6SAF

The Fk1 domain of FKBP51 in complex with (S)-(R)-3-(3,4-dimethoxyphenyl)-1-(3-(2-morpholinoethoxy)phenyl)propyl 1-((1R,4aR,8aR)-4-oxodecahydronaphthalene-1-carbonyl)piperidine-2-carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Novel Decalin-Based Bicyclic Scaffold for FKBP51-Selective Ligands.

Feng, X.Sippel, C.Knaup, F.H.Bracher, A.Staibano, S.Romano, M.F.Hausch, F.

(2020) J Med Chem 63: 231-240

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01157
  • Primary Citation of Related Structures:  
    6SAF

  • PubMed Abstract: 

    Selective inhibition of FKBP51 has emerged as possible novel treatment for diseases like major depressive disorder, obesity, chronic pain, and certain cancers. The current FKBP51 inhibitors are rather large, flexible, and have to be further optimized. By using a structure-based rigidification strategy, we hereby report the design and synthesis of a novel promising bicyclic scaffold for FKBP51 ligands. The structure-activity analysis revealed the decalin scaffold as the best moiety for the selectivity-enabling subpocket of FBKP51. The resulting compounds retain high potency for FKBP51 and excellent selectivity over the close homologue FKBP52. With the cocrystal structure of an advanced ligand in this novel series, we show how the decalin locks the key selectivity-inducing cyclohexyl moiety of the ligand in a conformation typical for FKBP51-selective binding. The best compound 29 produces cell death in a HeLa-derived KB cell line, a cellular model of cervical adenocarcinoma, where FKBP51 is highly overexpressed. Our results show how FKBP51 inhibitors can be rigidified and extended while preserving FKBP51 selectivity. Such inhibitors might be novel tools in the treatment of human cancers with deregulated FKBP51.


  • Organizational Affiliation

    Department of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , Kraepelinstrasse 2 , 80804 Munich , 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): 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L2Q (Subject of Investigation/LOI)
Query on L2Q

Download Ideal Coordinates CCD File 
B [auth A][(1~{R})-3-(3,4-dimethoxyphenyl)-1-[3-(2-morpholin-4-ylethoxy)phenyl]propyl] (2~{S})-1-[[(1~{R},4~{a}~{R},8~{a}~{R})-4-oxidanylidene-2,3,4~{a},5,6,7,8,8~{a}-octahydro-1~{H}-naphthalen-1-yl]carbonyl]piperidine-2-carboxylate
C40 H54 N2 O8
UGIVXHVIZXJHDG-YGYPXORBSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
L2Q Binding MOAD:  6SAF Ki: 230 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.555α = 90
b = 50.334β = 90
c = 62.776γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description