8R5K

The Fk1 domain of FKBP51 in complex with Antascomicine B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 

Starting Model: experimental
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Literature

Antascomicin B stabilizes FKBP51-Akt1 complexes as a molecular glue.

Schafer, S.C.Voll, A.M.Bracher, A.Ley, S.V.Hausch, F.

(2024) Bioorg Med Chem Lett 104: 129728-129728

  • DOI: https://doi.org/10.1016/j.bmcl.2024.129728
  • Primary Citation of Related Structures:  
    8R5K

  • PubMed Abstract: 

    Antascomicin B is a natural product that similarly to the macrolides FK506 and Rapamycin binds to the FK506-binding protein 12 (FKBP12). FK506 and Rapamycin act as molecular glues by inducing ternary complexes between FKBPs and additional target proteins. Whether Antascomicin B can induce ternary complexes is unknown. Here we show that Antascomicin B binds tightly to larger human FKBP homologs. The cocrystal structure of FKBP51 in complex with Antascomicin B revealed that large parts of Antascomicin B are solvent-exposed and available to engage additional proteins. Cellular studies demonstrated that Antascomicin B enhances the interaction between human FKBP51 and human Akt. Our studies show that molecules with molecular glue-like properties are more prominent in nature than previously thought. We predict the existence of additional 'orphan' molecular glues that evolved to induce ternary protein complexes but where the relevant ternary complex partners are unknown.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Clemens-Schöpf-Institute Technical University Darmstadt Peter-Grünberg-Straße 4, 64287 Darmstadt, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5128Homo sapiensMutation(s): 1 
Gene Names: FKBP5AIG6FKBP51
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13451 (Homo sapiens)
Explore Q13451 
Go to UniProtKB:  Q13451
PHAROS:  Q13451
GTEx:  ENSG00000096060 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13451
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y6Z (Subject of Investigation/LOI)
Query on Y6Z

Download Ideal Coordinates CCD File 
B [auth A]Antascomicine B
C37 H57 N O10
PSAJCYLXNSDJCJ-FALYXAMCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.01α = 90
b = 54.89β = 90
c = 56.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

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: 2024-05-08
    Type: Initial release