4PCE | pdb_00004pce

Crystal Structure of the first bromodomain of human BRD4 in complex with compound B13

• PDB DOI: https://doi.org/10.2210/pdb4PCE/pdb

• Classification: Transcription/transcription Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-15 Released: 2014-05-07 
• Deposition Author(s): Dong, J., Caflisch, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.164 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Literature

Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking.

Zhao, H., Gartenmann, L., Dong, J., Spiliotopoulos, D., Caflisch, A.

(2014) Bioorg Med Chem Lett 24: 2493-2496

• PubMed: 24767840 
• DOI: https://doi.org/10.1016/j.bmcl.2014.04.017
• Primary Citation Related Structures: 
  4PCE, 4PCI


• PubMed Abstract: 
  

  Bromodomains (BRDs) recognize acetyl-lysine modified histone tails mediating epigenetic processes. BRD4, a protein containing two bromodomains, has emerged as an attractive therapeutic target for several types of cancer as well as inflammatory diseases. Using a fragment-based in silico screening approach, we identified two small molecules that bind to the first bromodomain of BRD4 with low-micromolar affinity and favorable ligand efficiency (0.37 kcal/mol per non-hydrogen atom), selectively over other families of bromodomains. Notably, the hit rate of the fragment-based in silico approach is about 10% as only 24 putative inhibitors, from an initial library of about 9 million molecules, were tested in vitro.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. Electronic address: [e-mail].
Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. Electronic address: [e-mail].

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: 15.41 kDa 
• Atom Count: 1,289 
• 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
2N0	C [auth A]	1-benzyl-2-ethyl-1,5,6,7-tetrahydro-4H-indol-4-one C17 H19 N O WAZKIRPFJTZRDA-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2N0	BindingDB:  4PCE	IC50: 7000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.164 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.59	α = 90
b = 44.279	β = 90
c = 78.371	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Dong, J., Caflisch, A.

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Database references
• Version 1.2: 2014-06-04
  Changes: Data collection, Database references
• Version 1.3: 2015-02-04
  Changes: Derived calculations
• Version 1.4: 2017-11-22
  Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.5: 2023-12-27
  Changes: Advisory, Data collection, Database references, Refinement description