8SZ3

Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 7j


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Imidazolone as an Amide Bioisostere in the Development of beta-1,3- N -Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors.

Jackson, J.J.Siegmund, A.C.Bai, W.J.Reed, A.B.Birkholz, A.B.Campuzano, I.D.G.Crequer-Grandhomme, A.Hu, R.Modak, R.V.Sudom, A.Javier, N.Sanders, C.Lo, M.C.Xie, F.Cee, V.J.Manzanillo, P.Allen, J.G.

(2023) J Med Chem 66: 16120-16140

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01517
  • Primary Citation of Related Structures:  
    8SZ3, 8TIC, 8TJC

  • PubMed Abstract: 

    B3GNT2 is responsible for elongation of cell surface long-chain polylactosamine, which influences the regulation of the immune response, making it an attractive target for immunomodulation. In the development of amide containing B3GNT2 inhibitors guided by structure-based drug design, imidazolones were found to successfully serve as amide bioisosteres. This novel imidazolone isosteric strategy alleviated torsional strain of the amide bond on binding to B3GNT2 and improved potency, isoform selectivity, as well as certain physicochemical and pharmacokinetic properties. Herein, we present the synthesis, SAR, X-ray cocrystal structures, and in vivo PK properties of imidazol-4-ones in the context of B3GNT2 inhibition.


  • Organizational Affiliation

    Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
A, B
397Homo sapiensMutation(s): 0 
Gene Names: B3GNT2B3GALT7B3GNT1
EC: 2.4.1.149
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY97 (Homo sapiens)
Explore Q9NY97 
Go to UniProtKB:  Q9NY97
PHAROS:  Q9NY97
GTEx:  ENSG00000170340 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NY97
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.375α = 90
b = 76.405β = 102.58
c = 128.019γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references