4AKN

N-Terminal Bromodomain of Human BRD2 With tbutyl-phenyl-amino- dimethyl-oxazolyl-quinoline-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb4AKN/pdb

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

Deposited: 2012-02-26 Released: 2012-07-04
Deposition Author(s): Chung, C., Lamotte, Y., Donche, F., Bouillot, A., Mirguet, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.197
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Identification of a Novel Series of Bet Family Bromodomain Inhibitors: Binding Mode and Profile of I-Bet151 (Gsk1210151A).

Seal, J., Lamotte, Y., Donche, F., Bouillot, A., Mirguet, O., Gellibert, F., Nicodeme, E., Krysa, G., Kirilovsky, J., Beinke, S., Mccleary, S., Rioja, I., Bamborough, P., Chung, C., Gordon, L., Lewis, T., Walker, A.L., Cutler, L., Lugo, D., Wilson, D.M., Witherington, J., Lee, K., Prinjha, R.K.

(2012) Bioorg Med Chem Lett 22: 2968

PubMed: 22437115 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2012.02.041
Primary Citation of Related Structures:
4AKN, 4ALG

PubMed Abstract:
A novel series of quinoline isoxazole BET family bromodomain inhibitors are discussed. Crystallography is used to illustrate binding modes and rationalize their SAR. One member, I-BET151 (GSK1210151A), shows good oral bioavailability in both the rat and minipig as well as demonstrating efficient suppression of bacterial induced inflammation and sepsis in a murine in vivo endotoxaemia model.

Organizational Affiliation

Epinova DPU, GlaxoSmithKline R&D, Medicines Research Centre, Stevenage, Hertfordshire, UK. jon.t.seal@gsk.com

Macromolecule Content

Total Structure Weight: 54.6 kDa
Atom Count: 3,282
Modelled Residue Count: 330
Deposited Residue Count: 459
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 2	A, B, C	153	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440 Go to UniProtKB: P25440
PHAROS: P25440 GTEx: ENSG00000204256
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25440
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S5B Query on S5B Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	4-[(2-tert-butylphenyl)amino]-7-(3,5-dimethyl-1,2-oxazol-4-yl)quinoline-3-carboxylic acid C₂₅ H₂₅ N₃ O₃ OWUQUQCSBQATFQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C]	F [auth A], G [auth A], J [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
S5B	PDBBind: 4AKN	IC50: 790 (nM) from 1 assay(s)
S5B	BindingDB: 4AKN	IC50: 794.33 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.197
R-Value Work: 0.168
R-Value Observed: 0.170
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.314	α = 90
b = 55.73	β = 94.34
c = 67.991	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-07-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-04
Type: Initial release
Version 1.1: 2012-11-14
Changes: Database references
Version 1.2: 2019-05-15
Changes: Advisory, Data collection, Experimental preparation, Other
Version 1.3: 2024-05-08
Changes: Advisory, Data collection, Database references, Derived calculations, Other