6VUJ

Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 15c (N,N-diethyl-3',4'-dimethoxy-6-(1-methyl-5-oxopyrrolidin-3-yl)-[1,1'-biphenyl]-3-sulfonamide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.ejmech.2020.112120
  • Primary Citation of Related Structures:  
    6VUF, 6VUJ, 6VUB, 6VUC

  • 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-phenylpyrro ...

    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. Electronic address: philip.thompson@monash.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A126Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RLY
Query on RLY

Download CCD File 
A
N,N-diethyl-3',4'-dimethoxy-6-[(3S)-1-methyl-5-oxopyrrolidin-3-yl][1,1'-biphenyl]-3-sulfonamide
C23 H30 N2 O5 S
CZOWHOAXNNGART-QGZVFWFLSA-N
 Ligand Interaction
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.83α = 90
b = 52.047β = 90
c = 57.354γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references