8Q34

Crystal structure of the first bromodomain of human BRD4 in complex with the ligand ZZ001229a

• PDB DOI: https://doi.org/10.2210/pdb8Q34/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-08-03 Released: 2024-02-07 
• Deposition Author(s): MacLean, E.M., Gao, Q., Williams, E., Balcomb, B.H., von Delft, F., Bajusz, D., Keeley, A., Abranyi-Balogh, P., Koekemoer, L., Keseru, G.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.216 
• R-Value Work: 0.184 

Literature

Mapping protein binding sites by photoreactive fragment pharmacophores

Keseru, G.M.

(2023) Res Sq 

• DOI: https://doi.org/10.21203/rs.3.rs-3379575/v1

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.05 kDa 
• Atom Count: 5,166 
• Modelled Residue Count: 506 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B, C, D	130	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
IX4 (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	~{N}-(1~{H}-imidazo[4,5-b]pyridin-2-ylmethyl)-3-(3-methyl-1,2-diazirin-3-yl)propanamide C12 H14 N6 O NHWWLVCZMAELEF-UHFFFAOYSA-N
EDO	E [auth A], G [auth B], I [auth C], K [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.216 
• R-Value Work: 0.184 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.239	α = 90.033
b = 44.093	β = 90
c = 78.479	γ = 90.026

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): MacLean, E.M., Gao, Q., Williams, E., Balcomb, B.H., von Delft, F., Bajusz, D., Keeley, A., Abranyi-Balogh, P., Koekemoer, L., Keseru, G.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release