5OWW

Crystal structure of human BRD4(1) bromodomain in complex with UT22B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple).

Batiste, L.Unzue, A.Dolbois, A.Hassler, F.Wang, X.Deerain, N.Zhu, J.Spiliotopoulos, D.Nevado, C.Caflisch, A.

(2018) Acs Cent.Sci. 4: 180-188

  • DOI: 10.1021/acscentsci.7b00401
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Expanding the chemical space and simultaneously ensuring synthetic accessibility is of upmost importance, not only for the discovery of effective binders for novel protein classes but, more importantly, for the development of compounds against hard-t ...

    Expanding the chemical space and simultaneously ensuring synthetic accessibility is of upmost importance, not only for the discovery of effective binders for novel protein classes but, more importantly, for the development of compounds against hard-to-drug proteins. Here, we present AutoCouple, a de novo approach to computational ligand design focused on the diversity-oriented generation of chemical entities via virtual couplings. In a benchmark application, chemically diverse compounds with low-nanomolar potency for the CBP bromodomain and high selectivity against the BRD4(1) bromodomain were achieved by the synthesis of about 50 derivatives of the original fragment. The binding mode was confirmed by X-ray crystallography, target engagement in cells was demonstrated, and antiproliferative activity was showcased in three cancer cell lines. These results reveal AutoCouple as a useful in silico coupling method to expand the chemical space in hit optimization campaigns resulting in potent, selective, and cell permeable bromodomain ligands.


    Organizational Affiliation

    Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.,Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A, B, C, D
127Homo sapiensMutation(s): 0 
Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens)
Go to Gene View: BRD4
Go to UniProtKB:  O60885
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B0Q
Query on B0Q

Download SDF File 
Download CCD File 
A, B, C, D
~{N}-(3-methylbenzotriazol-5-yl)-1-(phenylmethyl)imidazole-2-carboxamide
C18 H16 N6 O
KXKQPHQDIFTLEB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.877α = 90.00
b = 41.924β = 92.03
c = 109.416γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-04 
  • Released Date: 2018-10-10 
  • Deposition Author(s): Zhu, J., Caflisch, A.

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Database references, Structure summary