7NPY | pdb_00007npy

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 6-benzyl-N2-methyl-N4-((1S,2S)-2-methylcyclopropyl)pyridine-2,4-dicarboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.173 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.146 (Depositor) 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 13.94 kDa 
  • Atom Count: 1,136 
  • Modeled Residue Count: 111 
  • Deposited Residue Count: 115 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.173 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.146 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.047α = 90
b = 52.31β = 90
c = 32.087γ = 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