5EI4

First domain of human bromodomain BRD4 in complex with inhibitor 8-(5-Amino-1H-[1,2,4]triazol-3-ylsulfanylmethyl)-3-(4-chlorobenzyl)-7-ethyl-3,7-dihydropurine-2,6-dione

• PDB DOI:  https://doi.org/10.2210/pdb5EI4/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-29 Released: 2016-01-20 
• Deposition Author(s): Raux, B., Rebuffet, E., Betzi, S., Morelli, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.192 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Literature

Exploring Selective Inhibition of the First Bromodomain of the Human Bromodomain and Extra-terminal Domain (BET) Proteins.

Raux, B., Voitovich, Y., Derviaux, C., Lugari, A., Rebuffet, E., Milhas, S., Priet, S., Roux, T., Trinquet, E., Guillemot, J.C., Knapp, S., Brunel, J.M., Fedorov, A.Y., Collette, Y., Roche, P., Betzi, S., Combes, S., Morelli, X.

(2016) J Med Chem 59: 1634-1641

• PubMed: 26735842 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01708
• Primary Citation of Related Structures:  
  5EGU, 5EI4, 5EIS


• PubMed Abstract: 
  

A midthroughput screening follow-up program targeting the first bromodomain of the human BRD4 protein, BRD4(BD1), identified an acetylated-mimic xanthine derivative inhibitor. This compound binds with an affinity in the low micromolar range yet exerts suitable unexpected selectivity in vitro against the other members of the bromodomain and extra-terminal domain (BET) family. A structure-based program pinpointed a role of the ZA loop, paving the way for the development of potent and selective BET-BRDi probes.

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Organizational Affiliation: 

Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France.

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: 15.59 kDa 
• Atom Count: 1,312 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5NV	C [auth A]	8-[(3-azanyl-1~{H}-1,2,4-triazol-5-yl)sulfanylmethyl]-3-[(4-chlorophenyl)methyl]-7-ethyl-purine-2,6-dione C17 H17 Cl N8 O2 S HZXIXZPCCYPTDC-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5NV	Binding MOAD:  5EI4	IC50: 2.64e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.192 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.353	α = 90
b = 44.069	β = 90
c = 78.272	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
REFMAC	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Raux, B., Rebuffet, E., Betzi, S., Morelli, X.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references