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: 15.53 kDa 
• Atom Count: 1,250 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

 5A5S

NN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 5-5-methoxypyridin-3-yl-3- methyl-8-piperidin-4-ylamino-1,2-dihydro-1,7-naphthyridin-2-one

• PDB DOI: 10.2210/pdb5A5S/pdb

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


• Deposited: 2015-06-20 Released: 2015-07-22 
• Deposition Author(s): Chung, C., Bamborough, P., Demont, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.218 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Fragment-Based Discovery of Low-Micromolar Atad2 Bromodomain Inhibitors.

Demont, E.H., Chung, C., Furze, R.C., Grandi, P., Michon, A., Wellaway, C., Barrett, N., Bridges, A.M., Craggs, P.D., Diallo, H., Dixon, D.P., Douault, C., Emmons, A.J., Jones, E.J., Karamshi, B.V., Locke, K., Mitchell, D.J., Mouzon, B.H., Prinjha, R.K., Roberts, A.D., Sheppard, R.J., Watson, R.J., Bamborough, P.

(2015) J Med Chem 58: 5649

• PubMed: 26155854 
• DOI: 10.1021/acs.jmedchem.5b00772
• Primary Citation of Related Structures:  
  5A5N, 5A5O, 5A5P, 5A5Q, 5A5R, 5A5S


• PubMed Abstract: 
  

Overexpression of ATAD2 (ATPase family, AAA domain containing 2) has been linked to disease severity and progression in a wide range of cancers, and is implicated in the regulation of several drivers of cancer growth. Little is known of the dependence of these effects upon the ATAD2 bromodomain, which has been categorized as among the least tractable of its class. The absence of any potent, selective inhibitors limits clear understanding of the therapeutic potential of the bromodomain. Here, we describe the discovery of a hit from a fragment-based targeted array. Optimization of this produced the first known micromolar inhibitors of the ATAD2 bromodomain.

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Organizational Affiliation: 

∥Drug Metabolism and Pharmacokinetics (DMPK), GlaxoSmithKline, Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NP8	C [auth A]	5-(5-methoxypyridin-3-yl)-3-methyl-8-[(piperidin-4-yl)amino]-1,2-dihydro-1,7-naphthyridin-2-one C20 H23 N5 O2 FPQQERRFPULCIK-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NP8	BindingDB:  5A5S	IC50: min: 1259, max: 1.58e+4 (nM) from 2 assay(s)
	Binding MOAD:  5A5S	IC50: 1300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.218 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.39	α = 90
b = 49.39	β = 90
c = 59.23	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Chung, C., Bamborough, P., Demont, E.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Database references