Crystal structure of the first bromodomain of human BRD4 in complex with MA4-022-1

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.127 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Potent Dual BET Bromodomain-Kinase Inhibitors as Value-Added Multitargeted Chemical Probes and Cancer Therapeutics.

Ember, S.W.Lambert, Q.T.Berndt, N.Gunawan, S.Ayaz, M.Tauro, M.Zhu, J.Y.Cranfill, P.J.Greninger, P.Lynch, C.C.Benes, C.H.Lawrence, H.R.Reuther, G.W.Lawrence, N.J.Schonbrunn, E.

(2017) Mol Cancer Ther 16: 1054-1067

  • DOI: https://doi.org/10.1158/1535-7163.MCT-16-0568-T
  • Primary Citation of Related Structures:  
    5F5Z, 5F60, 5F61, 5F62, 5F63

  • PubMed Abstract: 

    Synergistic action of kinase and BET bromodomain inhibitors in cell killing has been reported for a variety of cancers. Using the chemical scaffold of the JAK2 inhibitor TG101348, we developed and characterized single agents which potently and simultaneously inhibit BRD4 and a specific set of oncogenic tyrosine kinases including JAK2, FLT3, RET, and ROS1. Lead compounds showed on-target inhibition in several blood cancer cell lines and were highly efficacious at inhibiting the growth of hematopoietic progenitor cells from patients with myeloproliferative neoplasm. Screening across 931 cancer cell lines revealed differential growth inhibitory potential with highest activity against bone and blood cancers and greatly enhanced activity over the single BET inhibitor JQ1. Gene drug sensitivity analyses and drug combination studies indicate synergism of BRD4 and kinase inhibition as a plausible reason for the superior potency in cell killing. Combined, our findings indicate promising potential of these agents as novel chemical probes and cancer therapeutics. Mol Cancer Ther; 16(6); 1054-67. ©2017 AACR .

  • Organizational Affiliation

    Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4
A, B
127Homo 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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5W0

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B]
C26 H34 F N7 O2 S
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
F [auth B]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
5W0 Binding MOAD:  5F61 Kd: 35 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.85α = 90
b = 78.51β = 91.74
c = 47.09γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-06-14
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description