8CCB

The Fk1 domain of FKBP51 in complex with 2-(3-((1R)-1-(((2S)-1-(2-(5-chlorothiophen-2-yl)-2-cyclohexylacetyl)piperidine-2-carbonyl)oxy)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure-Based Discovery of a New Selectivity-Enabling Motif for the FK506-Binding Protein 51.

Knaup, F.H.Meyners, C.Sugiarto, W.O.Wedel, S.Springer, M.Walz, C.Geiger, T.M.Schmidt, M.Sisignano, M.Hausch, F.

(2023) J Med Chem 66: 5965-5980

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00249
  • Primary Citation of Related Structures:  
    8CCA, 8CCB, 8CCC, 8CCD, 8CCE, 8CCF, 8CCG, 8CCH

  • PubMed Abstract: 

    In recent years, the selective inhibition of FKBP51 has emerged as a possible treatment for chronic pain, obesity-induced diabetes, or depression. All currently known advanced FKBP51-selective inhibitors, including the widely used SAFit2, contain a cyclohexyl residue as a key motif for enabling selectivity over the closest homologue and anti-target FKBP52. During a structure-based SAR exploration, we surprisingly discovered thiophenes as highly efficient cyclohexyl replacement moieties that retain the strong selectivity of SAFit-type inhibitors for FKBP51 over FKBP52. Cocrystal structures revealed that the thiophene-containing moieties enable selectivity by stabilizing a flipped-out conformation of Phe 67 of FKBP51. Our best compound, 19b , potently binds to FKBP51 biochemically as well as in mammalian cells, desensitize TRPV1 in primary sensory neurons, and has an acceptable PK profile in mice, suggesting its use as a novel tool compound for studying FKBP51 in animal models of neuropathic pain.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5128Homo 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 
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
U83 (Subject of Investigation/LOI)
Query on U83

Download Ideal Coordinates CCD File 
B [auth A]2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-(5-chloranylthiophen-2-yl)-2-cyclohexyl-ethanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid
C37 H44 Cl N O8 S
GTUUVVDLKBPWFG-JVLQLMMJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.328α = 90
b = 54.115β = 90
c = 57.158γ = 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: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection
  • Version 1.3: 2024-02-14
    Changes: Refinement description