Increasing the Efficiency Efficiency of Ligands for the FK506-Binding Protein 51 by Conformational Control: Complex of FKBP51 with 6-({(1S,5R)-3-[2-(3,4-dimethoxyphenoxy)ethyl]-2-oxo-3,9-diazabicyclo[3.3.1]non-9-yl}sulfonyl)-1,3-benzothiazol-2(3H)-one

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

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Increasing the efficiency of ligands for FK506-binding protein 51 by conformational control.

Wang, Y.Kirschner, A.Fabian, A.K.Gopalakrishnan, R.Kress, C.Hoogeland, B.Koch, U.Kozany, C.Bracher, A.Hausch, F.

(2013) J Med Chem 56: 3922-3935

  • DOI: https://doi.org/10.1021/jm400087k
  • Primary Citation of Related Structures:  
    4JFI, 4JFJ, 4JFK, 4JFL, 4JFM

  • PubMed Abstract: 

    The design of efficient ligands remains a key challenge in drug discovery. In the quest for lead-like ligands for the FK506-binding protein 51 (FKBP51), we designed two new classes of bicyclic sulfonamides to probe the contribution of conformational energy in these ligands. The [4.3.1] scaffold had consistently higher affinity compared to the [3.3.1] or monocyclic scaffolds, which could be attributed to better preorganization of two key recognition motifs. Surprisingly, the binding of the rigid [4.3.1] scaffold was enthalpy-driven and entropically disfavored compared to the flexible analogues. Cocrystal structures at atomic resolution revealed that the sulfonamide nitrogen in the bicyclic scaffolds can accept an unusual hydrogen bond from Tyr(113) that mimics the putative FKBP transition state. This resulted in the first lead-like, functionally active ligand for FKBP51. Our work exemplifies how atom-efficient ligands can be achieved by careful conformational control even in very open and thus difficult binding sites such as FKBP51.

  • Organizational Affiliation

    AG Chemical Genomics, Max Planck Institute of Psychiatry , Kraepelinstraße 2, 80804 Munich, Germany.

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: AIG6FKBP5FKBP51
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1KY

Download Ideal Coordinates CCD File 
B [auth A]6-({(1S,5R)-3-[2-(3,4-dimethoxyphenoxy)ethyl]-2-oxo-3,9-diazabicyclo[3.3.1]non-9-yl}sulfonyl)-1,3-benzothiazol-2(3H)-one
C24 H27 N3 O7 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
1KY BindingDB:  4JFL Ki: 1.39e+4 (nM) from 1 assay(s)
Kd: 1.05e+4 (nM) from 1 assay(s)
Binding MOAD:  4JFL Kd: 1.05e+4 (nM) from 1 assay(s)
PDBBind:  4JFL Kd: 1.05e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.158α = 90
b = 54.178β = 90
c = 56.244γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations