7B1T

Crystal structure of BRD4(1) in complex with the inhibitor MPM6

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

A novel pan-selective bromodomain inhibitor for epigenetic drug design.

Warstat, R., Pervaiz, M., Regenass, P., Amann, M., Schmidtkunz, K., Einsle, O., Jung, M., Breit, B., Hugle, M., Gunther, S.

(2023) Eur J Med Chem 249: 115139-115139

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115139
  • Primary Citation of Related Structures:  
    7B1T

  • PubMed Abstract: 

    For a long time, the development of bromodomain (BD) inhibitors (BDi) was almost exclusively related to the BET family. More recently, BDi for BDs outside the BET family have also been developed. Here we present a novel pan-BDi with micromolar affinities to various BDs, and nanomolar affinities to representatives of BD families I, II (Bromodomain and Extra-Terminal Domain (BET) family), III, and IV. The inhibitor shows a broad activity profile with nanomolar growth inhibition (GI50) values on various cancer cell lines. Subsequently, we were able to control the selectivity of the inhibitor by simple modifications and turned it into a highly selective BRD9 inhibitor.

    • Organizational Affiliation: 

    Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, D-79104, Freiburg, Germany.


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: BRD4, HUNK1
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SOK (Subject of Investigation/LOI)
Query on SOK
Download Ideal Coordinates CCD File 
B [auth A]3-(5-azanyl-2-chloranyl-phenyl)-1-methyl-4,7-dihydro-2~{H}-cyclohepta[c]pyrrol-8-one
C16 H15 Cl N2 O
NHRQHOMIYFOZIR-UHFFFAOYSA-N
DMS
Query on DMS
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.31α = 90
b = 44.43β = 90
c = 76.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-06-08 
    • Deposition Author(s): Huegle, M.
Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyGU 1225 3 1

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description