5EIS | pdb_00005eis

FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-(4-Chlorobenzyl)-7-ethyl-3,7-dihydropurine-2,6-dione

• PDB DOI: https://doi.org/10.2210/pdb5EIS/pdb

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


• Deposited: 2015-10-30 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: 1.60 Å
• R-Value Free: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

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 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.
Department of Organic Chemistry, Lobachevsky State University of Nizhni Novgorod , Gagarina av. 23, Nizhni Novgorod 603950, Russia.
Screening Platform AD2P, CNRS, AFMB UMR 7257, Aix-Marseille Université , 13288 Marseille, France.
Cisbio Bioassays, R&D , Parc Marcel Boiteux, BP 84175, 30200 Codolet, France.
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K.
Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
Goethe-University , Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Science, Campus Riedberg, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany.

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: 1,204 
• Modeled 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
5OU	B [auth A]	3-[(4-chlorophenyl)methyl]-7-ethyl-purine-2,6-dione C14 H13 Cl N4 O2 ZUHFEYWVQFKDLX-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5OU	BindingDB:  5EIS	Kd: 1800 (nM) from 1 assay(s)
		IC50: min: 1900, max: 2600 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.935	α = 90
b = 46.545	β = 90
c = 77.658	γ = 90

Software Package:

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

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
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description