6Y7I

Structure of the BRD9 bromodomain and compound 2

• PDB DOI: https://doi.org/10.2210/pdb6Y7I/pdb

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


• Deposited: 2020-03-01 Released: 2021-03-31 
• Deposition Author(s): Diaz-Saez, L., Krojer, T., Picaud, S., von Delft, F., Filippakopoulos, P., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K.V.M., Structural Genomics Consortium (SGC)
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.215 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Structure of the BRD9 bromodomain and compound 2

Diaz-Saez, L., Krojer, T., Picaud, S., von Delft, F., Filippakopoulos, P., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K.V.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.6 kDa 
• Atom Count: 2,301 
• Modelled Residue Count: 228 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 9	A, B	121	Homo sapiens	Mutation(s): 0  Gene Names: BRD9, UNQ3040/PRO9856
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8M2 (Homo sapiens) Explore Q9H8M2  Go to UniProtKB:  Q9H8M2
PHAROS:  Q9H8M2 GTEx:  ENSG00000028310

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OF8 (Subject of Investigation/LOI)	C [auth A], E [auth B]	1-(8-pyridin-2-ylpyrrolo[1,2-a]pyrimidin-6-yl)ethanone C14 H11 N3 O LNUJODOPWTZPCA-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.215 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.139	α = 90
b = 38.38	β = 107.13
c = 60.839	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Diaz-Saez, L., Krojer, T., Picaud, S., von Delft, F., Filippakopoulos, P., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K.V.M., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative		--

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description