5Z9K

BRD4 Bromodomain 1 with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5Z9K/pdb

• Classification: TRANSCRIPTION/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-03 Released: 2019-02-06 
• Deposition Author(s): Xiao, S., Chen, S., Chen, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.258 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

BRD4 Bromodomain 1 with an inhibitor

Xiao, S., Chen, S., Chen, H.

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)

Macromolecule Content

• Total Structure Weight: 15.46 kDa 
• Atom Count: 1,082 
• Modelled Residue Count: 123 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
99X (Subject of Investigation/LOI)	B [auth A]	1-ethyl-6-[(2R)-2-(hydroxymethyl)pyrrolidin-1-yl]sulfonyl-benzo[cd]indol-2-one C18 H20 N2 O4 S LBIMQKNDHURLPV-GFCCVEGCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.258 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.918	α = 90
b = 48.245	β = 90
c = 80.238	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Xiao, S., Chen, S., Chen, H.

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references