6UVJ

Cocrystal of BRD4(D1) with a methyl carbamate thiazepane inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report



Literature

Evaluating the Advantages of Using 3D-Enriched Fragments for Targeting BET Bromodomains.

Johnson, J.A.Nicolaou, C.A.Kirberger, S.E.Pandey, A.K.Hu, H.Pomerantz, W.C.K.

(2019) ACS Med Chem Lett 10: 1648-1654

  • DOI: 10.1021/acsmedchemlett.9b00414
  • Primary Citation of Related Structures:  
    6UVJ, 6UVM, 6UWX

  • PubMed Abstract: 
  • Fragment-based ligand discovery has been successful in targeting diverse proteins. Despite drug-like molecules having more 3D character, traditional fragment libraries are largely composed of flat, aromatic fragments. The use of 3D-enriched fragments ...

    Fragment-based ligand discovery has been successful in targeting diverse proteins. Despite drug-like molecules having more 3D character, traditional fragment libraries are largely composed of flat, aromatic fragments. The use of 3D-enriched fragments for enhancing library diversity is underexplored especially against protein-protein interactions. Here, we evaluate using 3D-enriched fragments against bromodomains. Bromodomains are highly ligandable, but selectivity remains challenging, particularly for bromodomain and extraterminal (BET) family bromodomains. We screened a 3D-enriched fragment library against BRD4(D1) via 1 H CPMG NMR with a protein-observed 19 F NMR secondary assay. The screen led to 29% of the hits that are selective over two related bromodomains, BRDT(D1) and BPTF, and the identification of underrepresented chemical bromodomain inhibitor scaffolds. Initial structure-activity relationship studies guided by X-ray crystallography led to a ligand-efficient thiazepane, with good selectivity and affinity for BET bromodomains. These results suggest that the incorporation of 3D-enriched fragments to increase library diversity can benefit bromodomain screening.


    Organizational Affiliation

    Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A127Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QJ1
Query on QJ1

Download CCD File 
A
methyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate
C11 H15 N O2 S2
GTUMUZDXWXZZSA-JTQLQIEISA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QJ1Kd:  20000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.41α = 90
b = 44.31β = 90
c = 78.24γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)United States5T32GM008347-23

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release