4IOO | pdb_00004ioo

Crystal Structure of the first bromodomain of BRD4 in complex with N-methyltrimethylacetamide

• PDB DOI: https://doi.org/10.2210/pdb4IOO/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-01-08 Released: 2013-10-02 
• Deposition Author(s): Lolli, G., Battistutta, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.149 (Depositor) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Different orientations of low-molecular-weight fragments in the binding pocket of a BRD4 bromodomain.

Lolli, G., Battistutta, R.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2161-2164

• PubMed: 24100334 
• DOI: https://doi.org/10.1107/S090744491301994X
• Primary Citation Related Structures: 
  4IOO, 4IOQ, 4IOR


• PubMed Abstract: 
  

  Bromodomains are involved in the regulation of chromatin architecture and transcription through the recognition of acetylated lysines in histones and other proteins. Many of them are considered to be relevant pharmacological targets for different pathologies. Three crystallographic structures of the N-terminal bromodomain of BRD4 in complex with low-molecular-weight fragments are presented. They show that similar molecules mimicking acetylated lysine bind the bromodomain with different orientations and exploit different interactions. It is also advised to avoid DMSO when searching for low-affinity fragments that interact with bromodomains since DMSO binds in the acetylated lysine-recognition pocket of BRD4.

---

Organizational Affiliation: 
• Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.

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: 15.6 kDa 
• Atom Count: 1,357 
• Modeled Residue Count: 126 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BAE	G [auth A]	N-methyltrimethylacetamide C6 H13 N O QMKKJBRRKIKWFK-UHFFFAOYSA-N
DMS	H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.149 (Depositor) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.199	α = 90
b = 44.128	β = 90
c = 77.963	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Lolli, G., Battistutta, R.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-11-13
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations