7MLR | pdb_00007mlr

X-ray crystal structure of human BRD4(D1) in complex with 2-(4-{5-[6-(3,5-dimethylphenoxy)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1- yl}piperidin-1-yl)-N,N-dimethylethan-1-amine (DW34)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.164 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.136 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.137 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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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
ZHS (Subject of Investigation/LOI)
Query on ZHS

Download Ideal Coordinates CCD File 
G [auth A]2-(4-{5-[6-(3,5-dimethylphenoxy)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1-yl}piperidin-1-yl)-N,N-dimethylethan-1-amine
C25 H34 N6 O
PIKWYDHWUKSWAQ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ZHS BindingDB:  7MLR Kd: min: 12, max: 67 (nM) from 2 assay(s)
IC50: min: 137, max: 1020 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.164 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.136 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.137 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.098α = 90
b = 44.336β = 90
c = 78.936γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ZHSClick on this verticalbar to view details

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