7B1T

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

• PDB DOI: https://doi.org/10.2210/pdb7B1T/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-25 Released: 2022-06-08 
• Deposition Author(s): Huegle, M.
• Funding Organization(s): German Research Foundation (DFG)

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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 

Starting Model: experimental

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

• PubMed: 36736153 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.54 kDa 
• Atom Count: 1,288 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SOK (Subject of Investigation/LOI)	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	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 = 37.31	α = 90
b = 44.43	β = 90
c = 76.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Huegle, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	GU 1225 3 1

Revision History  

• 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