7Q6T

Crystal structure of the bromodomain of ATAD2 with AZ13824374


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of a Potent and Selective ATAD2 Bromodomain Inhibitor with Antiproliferative Activity in Breast Cancer Models.

Winter-Holt, J.J.Bardelle, C.Chiarparin, E.Dale, I.L.Davey, P.R.J.Davies, N.L.Denz, C.Fillery, S.M.Guerot, C.M.Han, F.Hughes, S.J.Kulkarni, M.Liu, Z.Milbradt, A.Moss, T.A.Niu, H.Patel, J.Rabow, A.A.Schimpl, M.Shi, J.Sun, D.Yang, D.Guichard, S.

(2022) J Med Chem 65: 3306-3331

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01871
  • Primary Citation of Related Structures:  
    7Q6T, 7Q6U, 7Q6V, 7Q6W

  • PubMed Abstract: 

    ATAD2 is an epigenetic bromodomain-containing target which is overexpressed in many cancers and has been suggested as a potential oncology target. While several small molecule inhibitors have been described in the literature, their cellular activity has proved to be underwhelming. In this work, we describe the identification of a novel series of ATAD2 inhibitors by high throughput screening, confirmation of the bromodomain region as the site of action, and the optimization campaign undertaken to improve the potency, selectivity, and permeability of the initial hit. The result is compound 5 (AZ13824374), a highly potent and selective ATAD2 inhibitor which shows cellular target engagement and antiproliferative activity in a range of breast cancer models.


  • Organizational Affiliation

    BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase family AAA domain-containing protein 2130Homo sapiensMutation(s): 0 
Gene Names: ATAD2L16PRO2000
EC: 3.6.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens)
Explore Q6PL18 
Go to UniProtKB:  Q6PL18
PHAROS:  Q6PL18
GTEx:  ENSG00000156802 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PL18
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
96L (Subject of Investigation/LOI)
Query on 96L

Download Ideal Coordinates CCD File 
D [auth A](1R,9S,12R)-13-[[8-[[1-(2-fluoranyl-2-methyl-propyl)piperidin-4-yl]amino]-3-methyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl]carbonyl]-12-propan-2-yl-11,13-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4,6-trien-10-one
C30 H39 F N8 O2
NGXAMXNWIHBLBN-JIMJEQGWSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.414α = 90
b = 79.414β = 90
c = 139.478γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-03-09
    Changes: Database references