4TYL

Fragment-Based Screening of the Bromodomain of ATAD2

• PDB DOI: https://doi.org/10.2210/pdb4TYL/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-08 Released: 2014-10-29 
• Deposition Author(s): Harner, M.J., Chauder, B.A., Phan, J., Fesik, S.W.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.197 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 

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

• PubMed: 25314628 
• DOI: https://doi.org/10.1021/jm501035j
• Primary Citation of Related Structures:  
  4TYL, 4TZ2, 4TZ8


• 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 identified using NMR spectroscopy, and ATAD2 was crystallized with three of the hits identified in the fragment screen.

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Organizational Affiliation: 

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

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: 15.88 kDa 
• Atom Count: 1,360 
• Modelled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family AAA domain-containing protein 2	A	130	Homo sapiens	Mutation(s): 0  Gene Names: ATAD2, L16, PRO2000 EC: 3.6.1.3 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens) Explore Q6PL18  Go to UniProtKB:  Q6PL18
PHAROS:  Q6PL18 GTEx:  ENSG00000156802

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
39O	D [auth A]	5-amino-1,3,6-trimethyl-1,3-dihydro-2H-benzimidazol-2-one C10 H13 N3 O DHPXTEFKFUCWDK-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
39O	BindingDB:  4TYL	Kd: 6.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.197 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.492	α = 90
b = 79.492	β = 90
c = 137.508	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Harner, M.J., Chauder, B.A., Phan, J., Fesik, S.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	DP1OD006933/DP1CA174419

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2014-12-03
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2017-09-06
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence
• Version 1.5: 2023-12-27
  Changes: Advisory, Data collection, Database references, Refinement description