FKBP12 in complex with PROTAC 6a2

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.152 

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This is version 1.4 of the entry. See complete history


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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1A107Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
PHAROS:  P62942
GTEx:  ENSG00000088832 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62942
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y5Q (Subject of Investigation/LOI)
Query on Y5Q

Download Ideal Coordinates CCD File 
B [auth A](2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[4-[(1~{S})-1-[(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-ethenyl-2-oxidanylidene-3,10-diazabicyclo[4.3.1]decan-3-yl]ethyl]-1,2,3-triazol-1-yl]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
C48 H61 Cl2 N9 O9 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.993α = 90
b = 36.506β = 102.186
c = 44.217γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

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