4TX0 | pdb_00004tx0

The Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-[(3,5-dichlorophenyl)sulfonyl]-5-(2-methoxyethoxy)-3-(2-methoxyethyl)-3,10-diazabicyclo[4.3.1]decan-2-one

• PDB DOI: https://doi.org/10.2210/pdb4TX0/pdb

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


• Deposited: 2014-07-02 Released: 2014-10-15 
• Deposition Author(s): Bischoff, M., Sippel, C., Bracher, A., Hausch, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 
  0.149 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.129 (Depositor) 
• R-Value Observed: 
  0.130 (Depositor) 

Starting Model: experimental

Literature

Stereoselective Construction of the 5-Hydroxy Diazabicyclo[4.3.1]decane-2-one Scaffold, a Privileged Motif for FK506-Binding Proteins.

Bischoff, M., Sippel, C., Bracher, A., Hausch, F.

(2014) Org Lett 16: 5254-5257

• PubMed: 25286062 
• DOI: https://doi.org/10.1021/ol5023195
• Primary Citation Related Structures: 
  4TX0


• PubMed Abstract: 
  

  A stereoselective synthesis of a derivatized bicyclic [4.3.1]decane scaffold based on an acyclic precursor is described. The key steps involve a Pd-catalyzed sp(3)-sp(2) Negishi-coupling, an asymmetric Shi epoxidation, and an intramolecular epoxide opening. Representative derivatives of this novel scaffold were synthesized and found to be potent inhibitors of the psychiatric risk factor FKBP51, which bound to FKBP51 with the intended molecular binding mode.

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Organizational Affiliation: 
• Max Planck Institute of Psychiatry , Kraepelinstr. 2, 80804 München, 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: 14.52 kDa 
• Atom Count: 1,345 
• Modeled 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
384	B [auth A]	(1S,5S,6R)-10-[(3,5-dichlorophenyl)sulfonyl]-5-(2-methoxyethoxy)-3-(2-methoxyethyl)-3,10-diazabicyclo[4.3.1]decan-2-one C20 H28 Cl2 N2 O6 S NVEGGBQTNWZDFS-QYZOEREBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free:  0.149 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.129 (Depositor) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.821	α = 90
b = 54.872	β = 90
c = 56.665	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Bischoff, M., Sippel, C., Bracher, A., Hausch, F.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2014-10-29
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Refinement description