4JFM

Increasing the Efficiency Efficiency of Ligands for the FK506-Binding Protein 51 by Conformational Control: Complex of FKBP51 with 2-(3,4-dimethoxyphenoxy)ethyl (2S)-1-[(2-oxo-2,3-dihydro-1,3-benzothiazol-6-yl)sulfonyl]piperidine-2-carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report



Literature

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: 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 ener ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5 A128Homo sapiensMutation(s): 1 
Gene Names: AIG6FKBP5FKBP51
EC: 5.2.1.8
Find proteins for Q13451 (Homo sapiens)
Explore Q13451 
Go to UniProtKB:  Q13451
NIH Common Fund Data Resources
PHAROS:  Q13451
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1KZ
Query on 1KZ

Download Ideal Coordinates CCD File 
A
2-(3,4-dimethoxyphenoxy)ethyl (2S)-1-[(2-oxo-2,3-dihydro-1,3-benzothiazol-6-yl)sulfonyl]piperidine-2-carboxylate
C23 H26 N2 O8 S2
LKFOEMMDLYEDRW-SFHVURJKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1KZKi:  7600   nM  BindingDB
1KZKd :  3300   nM  PDBBind
1KZKi:  7600   nM  Binding MOAD
1KZKd:  3300   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.155α = 90
b = 54.497β = 90
c = 56.418γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release