9EY3 | pdb_00009ey3

The FK1 domain of FKBP51 in complex with (3S,11S,11aS)-12-((3,5-dichlorophenyl)sulfonyl)-5-oxo-11-vinyldecahydro-1H-6,10-epiminopyrrolo[1,2-a]azonine-3-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 
    0.168 (Depositor), 0.171 (DCC) 
  • R-Value Work: 
    0.139 (Depositor), 0.150 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9EY3

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Design of Ultrapotent Tricyclic Ligands for FK506-Binding Proteins.

Krajczy, P.Meyners, C.Repity, M.L.Hausch, F.

(2024) Chemistry 30: e202401405-e202401405

  • DOI: https://doi.org/10.1002/chem.202401405
  • Primary Citation Related Structures: 
    9EY3, 9EY4

  • PubMed Abstract: 

    Access to small, rigid, and sp3-rich molecules is a major limitation in the drug discovery for challenging protein targets. FK506-binding proteins hold high potential as drug targets or enablers of molecular glues but are fastidious in the chemotypes accepted as ligands. We here report an enantioselective synthesis of a highly rigidified pipecolate-mimicking tricyclic scaffold that precisely position functional groups for interacting with FKBPs. This was enabled by a 14-step gram-scale synthesis featuring anodic oxidation, stereospecific vinylation, and N-acyl iminium cyclization. Structure-based optimization resulted in the discovery of FKBP inhibitors with picomolar biochemical and subnanomolar cellular activity that represent the most potent FKBP ligands known to date.


  • Organizational Affiliation
    • Technische Universitat Darmstadt, Chemistry, GERMANY.

Macromolecule Content 

  • Total Structure Weight: 14.48 kDa 
  • Atom Count: 1,233 
  • Modeled Residue Count: 127 
  • Deposited Residue Count: 128 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5128Homo sapiensMutation(s): 3 
Gene Names: FKBP5AIG6FKBP51
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13451
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H70
(Subject of Investigation/LOI)

Query on A1H70



Download:Ideal Coordinates CCD File
B [auth A](1~{S},4~{S},7~{S},8~{S},9~{R})-13-[3,5-bis(chloranyl)phenyl]sulfonyl-8-ethenyl-2-oxidanylidene-3,13-diazatricyclo[7.3.1.0^{3,7}]tridecane-4-carboxylic acid
C20 H22 Cl2 N2 O5 S
SRHNUYKTBCXYAO-JCECYMMASA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free:  0.168 (Depositor), 0.171 (DCC) 
  • R-Value Work:  0.139 (Depositor), 0.150 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.077α = 90
b = 54.553β = 90
c = 56.322γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Database references
  • Version 1.2: 2024-08-28
    Changes: Database references