Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.63 kDa 
• Atom Count: 1,119 
• Modelled Residue Count: 126 
• Deposited Residue Count: 127 
• Unique protein chains: 1

 5DX4

Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand

• PDB DOI:  https://doi.org/10.2210/pdb5DX4/pdb

• Classification: SIGNALING PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-23 Released: 2016-01-13 
• Deposition Author(s): Zhang, Y., Song, M., Liu, Z., Xue, X., Xu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.239 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Literature

Discovery of Benzo[cd]indol-2(1H)-ones as Potent and Specific BET Bromodomain Inhibitors: Structure-Based Virtual Screening, Optimization, and Biological Evaluation

Xue, X., Zhang, Y., Liu, Z., Song, M., Xing, Y., Xiang, Q., Wang, Z., Tu, Z., Zhou, Y., Ding, K., Xu, Y.

(2016) J Med Chem 59: 1565-1579

• PubMed: 26731490 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01511
• Primary Citation of Related Structures:  
  5COI, 5CP5, 5CPE, 5CQT, 5CRM, 5CRZ, 5CS8, 5CTL, 5CY9, 5D0C, 5DX4


• PubMed Abstract: 
  

The discovery of inhibitors of bromodomain and extra terminal domain (BET) has achieved great progress, and at least seven inhibitors have progressed into clinical trials for the treatment of cancer or inflammatory diseases. Here, we describe the identification, optimization, and evaluation of benzo[cd]indol-2(1H)-one containing compounds as a new class of BET bromodomain inhibitors, starting from structure-based virtual screening (SBVS). Through structure-based optimization, potent compounds were obtained with significantly improved activity. The two most potent compounds bind to the BRD4 bromodomain, with Kd values of 124 and 137 nM. Selected compounds exhibited high selectivity over other non-BET subfamily members. Notably, compound 85 demonstrated a reasonable antiproliferation effect on MV4;11 leukemia cells and exhibited a good pharmacokinetic profile with high oral bioavailability (75.8%) and moderate half-life (T1/2 = 3.95 h). The resulting lead molecule 85 represents a new, potent, and selective class of BET bromodomain inhibitors for the development of therapeutics to treat cancer and inflammatory diseases.

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Organizational Affiliation: 

Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, China.

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E0C	B [auth A]	5-bromo-N-(1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indol-6-yl)-2-methoxybenzenesulfonamide C20 H17 Br N2 O4 S JTOXINSTQFVILZ-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E0C	Binding MOAD:  5DX4	Kd: 137 (nM) from 1 assay(s)
	BindingDB:  5DX4	Kd: 137 (nM) from 1 assay(s)
		IC50: 410 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.239 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.83	α = 90
b = 48.44	β = 90
c = 77.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Zhang, Y., Song, M., Liu, Z., Xue, X., Xu, Y.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Data collection, Database references
• Version 1.2: 2016-03-09
  Changes: Database references