8JVD

Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

Starting Model: experimental
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Literature

Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening.

Loh, Y.Y.Anantharajan, J.Huang, Q.Xu, W.Fulwood, J.Ng, H.Q.Ng, E.Y.Gea, C.Y.Choong, M.L.Tan, Q.W.Koh, X.Lim, W.H.Nacro, K.Cherian, J.Baburajendran, N.Ke, Z.Kang, C.

(2024) Protein Sci 33: e4904-e4904

  • DOI: https://doi.org/10.1002/pro.4904
  • Primary Citation of Related Structures:  
    8JUC, 8JVD

  • PubMed Abstract: 

    UBE2T is an attractive target for drug development due to its linkage with several types of cancers. However, the druggability of ubiquitin-conjugating E2 (UBE2T) is low because of the lack of a deep and hydrophobic pocket capable of forming strong binding interactions with drug-like small molecules. Here, we performed fragment screening using 19 F-nuclear magnetic resonance (NMR) and validated the hits with 1 H- 15 N-heteronuclear single quantum coherence (HSQC) experiment and X-ray crystallographic studies. The cocrystal structures obtained revealed the binding modes of the hit fragments and allowed for the characterization of the fragment-binding sites. Further screening of structural analogues resulted in the identification of a compound series with inhibitory effect on UBE2T activity. Our current study has identified two new binding pockets in UBE2T, which will be useful for the development of small molecules to regulate the function of this protein. In addition, the compounds identified in this study can serve as chemical starting points for the development of UBE2T modulators.


  • Organizational Affiliation

    Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 T156Homo sapiensMutation(s): 0 
Gene Names: UBE2T
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPD8 (Homo sapiens)
Explore Q9NPD8 
Go to UniProtKB:  Q9NPD8
PHAROS:  Q9NPD8
GTEx:  ENSG00000077152 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPD8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V2R (Subject of Investigation/LOI)
Query on V2R

Download Ideal Coordinates CCD File 
B [auth A]5-fluoranyl-1,3-benzoxazol-2-amine
C7 H5 F N2 O
PFPSBRGOJCFWKD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.636α = 90
b = 54.636β = 90
c = 182.728γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release