8PC2

SelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.210 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history


Literature

Discovery of a Potent Proteolysis Targeting Chimera Enables Targeting the Scaffolding Functions of FK506-Binding Protein 51 (FKBP51).

Geiger, T.M.Walz, M.Meyners, C.Kuehn, A.Dreizler, J.K.Sugiarto, W.O.Maciel, E.V.S.Zheng, M.Lermyte, F.Hausch, F.

(2024) Angew Chem Int Ed Engl 63: e202309706-e202309706

  • DOI: https://doi.org/10.1002/anie.202309706
  • Primary Citation of Related Structures:  
    8PC2, 8PDF

  • PubMed Abstract: 

    The FK506-binding protein 51 (FKBP51) is a promising target in a variety of disorders including depression, chronic pain, and obesity. Previous FKBP51-targeting strategies were restricted to occupation of the FK506-binding site, which does not affect core functions of FKBP51. Here, we report the discovery of the first FKBP51 proteolysis targeting chimera (PROTAC) that enables degradation of FKBP51 abolishing its scaffolding function. Initial synthesis of 220 FKBP-focused PROTACs yielded a plethora of active PROTACs for FKBP12, six for FKBP51, and none for FKBP52. Structural analysis of a binary FKBP12:PROTAC complex revealed the molecular basis for negative cooperativity. Linker-based optimization of first generation FKBP51 PROTACs led to the PROTAC SelDeg51 with improved cellular activity, selectivity, and high cooperativity. The structure of the ternary FKBP51:SelDeg51:VCB complex revealed how SelDeg51 establishes cooperativity by dimerizing FKBP51 and the von Hippel-Lindau protein (VHL) in a glue-like fashion. SelDeg51 efficiently depletes FKBP51 and reactivates glucocorticoid receptor (GR)-signalling, highlighting the enhanced efficacy of full protein degradation compared to classical FKBP51 binding.


  • 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
von Hippel-Lindau disease tumor suppressorA [auth B],
E [auth A]
162Homo sapiensMutation(s): 0 
Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens)
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Go to UniProtKB:  P40337
PHAROS:  P40337
GTEx:  ENSG00000134086 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40337
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CB [auth C],
F [auth E]
97Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
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Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
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UniProt GroupQ15369
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-BC [auth D],
G [auth F]
104Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
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Go to UniProtKB:  Q15370
PHAROS:  Q15370
GTEx:  ENSG00000103363 
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UniProt GroupQ15370
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5D [auth G],
H
128Homo sapiensMutation(s): 3 
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 
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UniProt GroupQ13451
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XZW (Subject of Investigation/LOI)
Query on XZW

Download Ideal Coordinates CCD File 
I [auth B],
J [auth A]
[(1~{R})-3-(3,4-dimethoxyphenyl)-1-[4-[[1-[3-[2-[[[(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidin-2-yl]carbonylamino]methyl]-5-(4-methyl-1,3-thiazol-5-yl)phenoxy]propyl]-1,2,3-triazol-4-yl]methoxy]phenyl]propyl] (2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate
C72 H91 F N8 O14 S
FKTLFLSCPIJSAI-RXUWPDNZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.210 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.646α = 90
b = 68.425β = 114.453
c = 159.256γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references
  • Version 1.2: 2023-12-27
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Database references
  • Version 1.4: 2024-01-24
    Changes: Database references