7MLQ

X-ray crystal structure of human BRD4(D1) in complex with 2-(4-{5-[6-(2,5-dibromophenoxy)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1-yl}piperidin-1-yl)-N,N-dimethylethan-1-amine (compound 26)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

4-Methyl-1,2,3-Triazoles as N -Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity.

Cui, H.Carlson, A.S.Schleiff, M.A.Divakaran, A.Johnson, J.A.Buchholz, C.R.Zahid, H.Vail, N.R.Shi, K.Aihara, H.Harki, D.A.Miller, G.P.Topczewski, J.J.Pomerantz, W.C.K.

(2021) J Med Chem 64: 10497-10511

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00933
  • Primary Citation of Related Structures:  
    7MLQ, 7MLR, 7MLS

  • PubMed Abstract: 

    The bromodomain and extra terminal (BET) protein family recognizes acetylated lysines within histones and transcription factors using two N-terminal bromodomains, D1 and D2. The protein-protein interactions between BET bromodomains, acetylated histones, and transcription factors are therapeutic targets for BET-related diseases, including inflammatory disease and cancer. Prior work demonstrated that methylated-1,2,3-triazoles are suitable N -acetyl lysine mimetics for BET inhibition. Here we describe a structure-activity relationship study of triazole-based inhibitors that improve affinity, D1 selectivity, and microsomal stability. These outcomes were accomplished by targeting a nonconserved residue, Asp144 and a conserved residue, Met149, on BRD4 D1. The lead inhibitors DW34 and 26 have a BRD4 D1 K d of 12 and 6.4 nM, respectively. Cellular activity was demonstrated through suppression of c-Myc expression in MM.1S cells and downregulation of IL-8 in TNF-α-stimulated A549 cells. These data indicate that DW34 and 26 are new leads to investigate the anticancer and anti-inflammatory activity of BET proteins.


  • Organizational Affiliation

    Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.


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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZHV (Subject of Investigation/LOI)
Query on ZHV

Download Ideal Coordinates CCD File 
C [auth A]2-(4-{5-[6-(2,5-dibromophenoxy)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1-yl}piperidin-1-yl)-N,N-dimethylethan-1-amine
C23 H28 Br2 N6 O
RSOZHLZHAXOEGJ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
ZHV BindingDB:  7MLQ Kd: min: 6.4, max: 28 (nM) from 2 assay(s)
IC50: min: 856, max: 1020 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.123α = 90
b = 44.019β = 90
c = 79.56γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047
National Institutes of Health/National Library of Medicine (NIH/NLM)United States5T32GM008347-23

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description