Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 14.59 kDa 
• Atom Count: 1273 
• Residue Count: 127 
• Unique protein chains: 1

4JFI

Increasing the Efficiency Efficiency of Ligands for the FK506-Binding Protein 51 by Conformational Control: Complex of FKBP51 with compound 1-[(9S,13R,13aR)-1,3-dimethoxy-8-oxo-5,8,9,10,11,12,13,13a-octahydro-6H-9,13-epiminoazocino[2,1-a]isoquinolin-14-yl]-2-(3,4,5-trimethoxyphenyl)ethane-1,2-dione

• DOI: 10.2210/pdb4JFI/pdb

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


• Deposited: 2013-02-28 Released: 2013-08-28 
• Deposition Author(s): Wang, Y., Kirschner, A., Fabian, A., Gopalakrishnan, R., Kress, C., Hoogeland, B., Koch, U., Kozany, C., Bracher, A., Hausch, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.158 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

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

• PubMed: 23647266 
• 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 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.

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Organizational Affiliation: 

AG Chemical Genomics, Max Planck Institute of Psychiatry , Kraepelinstraße 2, 80804 Munich, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP5	A	127	Homo sapiens	Mutation(s): 1  Gene Names: AIG6, FKBP5, FKBP51 EC: 5.2.1.8
Find proteins for Q13451 (Homo sapiens) Explore Q13451  Go to UniProtKB:  Q13451
NIH Common Fund Data Resources
PHAROS:  Q13451 GTEx:  ENSG00000096060

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1KT	A	1-[(9S,13R,13aR)-1,3-dimethoxy-8-oxo-5,8,9,10,11,12,13,13a-octahydro-6H-9,13-epiminoazocino[2,1-a]isoquinolin-14-yl]-2-(3,4,5-trimethoxyphenyl)ethane-1,2-dione C28 H32 N2 O8 ODLXCGSAEOWAKV-IMWIBFENSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1KT	Ki:  18100   nM  Binding MOAD
1KT	Ki :  18100   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.158 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.051	α = 90
b = 54.192	β = 90
c = 55.96	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-28 
• Released Date: 2013-08-28 
Deposition Author(s): Wang, Y., Kirschner, A., Fabian, A., Gopalakrishnan, R., Kress, C., Hoogeland, B., Koch, U., Kozany, C., Bracher, A., Hausch, F.

Revision History 

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