6Y7J | pdb_00006y7j

Structure of the BRD9 bromodomain and compound 15

• PDB DOI: https://doi.org/10.2210/pdb6Y7J/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.
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structure of the BRD9 bromodomain

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: 28.75 kDa 
• Atom Count: 2,186 
• Modeled Residue Count: 226 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OF5 (Subject of Investigation/LOI)	C [auth A], D [auth B]	1-[8-(2,5-dimethoxyphenyl)pyrrolo[1,2-a]pyrimidin-6-yl]ethanone C17 H16 N2 O3 VNCOLZXZXMUDIT-UHFFFAOYSA-N
ACT	E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.11	α = 90
b = 118.69	β = 90
c = 28.33	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
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.

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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