7B9Y

Structure of the FKBP51FK1 domain in complex with the macrocyclic SAFit analogue 64a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.158 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.135 (Depositor), 0.140 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Structure-Based Design of High-Affinity Macrocyclic FKBP51 Inhibitors.

Bauder, M.Meyners, C.Purder, P.L.Merz, S.Sugiarto, W.O.Voll, A.M.Heymann, T.Hausch, F.

(2021) J Med Chem 64: 3320-3349

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02195
  • Primary Citation of Related Structures:  
    7A6W, 7A6X, 7AWX, 7B9Y, 7B9Z, 7BA0

  • PubMed Abstract: 

    The FK506-binding protein 51 (FKBP51) emerged as a key player in several diseases like stress-related disorders, chronic pain, and obesity. Linear analogues of FK506 called SAFit were shown to be highly selective for FKBP51 over its closest homologue FKBP52, allowing the proof-of-concept studies in animal models. Here, we designed and synthesized the first macrocyclic FKBP51-selective ligands to stabilize the active conformation. All macrocycles retained full FKBP51 affinity and selectivity over FKBP52 and the incorporation of polar functionalities further enhanced affinity. Six high-resolution crystal structures of macrocyclic inhibitors in complex with FKBP51 confirmed the desired selectivity-enabling binding mode. Our results show that macrocyclization is a viable strategy to target the shallow FKBP51 binding site selectively.


  • Organizational Affiliation

    Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5130Homo 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
T5B (Subject of Investigation/LOI)
Query on T5B

Download Ideal Coordinates CCD File 
B [auth A]2-cyclohexyl-12-[2-(3,4-dimethoxyphenyl)ethyl]-20,21-dihydroxy-25,26-dimethoxy-11,18,23-trioxa-4-azatetracyclo[22.3.1.113,17.04,9]nonacosa-1(27),13(29),14,16,24(28),25-hexaene-3,10-dione
C43 H55 N O11
KMMZNLFAOHLXKG-NXKLTUDVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
T5B BindingDB:  7B9Y Kd: min: 5, max: 6.9 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.158 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.135 (Depositor), 0.140 (DCC) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.51α = 90
b = 48.51β = 90
c = 105.935γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata collection
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted T5BClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyHA5565-5/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description