4LRG

Structure of BRD4 bromodomain 1 with a dimethyl thiophene isoxazole azepine carboxamide

• PDB DOI: https://doi.org/10.2210/pdb4LRG/pdb

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


• Deposited: 2013-07-19 Released: 2013-08-07 
• Deposition Author(s): Ravichandran, S., Jayaram, H., Poy, F., Gehling, V., Hewitt, M., Vaswani, R., Leblanc, Y., Cote, A., Nasveschuk, C., Taylor, A., Harmange, J.-C., Audia, J., Pardo, E., Joshi, S., Sandy, P., Mertz, J., Sims, R., Bergeron, L., Bryant, B., Yellapuntala, S., Nandana, B.S., Birudukota, S., Albrecht, B., Bellon, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.288 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 

Literature

Discovery, Design, and Optimization of Isoxazole Azepine BET Inhibitors.

Gehling, V.S., Hewitt, M.C., Vaswani, R.G., Leblanc, Y., Cote, A., Nasveschuk, C.G., Taylor, A.M., Harmange, J.C., Audia, J.E., Pardo, E., Joshi, S., Sandy, P., Mertz, J.A., Sims, R.J., Bergeron, L., Bryant, B.M., Bellon, S., Poy, F., Jayaram, H., Sankaranarayanan, R., Yellapantula, S., Bangalore Srinivasamurthy, N., Birudukota, S., Albrecht, B.K.

(2013) ACS Med Chem Lett 4: 835-840

• PubMed: 24900758 
• DOI: https://doi.org/10.1021/ml4001485
• Primary Citation of Related Structures:  
  4LR6, 4LRG


• PubMed Abstract: 
  

  The identification of a novel series of small molecule BET inhibitors is described. Using crystallographic binding modes of an amino-isoxazole fragment and known BET inhibitors, a structure-based drug design effort lead to a novel isoxazole azepine scaffold. This scaffold showed good potency in biochemical and cellular assays and oral activity in an in vivo model of BET inhibition.

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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: 15.53 kDa 
• Atom Count: 1,204 
• Modelled Residue Count: 128 
• 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, BRD4_HUMAN, 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
1XB	B [auth A]	2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-[1,2]oxazolo[5,4-c]thieno[2,3-e]azepin-6-yl]acetamide C20 H18 Cl N3 O2 S DRSQZZRFHBWKKZ-AWEZNQCLSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1XB	BindingDB:  4LRG	IC50: min: 26, max: 140 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.288 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.044	α = 90
b = 45.604	β = 90
c = 78.581	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Ravichandran, S., Jayaram, H., Poy, F., Gehling, V., Hewitt, M., Vaswani, R., Leblanc, Y., Cote, A., Nasveschuk, C., Taylor, A., Harmange, J.-C., Audia, J., Pardo, E., Joshi, S., Sandy, P., Mertz, J., Sims, R., Bergeron, L., Bryant, B., Yellapuntala, S., Nandana, B.S., Birudukota, S., Albrecht, B., Bellon, S.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Other, Structure summary
• Version 1.2: 2014-10-08
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Derived calculations