6DUV

Crystal structure of the second bromodomain of human BRD4 in complex with MS417 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6DUV/pdb

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


• Deposited: 2018-06-22 Released: 2019-06-26 
• Deposition Author(s): Babault, N., Zhou, M.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.188 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Role of Bound Water Molecules in Differential Recognition of Di-Acetylated Histone Peptides by the BRD4 Bromodomains

Babault, N., Zhang, Q., Zhang, G., Zhou, M.M., Zeng, L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.75 kDa 
• Atom Count: 2,122 
• Modelled Residue Count: 219 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B	112	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
0S6	C [auth A], D [auth A], G [auth B]	methyl [(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate C20 H19 Cl N4 O2 S GGRCIHACOIMRKY-HNNXBMFYSA-N
EDO	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0S6	BindingDB:  6DUV	Ki: 17 (nM) from 1 assay(s)
		IC50: 18.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.188 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.58	α = 90
b = 74.58	β = 90
c = 111.47	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Babault, N., Zhou, M.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01HG004508

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Refinement description