7OE4 | pdb_00007oe4

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N-methyl-4-propionyl-1H-pyrrole-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.185 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.157 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 7OE4

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Fragment-based Scaffold Hopping: Identification of Potent, Selective, and Highly Soluble Bromo and Extra Terminal Domain (BET) Second Bromodomain (BD2) Inhibitors.

Seal, J.T.Atkinson, S.J.Bamborough, P.Bassil, A.Chung, C.W.Foley, J.Gordon, L.Grandi, P.Gray, J.R.J.Harrison, L.A.Kruger, R.G.Matteo, J.J.McCabe, M.T.Messenger, C.Mitchell, D.Phillipou, A.Preston, A.Prinjha, R.K.Rianjongdee, F.Rioja, I.Taylor, S.Wall, I.D.Watson, R.J.Woolven, J.M.Wyce, A.Zhang, X.P.Demont, E.H.

(2021) J Med Chem 64: 10772-10805

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00365
  • Primary Citation Related Structures: 
    7OE4, 7OE5, 7OE6, 7OGY

  • PubMed Abstract: 

    The profound efficacy of pan-BET inhibitors is well documented, but these epigenetic agents have shown pharmacology-driven toxicity in oncology clinical trials. The opportunity to identify inhibitors with an improved safety profile by selective targeting of a subset of the eight bromodomains of the BET family has triggered extensive medicinal chemistry efforts. In this article, we disclose the identification of potent and selective drug-like pan-BD2 inhibitors such as pyrazole 23 (GSK809) and furan 24 (GSK743) that were derived from the pyrrole fragment 6 . We transpose the key learnings from a previous pyridone series (GSK620 2 as a representative example) to this novel class of inhibitors, which are characterized by significantly improved solubility relative to our previous research.


  • Organizational Affiliation
    • Cancer Epigenetics Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States.

Macromolecule Content 

  • Total Structure Weight: 14.22 kDa 
  • Atom Count: 1,192 
  • Modeled Residue Count: 113 
  • 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

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4

Query on PE4



Download:Ideal Coordinates CCD File
F [auth AAA]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
V9B
(Subject of Investigation/LOI)

Query on V9B



Download:Ideal Coordinates CCD File
G [auth AAA]N-methyl-4-propanoyl-1H-pyrrole-2-carboxamide
C9 H12 N2 O2
CWMKCPQGJKUMBN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth AAA],
C [auth AAA],
D [auth AAA],
E [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.185 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.157 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.325α = 90
b = 52.773β = 90
c = 31.845γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-07-28 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Derived calculations, Refinement description