5DIV

The Fk1 domain of FKBP51 in complex with the new synthetic ligand (S)-N-(1-carbamoylcyclopentyl)-1-((S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)acetyl)piperidine-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rapid, Structure-Based Exploration of Pipecolic Acid Amides as Novel Selective Antagonists of the FK506-Binding Protein 51.

Gaali, S.Feng, X.Hahle, A.Sippel, C.Bracher, A.Hausch, F.

(2016) J.Med.Chem. 59: 2410-2422

  • DOI: 10.1021/acs.jmedchem.5b01355
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The FK506-binding protein 51 (FKBP51) is a key regulator of stress hormone receptors and an established risk factor for stress-related disorders. Drug development for FKBP51 has been impaired by the structurally similar but functionally opposing homo ...

    The FK506-binding protein 51 (FKBP51) is a key regulator of stress hormone receptors and an established risk factor for stress-related disorders. Drug development for FKBP51 has been impaired by the structurally similar but functionally opposing homologue FKBP52. High selectivity between FKBP51 and FKBP52 can be achieved by ligands that stabilize a recently discovered FKBP51-favoring conformation. However, drug-like parameters for these ligands remained unfavorable. In the present study, we replaced the potentially labile pipecolic ester group of previous FKBP51 ligands by various low molecular weight amides. This resulted in the first series of pipecolic acid amides, which had much lower molecular weights without affecting FKBP51 selectivity. We discovered a geminally substituted cyclopentyl amide as a preferred FKBP51-binding motif and elucidated its binding mode to provide a new lead structure for future drug optimization.


    Organizational Affiliation

    Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry , Kraepelinstrasse 2, 80804 Munich, Germany.,Department of Cellular Biochemistry, Max Planck Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase FKBP5
A
127Homo sapiensMutation(s): 1 
Gene Names: FKBP5 (AIG6, FKBP51)
EC: 5.2.1.8
Find proteins for Q13451 (Homo sapiens)
Go to Gene View: FKBP5
Go to UniProtKB:  Q13451
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5BH
Query on 5BH

Download SDF File 
Download CCD File 
A
(2S)-N-(1-carbamoylcyclopentyl)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)acetyl]piperidine-2-carboxamide
C29 H43 N3 O6
CLJLSNLSXOZRQP-URXFXBBRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5BHKi: 140 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.261 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 82.160α = 90.00
b = 82.160β = 90.00
c = 50.194γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-06
    Type: Database references