6VUF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4
A, B
126Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RLV (Subject of Investigation/LOI)
Query on RLV

Download Ideal Coordinates CCD File 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
RLV Binding MOAD:  6VUF IC50: 1.47e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.03α = 90
b = 79.205β = 92.82
c = 46.819γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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