6HI7

The ATAD2 bromodomain in complex with compound 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1021/acsmedchemlett.0c00080
  • Primary Citation of Related Structures:  
    6HI4, 6HI3, 6HI6, 6HI5, 6HIB, 6HIA, 6HID, 6HIC, 6HIE, 6HI8

  • 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 ga ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase family AAA domain-containing protein 2A130Homo sapiensMutation(s): 0 
Gene Names: ATAD2L16PRO2000
EC: 3.6.1
Find proteins for Q6PL18 (Homo sapiens)
Explore Q6PL18 
Go to UniProtKB:  Q6PL18
NIH Common Fund Data Resources
PHAROS  Q6PL18
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6B
Query on G6B

Download Ideal Coordinates CCD File 
A
(2~{R})-~{N}-[5-(3-aminophenyl)-4-ethanoyl-1,3-thiazol-2-yl]-2-azanyl-propanamide
C14 H16 N4 O2 S
NZFSZJLKZIHQBY-SSDOTTSWSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.516α = 90
b = 80.516β = 90
c = 137.85γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references