7V2J

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design, synthesis and pharmacological characterization of N-(3-ethylbenzo[d]isoxazol-5-yl) sulfonamide derivatives as BRD4 inhibitors against acute myeloid leukemia.

Zhang, M.F.Luo, X.Y.Zhang, C.Wang, C.Wu, X.S.Xiang, Q.P.Xu, Y.Zhang, Y.

(2022) Acta Pharmacol Sin 43: 2735-2748

  • DOI: https://doi.org/10.1038/s41401-022-00881-y
  • Primary Citation of Related Structures:  
    7V1U, 7V2J

  • PubMed Abstract: 

    BRD4 plays a key role in the regulation of gene transcription and has been identified as an attractive target for cancer treatment. In this study, we designed 26 new compounds by modifying 3-ethyl-benzo[d]isoxazole core with sulfonamides. Most compounds exhibited potent BRD4 binding activities with ΔT m values exceeding 6 °C. Two crystal structures of 11h and 11r in complex with BRD4(1) were obtained to characterize the binding patterns. Compounds 11h and 11r were effective for BRD4(1) binding and showed remarkable anti-proliferative activity against MV4-11 cells with IC 50 values of 0.78 and 0.87 μM. Furthermore, 11r (0.5-10 μM) concentration-dependently inhibited the expression levels of oncogenes including c-Myc and CDK6 in MV4-11 cells. Moreover, 11r (0.5-10 μM) concentration-dependently blocked cell cycle in MV4-11 cells at G 0 /G 1 phase and induced cell apoptosis. Compound 11r may serve as a new lead compound for further drug development.


  • Organizational Affiliation

    College of Pharmacy, Taizhou Polytechnic College, Taizhou, 225300, China. zhang_maofeng@163.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4141Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5FZ (Subject of Investigation/LOI)
Query on 5FZ

Download Ideal Coordinates CCD File 
B [auth A]~{N}-(3-ethyl-6-methoxy-1,2-benzoxazol-5-yl)-4-methoxy-benzenesulfonamide
C17 H18 N2 O5 S
QDPZIJXJBVSBJA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.215α = 90
b = 47.347β = 90
c = 77.977γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81673357

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description