Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 15.01 kDa 
• Atom Count: 1050 
• Modelled Residue Count: 119 
• Deposited Residue Count: 126 
• Unique protein chains: 1

6V1E

Crystal structure of the bromodomain of human BRD7 bound to BI7273

• PDB DOI: 10.2210/pdb6V1E/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-20 Released: 2020-03-11 
• Deposition Author(s): Chan, A., Karim, M.R., Schonbrunn, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains.

Karim, R.M., Chan, A., Zhu, J.Y., Schonbrunn, E.

(2020) J Med Chem 63: 3227-3237

• PubMed: 32091206 
• DOI: 10.1021/acs.jmedchem.9b01980
• Primary Citation of Related Structures:  
  6PPA, 6UZF, 6V0Q, 6V0S, 6V0U, 6V0X, 6V14, 6V16, 6V17, 6V1B, 6V1E, 6V1F, 6V1H, 6V1K, 6V1L, 6V1U


• PubMed Abstract: 
  

Inhibition of the bromodomain containing protein 9 (BRD9) by small molecules is an attractive strategy to target mutated SWI/SNF chromatin-remodeling complexes in cancer. However, reported BRD9 inhibitors also inhibit the closely related bromodomain-containing protein 7 (BRD7), which has different biological functions. The structural basis for differential potency and selectivity of BRD9 inhibitors is largely unknown because of the lack of structural information on BRD7. Here, we biochemically and structurally characterized diverse inhibitors with varying degrees of potency and selectivity for BRD9 over BRD7. Novel cocrystal structures of BRD7 liganded with new and previously reported inhibitors of five different chemical scaffolds were determined alongside BRD9 and BRD4. We also report the discovery of first-in-class dual bromodomain-kinase inhibitors outside the bromodomain and extraterminal family targeting BRD7 and BRD9. Combined, the data provide a new framework for the development of BRD7/9 inhibitors with improved selectivity or additional polypharmacologic properties.

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Organizational Affiliation: 

Department of Molecular Medicine, USF Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 7	A	126	Homo sapiens	Mutation(s): 0  Gene Names: BRD7, BP75, CELTIX1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPI1 (Homo sapiens) Explore Q9NPI1  Go to UniProtKB:  Q9NPI1
PHAROS:  Q9NPI1 GTEx:  ENSG00000166164

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5SW (Subject of Investigation/LOI)	B [auth A]	4-[4-[(dimethylamino)methyl]-3,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one C20 H23 N3 O3 RBUYFHLQNPJMQM-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5SW	BindingDB:  6V1E	Kd: min: 0.3, max: 121 (nM) from 3 assay(s)
		IC50: 117 (nM) from 1 assay(s)
	Binding MOAD:  6V1E	Kd: 121 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.73	α = 90
b = 108.49	β = 90
c = 36.12	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-11-20 
• Released Date: 2020-03-11 
Deposition Author(s): Chan, A., Karim, M.R., Schonbrunn, E.

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2020-04-08
  Changes: Database references