6VUF | pdb_00006vuf

Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 7h (4-(1-methyl-5-oxopyrrolidin-3-yl)-N-propylbenzenesulfonamide)

• PDB DOI: https://doi.org/10.2210/pdb6VUF/pdb

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


• Deposited: 2020-02-15 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: 1.59 Å
• R-Value Free: 
  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

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 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.
Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.
Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, 246 Clayton Road, Clayton, Victoria, Australia; Monash Haematology, Monash Health, 246 Clayton Road, Clayton, Victoria, Australia.
Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, Australia. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.53 kDa 
• Atom Count: 2,575 
• Modeled Residue Count: 251 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B	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
RLV (Subject of Investigation/LOI)	C [auth A], D [auth B]	4-[(3R)-1-methyl-5-oxopyrrolidin-3-yl]-N-propylbenzene-1-sulfonamide C14 H20 N2 O3 S UOJMSGYUFCDFLH-LBPRGKRZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.03	α = 90
b = 79.205	β = 92.82
c = 46.819	γ = 90

Software Package:

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

Structure Validation

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