6ZEL

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F5

• PDB DOI: https://doi.org/10.2210/pdb6ZEL/pdb

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


• Deposited: 2020-06-16 Released: 2020-07-29 
• Deposition Author(s): Krojer, T., Martinez-Cartro, M., Picaud, S., Filippakopoulos, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Barril, X., von Delft, F.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 0.147 
• R-Value Work: 0.125 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F5

Martinez-Cartro, M., Barril, X.

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

Macromolecule Content

• Total Structure Weight: 15.52 kDa 
• Atom Count: 1,303 
• Modelled 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 [auth AAA]	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
QGQ (Subject of Investigation/LOI)	E [auth AAA]	3,5-dimethyl-4-[(6-methylpyrimidin-4-yl)sulfanylmethyl]-1,2-oxazole C11 H13 N3 O S ROKHJFVYDKKVDA-UHFFFAOYSA-N
EDO	B [auth AAA], C [auth AAA], D [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QGQ	BindingDB:  6ZEL	IC50: 3.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 0.147 
• R-Value Work: 0.125 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.235	α = 90
b = 44.141	β = 90
c = 78.441	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Krojer, T., Martinez-Cartro, M., Picaud, S., Filippakopoulos, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Barril, X., von Delft, F.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2021-05-19
  Changes: Experimental preparation
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description