6KEJ

Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 6-[2-(diethylamino)ethoxy]-16-methoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Synthesis and Structure-Activity Relationships of Aristoyagonine Derivatives as Brd4 Bromodomain Inhibitors with X-ray Co-Crystal Research.

Yoo, M.Park, T.H.Yoo, M.Kim, Y.Lee, J.Y.Lee, K.M.Ryu, S.E.Lee, B.I.Jung, K.Y.Park, C.H.

(2021) Molecules 26

  • DOI: https://doi.org/10.3390/molecules26061686
  • Primary Citation of Related Structures:  
    6KEC, 6KEH, 6KEI, 6KEJ, 6KEK

  • PubMed Abstract: 

    Epigenetic regulation is known to play a key role in progression of anti-cancer therapeutics. Lysine acetylation is an important mechanism in controlling gene expression. There has been increasing interest in bromodomain owing to its ability to modulate transcription of various genes as an epigenetic 'reader.' Herein, we report the design, synthesis, and X-ray studies of novel aristoyagonine (benzo[6,7]oxepino[4,3,2- cd ]isoindol-2(1 H )-one) derivatives and investigate their inhibitory effect against Brd4 bromodomain. Five compounds 8ab , 8bc , 8bd , 8be , and 8bf have been discovered with high binding affinity over the Brd4 protein. Co-crystal structures of these five inhibitors with human Brd4 bromodomain demonstrated that it has a key binding mode occupying the hydrophobic pocket, which is known to be the acetylated lysine binding site. These novel Brd4 bromodomain inhibitors demonstrated impressive inhibitory activity and mode of action for the treatment of cancer diseases.


  • Organizational Affiliation

    Department of Medicinal Chemistry and Pharmacology, University of Science & Technology, Daejeon 34113, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4127Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D7F (Subject of Investigation/LOI)
Query on D7F

Download Ideal Coordinates CCD File 
B [auth A]6-[2-(diethylamino)ethoxy]-16-methoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one
C23 H26 N2 O4
GATTUJGPZVMLAL-UHFFFAOYSA-N
FMT (Subject of Investigation/LOI)
Query on FMT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.899α = 90
b = 47.213β = 90
c = 79.262γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2019R1A2C1002545

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2021-04-21
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description