4DRQ

Exploration of Pipecolate Sulfonamides as Binders of the FK506-Binding Proteins 51 and 52: Complex of FKBP51 with 2-(3-((R)-1-((S)-1-(3,5-dichlorophenylsulfonyl)piperidine-2-carbonyloxy)-3-(3,4-dimethoxy -phenyl)propyl)phenoxy)acetic acid

• PDB DOI: https://doi.org/10.2210/pdb4DRQ/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-17 Released: 2012-04-18 
• Deposition Author(s): Gopalakrishnan, R., Kozany, C., Wang, Y., Hoogeland, B., Bracher, A., Hausch, F., Schneider, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.151 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 

Starting Model: experimental

Literature

Exploration of Pipecolate Sulfonamides as Binders of the FK506-Binding Proteins 51 and 52.

Gopalakrishnan, R., Kozany, C., Wang, Y., Schneider, S., Hoogeland, B., Bracher, A., Hausch, F.

(2012) J Med Chem 55: 4123-4131

• PubMed: 22455398 
• DOI: https://doi.org/10.1021/jm201747c
• Primary Citation of Related Structures:  
  4DRQ


• PubMed Abstract: 
  

  FK506-binding proteins (FKBP) 51 and 52 are cochaperones that modulate the signal transduction of steroid hormone receptors. Single nucleotide polymorphisms in the gene encoding FKBP51 have been associated with a variety of psychiatric disorders. Rapamycin and FK506 are two macrocyclic natural products, which tightly bind to most FKBP family members, including FKBP51 and FKBP52. A bioisosteric replacement of the α-ketoamide moiety of rapamycin and FK506 with a sulfonamide was envisaged with the retention of the conserved hydrogen bonds. A focused solid support-based synthesis protocol was developed, which led to ligands with submicromolar affinity for FKBP51 and FKBP52. The molecular binding mode for one sulfonamide analogue was confirmed by X-ray crystallography.

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Organizational Affiliation: 

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: 14.69 kDa 
• Atom Count: 1,341 
• 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): 0  Gene Names: AIG6, FKBP5, 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
0OS	B [auth A]	{3-[(1S)-1-[({(2S)-1-[(3,5-dichlorophenyl)sulfonyl]piperidin-2-yl}carbonyl)oxy]-3-(3,4-dimethoxyphenyl)propyl]phenoxy}acetic acid C31 H33 Cl2 N O9 S AOMAGJKZRYWVSR-SVBPBHIXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.151 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.966	α = 90
b = 54.641	β = 90
c = 56.596	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Gopalakrishnan, R., Kozany, C., Wang, Y., Hoogeland, B., Bracher, A., Hausch, F., Schneider, S.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.3: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description