9PQE | pdb_00009pqe

Fem-1 homolog B (FEM1B) in complex with VU0412674


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.326 (Depositor), 0.327 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.264 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Nuclear Magnetic Resonance-based fragment screen of the E3 ligase Fem-1 homolog B.

Katinas, J.M.Amporndanai, K.Taylor, A.J.Rose, K.L.Gareiss, P.C.Crespo, R.A.Phan, J.Waterson, A.G.Fesik, S.W.

(2025) Protein Sci 34: e70365-e70365

  • DOI: https://doi.org/10.1002/pro.70365
  • Primary Citation of Related Structures:  
    9PQ9, 9PQA, 9PQE, 9PW8, 9PWJ, 9PXO, 9PXP

  • PubMed Abstract: 

    Targeted protein degradation using PROTACs (PROteolysis TArgeting Chimeras) has emerged as a transformative therapeutic strategy, largely relying on a small number of E3 ubiquitin ligases such as CRBN and VHL. However, resistance, toxicity, and poor oral bioavailability limit the utility of PROTACs and highlight the need to expand the E3 ligase toolbox. Fem-1 homolog B (FEM1B) is a lesser-known E3 ligase that offers a promising alternative due to its broad expression and ability to recognize diverse degron motifs. Here, we describe the development of a stable construct of FEM1B, the results of a protein-observed NMR-based fragment screen using this construct, and the X-ray structures of some of the fragment hits when bound to the protein. From these results, new PROTACs utilizing FEM1B as the E3 ligase may be discovered, providing an alternative E3 ligase for targeted protein degradation.


  • Organizational Affiliation
    • Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein fem-1 homolog B
A, B
357Homo sapiensMutation(s): 0 
Gene Names: FEM1BF1AAKIAA0396
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK73 (Homo sapiens)
Explore Q9UK73 
Go to UniProtKB:  Q9UK73
PHAROS:  Q9UK73
GTEx:  ENSG00000169018 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UK73
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.326 (Depositor), 0.327 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.264 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.015α = 90
b = 130.015β = 90
c = 140.431γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesArvinas Inc. research agreement AWD00000788

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release