4W9P

The Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-[(3,5-dichlorophenyl)sulfonyl]-5-[(1S)-1,2-dihydroxyethyl]-3-[2-(3,4-dimethoxyphenoxy)ethyl]-3,10-diazabicyclo[4.3.1]decan-2-one

• PDB DOI: https://doi.org/10.2210/pdb4W9P/pdb

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


• Deposited: 2014-08-27 Released: 2014-12-03 
• Deposition Author(s): Pomplun, S., Wang, Y., Kirschner, K., Kozany, C., Bracher, A., Hausch, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.207 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Rational Design and Asymmetric Synthesis of Potent and Neurotrophic Ligands for FK506-Binding Proteins (FKBPs).

Pomplun, S., Wang, Y., Kirschner, A., Kozany, C., Bracher, A., Hausch, F.

(2015) Angew Chem Int Ed Engl 54: 345-348

• PubMed: 25412894 
• DOI: https://doi.org/10.1002/anie.201408776
• Primary Citation of Related Structures:  
  4W9O, 4W9P, 4W9Q


• PubMed Abstract: 
  

  To create highly efficient inhibitors for FK506-binding proteins, a new asymmetric synthesis for pro-(S)-C(5) -branched [4.3.1] aza-amide bicycles was developed. The key step of the synthesis is an HF-driven N-acyliminium cyclization. Functionalization of the C(5)  moiety resulted in novel protein contacts with the psychiatric risk factor FKBP51, which led to a more than 280-fold enhancement in affinity. The most potent ligands facilitated the differentiation of N2a neuroblastoma cells with low nanomolar potency.

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Organizational Affiliation: 

Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804 Munich (Germany).

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 29.38 kDa 
• Atom Count: 2,345 
• Modelled Residue Count: 248 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP5	A, B [auth E]	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3JR	C [auth A], D [auth E]	(1S,5S,6R)-10-[(3,5-dichlorophenyl)sulfonyl]-5-[(1S)-1,2-dihydroxyethyl]-3-[2-(3,4-dimethoxyphenoxy)ethyl]-3,10-diazabicyclo[4.3.1]decan-2-one C26 H32 Cl2 N2 O8 S JKYLGBPUGDRSCP-GSPCLOLRSA-N
ACT	E, F [auth E]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.207 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.179	α = 90
b = 50.674	β = 115.65
c = 69.228	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Pomplun, S., Wang, Y., Kirschner, K., Kozany, C., Bracher, A., Hausch, F.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description