5DIT

The Fk1 domain of FKBP51 in complex with the new synthetic ligand (1R)-3-(3,4-dimethoxyphenyl)-1-f3-[2-(morpholin-4-yl)ethoxy]phenylgpropyl(2S)-1-[(2S,3R)-2-cyclohexyl-3-hydroxybutanoyl]piperidine-2-carboxylate

• PDB DOI: https://doi.org/10.2210/pdb5DIT/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-09-01 Released: 2015-10-14 
• Deposition Author(s): Feng, X., Sippel, C., Bracher, A., Hausch, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.284 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Literature

Structure-Affinity Relationship Analysis of Selective FKBP51 Ligands.

Feng, X., Sippel, C., Bracher, A., Hausch, F.

(2015) J Med Chem 58: 7796-7806

• PubMed: 26419422 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00785
• Primary Citation of Related Structures:  
  5DIT


• PubMed Abstract: 
  

  The FK506-binding protein 51 (FKBP51) is a promising drug target for the treatment of stress-related psychiatric or metabolic disorders. Just recently, the first selective ligands for FKBP51 were reported based on an induced fit mechanism, but they are too large for a further drug development process. We therefore designed and synthesized a novel series of selective ligands to explore the requirements necessary for binding to the induced-fit conformation. All ligands of this series show no binding toward the structurally very similar antitarget FKBP52. With the cocrystal structure of the best ligand in this novel series we confirmed the induced fit mechanism. Furthermore, the structure-affinity relationship provides information about beneficial structural features, which is valuable for the development of improved FKBP51-directed drugs.

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Organizational Affiliation: 

Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry , Kraepelinstrasse 2, 80804 Munich, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.71 kDa 
• Atom Count: 1,090 
• Modelled Residue Count: 128 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP5	A	128	Homo sapiens	Mutation(s): 1  Gene Names: FKBP5, AIG6, FKBP51 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5B8	B [auth A]	(1R)-3-(3,4-dimethoxyphenyl)-1-{3-[2-(morpholin-4-yl)ethoxy]phenyl}propyl (2S)-1-[(2S,3R)-2-cyclohexyl-3-hydroxybutanoyl]piperidine-2-carboxylate C39 H56 N2 O8 RUPZPRKPEAFHDB-JEPHQYQUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5B8	BindingDB:  5DIT	Ki: 700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.284 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.371	α = 90
b = 50.22	β = 90
c = 61.811	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Feng, X., Sippel, C., Bracher, A., Hausch, F.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2015-10-21
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references