The ATAD2 bromodomain in complex with compound 11

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers.

Dolbois, A.Batiste, L.Wiedmer, L.Dong, J.Brutsch, M.Huang, D.Deerain, N.M.Spiliotopoulos, D.Cheng-Sanchez, I.Laul, E.Nevado, C.Sledz, P.Caflisch, A.

(2020) ACS Med Chem Lett 11: 1573-1580

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00080
  • Primary Citation of Related Structures:  
    5F36, 6EPJ, 6EPT, 6EPU, 6EPV, 6EPX, 6HI3, 6HI4, 6HI5, 6HI6, 6HI7, 6HI8, 6HIA, 6HIB, 6HIC, 6HID, 6HIE

  • PubMed Abstract: 

    Small molecule ligand binding to the ATAD2 bromodomain is investigated here through the synergistic combination of molecular dynamics and protein crystallography. A previously unexplored conformation of the binding pocket upon rearrangement of the gatekeeper residue Ile1074 has been found. Further, our investigations reveal how minor structural differences in the ligands result in binding with different plasticity of the ZA loop for this difficult-to-drug bromodomain.

  • Organizational Affiliation

    Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens)
Explore Q6PL18 
Go to UniProtKB:  Q6PL18
GTEx:  ENSG00000156802 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PL18
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G6W (Subject of Investigation/LOI)
Query on G6W

Download Ideal Coordinates CCD File 
C [auth A]2-azanyl-~{N}-[5-(5-azanylpyridin-3-yl)-4-ethanoyl-1,3-thiazol-2-yl]-2-methyl-propanamide
C14 H17 N5 O2 S
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.413α = 90
b = 79.413β = 90
c = 137.344γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description