5HM0

Crystal structure of the first bromodomain of human BRD4 bound to benzoisoxazoloazepine 3

• PDB DOI:  https://doi.org/10.2210/pdb5HM0/pdb

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


• Deposited: 2016-01-15 Released: 2016-02-10 
• Deposition Author(s): Jayaram, H., Poy, F., Setser, J.W., Bellon, S.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Identification of a Benzoisoxazoloazepine Inhibitor (CPI-0610) of the Bromodomain and Extra-Terminal (BET) Family as a Candidate for Human Clinical Trials.

Albrecht, B.K., Gehling, V.S., Hewitt, M.C., Vaswani, R.G., Cote, A., Leblanc, Y., Nasveschuk, C.G., Bellon, S., Bergeron, L., Campbell, R., Cantone, N., Cooper, M.R., Cummings, R.T., Jayaram, H., Joshi, S., Mertz, J.A., Neiss, A., Normant, E., O'Meara, M., Pardo, E., Poy, F., Sandy, P., Supko, J., Sims, R.J., Harmange, J.C., Taylor, A.M., Audia, J.E.

(2016) J Med Chem 59: 1330-1339

• PubMed: 26815195 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01882
• Primary Citation of Related Structures:  
  5HLS, 5HM0


• PubMed Abstract: 
  

In recent years, inhibition of the interaction between the bromodomain and extra-terminal domain (BET) family of chromatin adaptors and acetyl-lysine residues on chromatin has emerged as a promising approach to regulate the expression of important disease-relevant genes, including MYC, BCL-2, and NF-κB. Here we describe the identification and characterization of a potent and selective benzoisoxazoloazepine BET bromodomain inhibitor that attenuates BET-dependent gene expression in vivo, demonstrates antitumor efficacy in an MV-4-11 mouse xenograft model, and is currently undergoing human clinical trials for hematological malignancies (CPI-0610).

---

Organizational Affiliation: 

Constellation Pharmaceuticals , 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States.

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: 15.44 kDa 
• Atom Count: 1,183 
• Modelled Residue Count: 125 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	128	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
62V	B [auth A]	6-(4-chlorophenyl)-1-methyl-4H-[1,2]oxazolo[5,4-d][2]benzazepine C18 H13 Cl N2 O LVBAGZIAQBWUJP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
62V	Binding MOAD:  5HM0	IC50: 440 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.682	α = 90
b = 47.722	β = 90
c = 78.184	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Jayaram, H., Poy, F., Setser, J.W., Bellon, S.F.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references