4GPJ

Crystal Structure of the first bromodomain of human BRD4 in complex with a isoxazolylbenzimidazole ligand

• PDB DOI: https://doi.org/10.2210/pdb4GPJ/pdb

• Classification: PROTEIN BINDING/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-21 Released: 2012-10-17 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Qi, J., Felletar, I., Heightman, T.D., Brennan, P., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

The design and synthesis of 5- and 6-isoxazolylbenzimidazoles as selective inhibitors of the BET bromodomains.

Hay, D., Fedorov, O., Filippakopoulos, P., Martin, S., Philpott, M., Picaud, S., Hewings, D.S., Uttakar, S., Heightman, T.D., Conway, S.J., Knapp, S., Brennan, P.E.

(2013) Medchemcomm 4: 140-144

• PubMed: 26682033 
• DOI: https://doi.org/10.1039/C2MD20189E
• Primary Citation of Related Structures:  
  4GPJ


• PubMed Abstract: 
  

  Simple 1-substituted 5- and 6-isoxazolyl-benzimidazoles have been shown to be potent inhibitors of the BET bromodomains with selectivity over the related bromodomain of CBP. The reported inhibitors were prepared from simple starting materials in two steps followed by separation of the regioisomers or regioselectively in three steps.

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Organizational Affiliation: 

Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.

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: 15.55 kDa 
• Atom Count: 1,260 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0Q1	B [auth A]	(1R)-6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-phenyl-2,3-dihydro-1H-inden-1-ol C20 H19 N O2 SEOJJNHYXOQNOZ-HXUWFJFHSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0Q1	BindingDB:  4GPJ	IC50: 1259 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.29	α = 90
b = 44.38	β = 90
c = 79.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Qi, J., Felletar, I., Heightman, T.D., Brennan, P., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2023-09-13
  Changes: Data collection, Refinement description