Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 15.37 kDa 
• Atom Count: 1226 
• Residue Count: 125 
• Unique protein chains: 1

4HXL

Brd4 Bromodomain 1 complex with 3-CYCLOHEXYL-N-{3-(2-OXO-2,3-DIHYDRO-1,3-THIAZOL-4-YL)-5-[(THIOPHEN-2-YLSULFONYL)AMINO]PHENYL}PROPANAMIDE inhibitor

• DOI: 10.2210/pdb4HXL/pdb

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


• Deposited: 2012-11-12 Released: 2013-04-03 
• Deposition Author(s): Chen, T.T., Cao, D.Y., Chen, W.Y., Xiong, B., Shen, J.K., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.191 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

Fragment-Based Drug Discovery of 2-Thiazolidinones as Inhibitors of the Histone Reader BRD4 Bromodomain.

Zhao, L., Cao, D., Chen, T., Wang, Y., Miao, Z., Xu, Y., Chen, W., Wang, X., Li, Y., Du, Z., Xiong, B., Li, J., Xu, C., Zhang, N., He, J., Shen, J.

(2013) J Med Chem 56: 3833-3851

• PubMed: 23530754 
• DOI: 10.1021/jm301793a
• Primary Citation of Related Structures:  
  4HXL, 4HXM, 4HXN, 4HXO, 4HXP, 4HXR, 4HXS, 4HXK


• PubMed Abstract: 
  

Recognizing acetyllysine of histone is a vital process of epigenetic regulation that is mediated by a protein module called bromodomain. To contribute novel scaffolds for developing into bromodomain inhibitors, we utilize a fragment-based drug discovery approach. By successively applying docking and X-ray crystallography, we were able to identify 9 fragment hits from diffracting more than 60 crystals. In the present work, we described four of them and carried out the integrated lead optimization for fragment 8, which bears a 2-thiazolidinone core. After several rounds of structure guided modifications, we assessed the druggability of 2-thiazolidinone by modulating in vitro pharmacokinetic studies and cellular activity assay. The results showed that two potent compounds of 2-thiazolidinones have good metabolic stability. Also, the cellular assay confirmed the activities of 2-thiazolidinones. Together, we hope the identified 2-thiazolidinone chemotype and other fragment hits described herein can stimulate researchers to develop more diversified bromodomain inhibitors.

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Organizational Affiliation: 

Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	125	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885 GTEx  ENSG00000141867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1A9	A	3-cyclohexyl-N-{3-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)-5-[(thiophen-2-ylsulfonyl)amino]phenyl}propanamide C22 H25 N3 O4 S3 WAUBHBSWJBQJEK-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1A9	IC50:  2200   nM  BindingDB
1A9	IC50:  2200   nM  Binding MOAD
1A9	IC50 :  2200   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.191 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.1	α = 90
b = 47.11	β = 90
c = 79.05	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-12 
• Released Date: 2013-04-03 
Deposition Author(s): Chen, T.T., Cao, D.Y., Chen, W.Y., Xiong, B., Shen, J.K., Xu, Y.C.

Revision History 

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-04-10
  Changes: Structure summary
• Version 1.2: 2013-06-19
  Changes: Database references