5LJ0

Crystal structure of human ATAD2 bromodomain in complex with 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one

• PDB DOI: https://doi.org/10.2210/pdb5LJ0/pdb

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


• Deposited: 2016-07-17 Released: 2016-08-31 
• Deposition Author(s): Chung, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.183 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

A Chemical Probe for the ATAD2 Bromodomain.

Bamborough, P., Chung, C.W., Demont, E.H., Furze, R.C., Bannister, A.J., Che, K.H., Diallo, H., Douault, C., Grandi, P., Kouzarides, T., Michon, A.M., Mitchell, D.J., Prinjha, R.K., Rau, C., Robson, S., Sheppard, R.J., Upton, R., Watson, R.J.

(2016) Angew Chem Int Ed Engl 55: 11382-11386

• PubMed: 27530368 
• DOI: https://doi.org/10.1002/anie.201603928
• Primary Citation of Related Structures:  
  5LJ0, 5LJ1, 5LJ2


• PubMed Abstract: 
  

  ATAD2 is a cancer-associated protein whose bromodomain has been described as among the least druggable of that target class. Starting from a potent lead, permeability and selectivity were improved through a dual approach: 1) using CF2 as a sulfone bio-isostere to exploit the unique properties of fluorine, and 2) using 1,3-interactions to control the conformation of a piperidine ring. This resulted in the first reported low-nanomolar, selective and cell permeable chemical probe for ATAD2.

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Organizational Affiliation: 

GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.33 kDa 
• Atom Count: 1,424 
• Modelled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family AAA domain-containing protein 2	A	130	Homo sapiens	Mutation(s): 0  Gene Names: ATAD2, L16, PRO2000 EC: 3.6.1.3 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens) Explore Q6PL18  Go to UniProtKB:  Q6PL18
PHAROS:  Q6PL18 GTEx:  ENSG00000156802

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6XX	F [auth A]	8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one C28 H35 F2 N5 O3 YDPMMWAOCCOULO-JBRSBNLGSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.183 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.158	α = 90
b = 79.158	β = 90
c = 135.857	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Chung, C.

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2016-09-14
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references