4NQN

Crystal Structure of the bromodomain of human BRD9 in complex with a triazolo-phthalazine ligand

• PDB DOI: https://doi.org/10.2210/pdb4NQN/pdb

• Classification: TRANSCRIPTION/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-25 Released: 2013-12-18 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.245 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Crystal Structure of the bromodomain of human BRD9 in complex with a triazolo-phthalazine ligand

Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

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)

Macromolecule Content

• Total Structure Weight: 14.78 kDa 
• Atom Count: 1,141 
• Modelled Residue Count: 113 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 9	A	123	Homo sapiens	Mutation(s): 0  Gene Names: BRD9
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
Y1Z	B [auth A]	2-chloro-N-[5-(3-methyl[1,2,4]triazolo[3,4-a]phthalazin-6-yl)-2-(morpholin-4-yl)phenyl]benzenesulfonamide C26 H23 Cl N6 O3 S WLUMGCPGWDQOSB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Y1Z	BindingDB:  4NQN	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.245 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.12	α = 90
b = 48.42	β = 90
c = 69.32	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description