7NQI | pdb_00007nqi

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 2-benzyl-N-cyclopropyl-6-(1-methyl-1H-1,2,3-triazol-4-yl)isonicotinamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.205 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7NQI

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Template-Hopping Approach Leads to Potent, Selective, and Highly Soluble Bromo and Extraterminal Domain (BET) Second Bromodomain (BD2) Inhibitors.

Aylott, H.E.Atkinson, S.J.Bamborough, P.Bassil, A.Chung, C.W.Gordon, L.Grandi, P.Gray, J.R.J.Harrison, L.A.Hayhow, T.G.Messenger, C.Mitchell, D.Phillipou, A.Preston, A.Prinjha, R.K.Rianjongdee, F.Rioja, I.Seal, J.T.Wall, I.D.Watson, R.J.Woolven, J.M.Demont, E.H.

(2021) J Med Chem 64: 3249-3281

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02156
  • Primary Citation Related Structures: 
    7NQ5, 7NQ7, 7NQ8, 7NQ9, 7NQI, 7NQJ

  • PubMed Abstract: 

    A number of reports have recently been published describing the discovery and optimization of bromo and extraterminal inhibitors which are selective for the second bromodomain (BD2); these include our own work toward GSK046 ( 3 ) and GSK620 ( 5 ). This paper describes our approach to mitigating the genotoxicity risk of GSK046 by replacement of the acetamide functionality with a heterocyclic ring. This was followed by a template-hopping and hybridization approach, guided by structure-based drug design, to incorporate learnings from other BD2-selective series, optimize the vector for the amide region, and explore the ZA cleft, leading to the identification of potent, selective, and bioavailable compounds 28 (GSK452), 39 (GSK737), and 36 (GSK217).


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

Macromolecule Content 

  • Total Structure Weight: 13.95 kDa 
  • Atom Count: 1,147 
  • 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 2115Homo 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:  0.205 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.016α = 90
b = 52.622β = 90
c = 32.091γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-03-24 
  • Deposition Author(s): Chung, C.W.

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection, Database references