5A81 | pdb_00005a81

Crystal structure of human ATAD2 bromodomain in complex with 8-(3R,4R) -3-(cyclohexylmethoxy)piperidin-4-yl-amino-3-methyl-1,2-dihydro-1,7- naphthyridin-2-one

• PDB DOI: https://doi.org/10.2210/pdb5A81/pdb

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


• Deposited: 2015-07-11 Released: 2015-08-12 
• Deposition Author(s): Chung, C., Bamborough, P., Demont, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Structure-Based Optimization of Naphthyridones Into Potent Atad2 Bromodomain Inhibitors.

Bamborough, P., Chung, C., Furze, R.C., Grandi, P., Michon, A., Sheppard, R.J., Barnett, H., Diallo, H., Dixon, D.P., Douault, C., Jones, E.J., Karamshi, B., Mitchell, D.J., Prinjha, R.K., Rau, C., Watson, R.J., Werner, T., Demont, E.H.

(2015) J Med Chem 58: 6151

• PubMed: 26230603 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00773
• Primary Citation of Related Structures:  
  5A81, 5A82, 5A83, 5A85


• PubMed Abstract: 
  

  ATAD2 is a bromodomain-containing protein whose overexpression is linked to poor outcomes in a number of different cancer types. To date, no potent and selective inhibitors of the bromodomain have been reported. This article describes the structure-based optimization of a series of naphthyridones from micromolar leads with no selectivity over the BET bromodomains to inhibitors with sub-100 nM ATAD2 potency and 100-fold BET selectivity.

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Organizational Affiliation: 

∥Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.14 kDa 
• Atom Count: 1,349 
• 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  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
78J	D [auth A]	(3R,4R)-3-(cyclohexylmethoxy)piperidin-4-yl]amino}-3-methyl-1,2-dihydro-1,7-naphthyridin-2-one C21 H30 N4 O2 DQJOFVKRLCBKNO-QZTJIDSGSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
78J	BindingDB:  5A81	Kd: min: 2900, max: 3162 (nM) from 3 assay(s)
		IC50: min: 2512, max: 3981 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.54	α = 90
b = 79.54	β = 90
c = 138.22	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Chung, C., Bamborough, P., Demont, E.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2015-08-26
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other