6VUB

Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 5 (1-methyl-4-phenylpyrrolidin-2-one)

• PDB DOI: https://doi.org/10.2210/pdb6VUB/pdb

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


• Deposited: 2020-02-14 Released: 2020-02-26 
• Deposition Author(s): Ilyichova, O.V., Scanlon, M.J., Thompson, P.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.177 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

Literature

Substituted 1-methyl-4-phenylpyrrolidin-2-ones - Fragment-based design of N-methylpyrrolidone-derived bromodomain inhibitors.

Hilton-Proctor, J.P., Ilyichova, O., Zheng, Z., Jennings, I.G., Johnstone, R.W., Shortt, J., Mountford, S.J., Scanlon, M.J., Thompson, P.E.

(2020) Eur J Med Chem 191: 112120-112120

• PubMed: 32120339 
• DOI: https://doi.org/10.1016/j.ejmech.2020.112120
• Primary Citation of Related Structures:  
  6VUB, 6VUC, 6VUF, 6VUJ


• PubMed Abstract: 
  

  N-Methylpyrrolidone is one of several chemotypes that have been described as a mimetic of acetyl-lysine in the development of bromodomain inhibitors. In this paper, we describe the synthesis of a 4-phenyl substituted analogue - 1-methyl-4-phenylpyrrolidin-2-one - and the use of aryl substitution reactions as a divergent route for derivatives. Ultimately, this has led to structurally complex, chiral compounds with progressively improved affinity as inhibitors of bromodomain-containing protein 4.

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Organizational Affiliation: 

Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.14 kDa 
• Atom Count: 1,406 
• Modelled Residue Count: 126 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	126	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RLG (Subject of Investigation/LOI)	B [auth A]	(4R)-1-methyl-4-phenylpyrrolidin-2-one C11 H13 N O NJSMSOSBMMZSSB-JTQLQIEISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RLG	Binding MOAD:  6VUB	IC50: 6.29e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.177 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.619	α = 90
b = 44.022	β = 90
c = 78.478	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Currently 6VUB does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Ilyichova, O.V., Scanlon, M.J., Thompson, P.E.

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2020-03-18
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description