9EUA | pdb_00009eua

The FK1 domain of FKBP51 in complex with SAFit-analog 23d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.304 (Depositor), 0.302 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.254 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

1,4-Pyrazolyl-Containing SAFit-Analogues are Selective FKBP51 Inhibitors With Improved Ligand Efficiency and Drug-Like Profile.

Buffa, V.Meyners, C.Sugiarto, W.O.Bauder, M.Gaali, S.Hausch, F.

(2024) ChemMedChem 19: e202400264-e202400264

  • DOI: https://doi.org/10.1002/cmdc.202400264
  • Primary Citation Related Structures: 
    9EU6, 9EU7, 9EU8, 9EU9, 9EUA, 9EUB, 9EUC, 9EUD, 9EUE

  • PubMed Abstract: 

    The FK506 binding protein 51 (FKBP51) is an appealing drug target due to its role in several diseases such as depression, anxiety, chronic pain and obesity. Towards this, selectivity versus the close homolog FKBP52 is essential. However, currently available FKBP51-selective ligands such as SAFit2 are too large and lack drug-like properties. Here, we present a structure activity relationship (SAR) analysis of the pipecolic ester moiety of SAFit1 and SAFit2, which culminated in the discovery of the 1,4-pyrazolyl derivative 23d, displaying a binding affinity of 0.077 µM for FKBP51, reduced molecular weight (541.7 g/mol), lower hydrophobicity (cLogP = 3.72) and higher ligand efficiency (LE = 0.25). Cocrystal structures revealed the importance of the 1,4- and 1,3,4- substitution patterns of the pyrazole ring versus the 1,4,5 arrangement.


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

Macromolecule Content 

  • Total Structure Weight: 29.09 kDa 
  • Atom Count: 1,860 
  • Modeled Residue Count: 256 
  • Deposited Residue Count: 256 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5
A, B
128Homo 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
A1H7D
(Subject of Investigation/LOI)

Query on A1H7D



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
(1-propylpyrazol-4-yl)methyl (2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate
C30 H43 N3 O6
HVWPRXIQGCFSII-IGKIAQTJSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.304 (Depositor), 0.302 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.254 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.952α = 90
b = 48.952β = 90
c = 195.947γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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: 2024-09-11
    Changes: Database references