744 displaced BRD4 from AR-containing super-enhancers and inhibited AR-dependent transcription, with less impact on global transcription compared with ABBV-075. These results underscore the potential value of selectively targeting the BD2 domain of BET family proteins for cancer therapy.


    Organizational Affiliation

    Oncology Discovery, AbbVie, North Chicago, IL, USA. yu.shen@abbvie.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 2A, B, C, D, E, F112Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HWV (Subject of Investigation/LOI)
Query on HWV

Download Ideal Coordinates CCD File 
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]N-ethyl-4-[2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl]-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide
C28 H30 F N3 O4
OEDSFMUSNZDJFD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.776α = 90
b = 107.776β = 90
c = 89.751γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Database references