4QST

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with 1-methylquinolin 2-one

PDB DOI: https://doi.org/10.2210/pdb4QST/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-06 Released: 2014-07-23
Deposition Author(s): Chaikuad, A., Felletar, I., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.222
R-Value Work: 0.178
R-Value Observed: 0.180

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure-based approaches towards identification of fragments for the low-druggability ATAD2 bromodomain

Chaikuad, A., Petros, A.M., Fedorov, O., Xu, J., Knapp, S.

(2014) Medchemcomm 5: 1843-1848

DOI: https://doi.org/10.1039/C4MD00237G

Macromolecule Content

Total Structure Weight: 16.74 kDa
Atom Count: 1,362
Modelled Residue Count: 130
Deposited Residue Count: 130
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens) Go to UniProtKB: Q6PL18
PHAROS: Q6PL18 GTEx: ENSG00000156802
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12Q Query on 12Q Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-METHYLQUINOLIN-2(1H)-ONE C₁₀ H₉ N O QYEMNJMSULGQRD-UHFFFAOYSA-N		Interactions Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain O [auth A] SDF format, chain S [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth A] mmCIF format, chain S [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
12Q	BindingDB: 4QST	IC50: 1.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.222
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.43	α = 90
b = 79.43	β = 90
c = 138.06	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-23

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-07-23
Type: Initial release
Version 1.1: 2015-01-14
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description