5E9V

Crystal structure of BRD9 bromodomain in complex with an indolizine ligand

• PDB DOI: https://doi.org/10.2210/pdb5E9V/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-15 Released: 2015-10-28 
• Deposition Author(s): Tallant, C., Hay, D.A., Krojer, T., Nunez-Alonso, G., Picaud, S., Fedorov, O., Schofield, C.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Crystal structure of BRD9 bromodomain in complex with an indolizine ligand

Tallant, C., Hay, D.A., Krojer, T., Nunez-Alonso, G., Picaud, S., Fedorov, O., Schofield, C.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.34 kDa 
• Atom Count: 2,038 
• Modelled Residue Count: 226 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 9	A, B	123	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
5L0	C [auth A], E [auth B]	1-[1-(imidazo[1,2-a]pyridin-5-yl)-7-(morpholin-4-yl)indolizin-3-yl]ethanone C21 H20 N4 O2 LBUBPCSKFDKKFO-UHFFFAOYSA-N
EDO	D [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5L0	BindingDB:  5E9V	IC50: 550 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.381	α = 90
b = 37.96	β = 106.17
c = 60.551	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Tallant, C., Hay, D.A., Krojer, T., Nunez-Alonso, G., Picaud, S., Fedorov, O., Schofield, C.J., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Knapp, S.

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description