4TYL

Fragment-Based Screening of the Bromodomain of ATAD2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Fragment-Based Screening of the Bromodomain of ATAD2.

Harner, M.J.Chauder, B.A.Phan, J.Fesik, S.W.

(2014) J.Med.Chem. 57: 9687-9692

  • DOI: 10.1021/jm501035j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cellular and genetic evidence suggest that inhibition of ATAD2 could be a useful strategy to treat several types of cancer. To discover small-molecule inhibitors of the bromodomain of ATAD2, we used a fragment-based approach. Fragment hits were ident ...

    Cellular and genetic evidence suggest that inhibition of ATAD2 could be a useful strategy to treat several types of cancer. To discover small-molecule inhibitors of the bromodomain of ATAD2, we used a fragment-based approach. Fragment hits were identified using NMR spectroscopy, and ATAD2 was crystallized with three of the hits identified in the fragment screen.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine , 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATPase family AAA domain-containing protein 2
A
130Homo sapiensMutation(s): 0 
Gene Names: ATAD2
EC: 3.6.1.3
Find proteins for Q6PL18 (Homo sapiens)
Go to Gene View: ATAD2
Go to UniProtKB:  Q6PL18
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
39O
Query on 39O

Download SDF File 
Download CCD File 
A
5-amino-1,3,6-trimethyl-1,3-dihydro-2H-benzimidazol-2-one
C10 H13 N3 O
DHPXTEFKFUCWDK-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
39OKd: 600000 nM (100) BINDINGDB
39OKd: 600000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.492α = 90.00
b = 79.492β = 90.00
c = 137.508γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesDP1OD006933/DP1CA174419

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Derived calculations
  • Version 1.3: 2017-09-06
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy