Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 15.53 kDa 
• Atom Count: 1,317 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

 5D3L

First bromodomain of BRD4 bound to inhibitor XD35

• PDB DOI:  https://doi.org/10.2210/pdb5D3L/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-08-06 Released: 2016-01-20 
• Deposition Author(s): Wohlwend, D., Huegle, M.
• Funding Organization(s): German Research Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1).

Hugle, M., Lucas, X., Weitzel, G., Ostrovskyi, D., Breit, B., Gerhardt, S., Einsle, O., Gunther, S., Wohlwend, D.

(2016) J Med Chem 59: 1518-1530

• PubMed: 26731611 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01267
• Primary Citation of Related Structures:  
  5D24, 5D25, 5D26, 5D3H, 5D3J, 5D3L, 5D3N, 5D3P, 5D3R, 5D3S, 5D3T


• PubMed Abstract: 
  

Several human diseases, including cancer, show altered signaling pathways resulting from changes in the activity levels of epigenetic modulators. In the past few years, small-molecule inhibitors against specific modulators, including the bromodomain and extra-terminal (BET) bromodomain family of acetylation readers, have shown early promise in the treatment of the genetically defined midline carcinoma and hematopoietic malignancies. We have recently developed a novel potent inhibitor of BET proteins, 1 (XD14[ Angew. Chem., Int. Ed. 2013, 52, 14055]), which exerts a strong inhibitory potential on the proliferation of specific leukemia cell lines. In the study presented here, we designed analogues of 1 to study the potential of substitutions on the 4-acyl pyrrole backbone to occupy additional sites within the substrate recognition site of BRD4(1). The compounds were profiled using ITC, DSF, and X-ray crystallography. We could introduce several substitutions that address previously untargeted areas of the substrate recognition site. This work may substantially contribute to the development of therapeutics with increased target specificity against BRD4-related malignancies.

---

Organizational Affiliation: 

Institut für Biochemie, Albert-Ludwigs-Universität Freiburg , Albertstrasse 21, D-79104 Freiburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 1  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
57F	B [auth A]	4-acetyl-N-[5-(diethylsulfamoyl)-2-hydroxy-4-methylphenyl]-3-ethyl-5-methyl-1H-pyrrole-2-carboxamide C21 H29 N3 O5 S CGYOKHBJOYVFIV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
57F	BindingDB:  5D3L	Kd: 880 (nM) from 1 assay(s)
	Binding MOAD:  5D3L	Kd: 880 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.58	α = 90
b = 47.94	β = 90
c = 58.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
iMOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Wohlwend, D., Huegle, M.

---

Funding Organization	Location	Grant Number
German Research Foundation	Germany	WO2012/1-1

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence