7W3D

Crystal structure of BRD4 bromodomain 1 (BD1) in complex with N2-(1,2,3-benzotriazol-5-yl)-N3-(dimethylsulfamoyl)-N6-[(2S)-1-methoxypropan-2-yl]pyridine-2,3,6-triamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.276 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of BET specific bromodomain inhibitors with a novel scaffold.

Pandit, N.Yoo, M.Hyun Park, T.Kim, J.Mi Kim, S.Myung Lee, K.Kim, Y.Min Bong, S.Il Lee, B.Jung, K.Y.Hoon Park, C.

(2022) Bioorg Med Chem 72: 116967-116967

  • DOI: https://doi.org/10.1016/j.bmc.2022.116967
  • Primary Citation of Related Structures:  
    7W3D

  • PubMed Abstract: 

    Bromodomain and extra-terminal domain (BET) proteins have been considered as potent candidates for anti-cancer drug development. As epigenetic readers, they modulate gene expression by recognizing acetylated lysine residues on histones. Therefore, the pharmacological inhibition of BET proteins has been extensively studied. Herein, we report the novel chemical scaffold of N-(pyridin-2-yl)-1H-benzo[d][1,2,3]triazol-5-amine as BET inhibitors using high-throughput screening assay. Through the analysis of structure-activity relationships, we developed a potent novel compound, which exhibited a better IC 50 value about 2-fold compared to iBet762 against the BRD4 bromodomain (BD). The addition of a sulfonyl group to the pyridine ring enhanced the inhibitory activity. Structural studies showed a clear electron density map for the inhibitor and revealed the structural basis for the critical role of the sulfonyl group in the interaction with BRD4.


  • Organizational Affiliation

    Department of Medicinal Chemistry and Pharmacology, University of Science & Technology, Daejeon 34113, Republic of Korea; Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
89T (Subject of Investigation/LOI)
Query on 89T

Download Ideal Coordinates CCD File 
B [auth A]N2-(1,2,3-benzotriazol-5-yl)-N3-(dimethylsulfamoyl)-N6-[(2S)-1-methoxypropan-2-yl]pyridine-2,3,6-triamine
C17 H24 N8 O3 S
YQVOHKBYIBRJBY-NSHDSACASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.276 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.991α = 90
b = 45.339β = 90
c = 78.197γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2019R1A2C100254513

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description