6Y7L

Structure of the BRD9 bromodomain and TP-472

• PDB DOI: https://doi.org/10.2210/pdb6Y7L/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: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 14.36 kDa 
• Atom Count: 1,031 
• Modelled Residue Count: 113 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 9	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QMG (Subject of Investigation/LOI)	B [auth A]	3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide C20 H19 N3 O2 RPBMXJHQYJLPDN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QMG	BindingDB:  6Y7L	Kd: min: 32, max: 82 (nM) from 3 assay(s)
		IC50: 550 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.075	α = 90
b = 41.435	β = 101.72
c = 29.681	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