7NQ0

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH oxabicyclo(hexan-6-yl)-N2-methyl-6-((S)-1-phenylethyl)pyridine-2,4-dicarboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of a Series of N -Methylpyridine-2-carboxamides as Potent and Selective Inhibitors of the Second Bromodomain (BD2) of the Bromo and Extra Terminal Domain (BET) Proteins.

Harrison, L.A.Atkinson, S.J.Bassil, A.Chung, C.W.Grandi, P.Gray, J.R.J.Levernier, E.Lewis, A.Lugo, D.Messenger, C.Michon, A.M.Mitchell, D.J.Preston, A.Prinjha, R.K.Rioja, I.Seal, J.T.Taylor, S.Wall, I.D.Watson, R.J.Woolven, J.M.Demont, E.H.

(2021) J Med Chem 64: 10742-10771

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02155
  • Primary Citation of Related Structures:  
    7NPY, 7NPZ, 7NQ0, 7NQ1, 7NQ2, 7NQ3

  • PubMed Abstract: 

    Domain-specific BET bromodomain ligands represent an attractive target for drug discovery with the potential to unlock the therapeutic benefits of antagonizing these proteins without eliciting the toxicological aspects seen with pan-BET inhibitors. While we have reported several distinct classes of BD2 selective compounds, namely, GSK620, GSK549, and GSK046, only GSK046 shows high aqueous solubility. Herein, we describe the lead optimization of a further class of highly soluble compounds based upon a picolinamide chemotype. Focusing on achieving >1000-fold selectivity for BD2 over BD1 ,while retaining favorable physical chemical properties, compound 36 was identified as being 2000-fold selective for BD2 over BD1 (Brd4 data) with >1 mg/mL solubility in FaSSIF media. 36 represents a valuable new in vivo ready molecule for the exploration of the BD2 phenotype.


  • Organizational Affiliation

    Epigenetics Discovery Performance Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2A [auth AAA]115Homo sapiensMutation(s): 0 
Gene Names: BRD2KIAA9001RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
GTEx:  ENSG00000204256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ULN (Subject of Investigation/LOI)
Query on ULN

Download Ideal Coordinates CCD File 
F [auth AAA]~{N}2-methyl-~{N}4-[(1~{R},5~{S})-3-oxabicyclo[3.1.0]hexan-6-yl]-6-[(1~{S})-1-phenylethyl]pyridine-2,4-dicarboxamide
C21 H23 N3 O3
VTIIKJCRYRUFLT-NALNUFGESA-N
PE4
Query on PE4

Download Ideal Coordinates CCD File 
E [auth AAA]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth AAA],
C [auth AAA],
D [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.17α = 90
b = 53.167β = 90
c = 32.511γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-07-21 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection, Derived calculations