EVALUATION OF SYNTHETIC FK506 ANALOGS AS LIGANDS FOR FKBP51 AND FKBP52: COMPLEX OF FKBP51 WITH (1R)-3-(3,4-dimethoxyphenyl)-1-phenylpropyl (2S)-1-{[(1R,2S)-2-ethyl-1-hydroxycyclohexyl](oxo)acetyl}piperidine-2-carboxylate

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Evaluation of Synthetic FK506 Analogues as Ligands for the FK506-Binding Proteins 51 and 52.

Gopalakrishnan, R.Kozany, C.Gaali, S.Kress, C.Hoogeland, B.Bracher, A.Hausch, F.

(2012) J Med Chem 55: 4114-4122

  • DOI: https://doi.org/10.1021/jm201746x
  • Primary Citation of Related Structures:  
    4DRK, 4DRM, 4DRN, 4DRO, 4DRP

  • PubMed Abstract: 

    The FK506-binding proteins (FKBP) 51 and 52 are cochaperones that modulate the signal transduction of steroid hormone receptors. Both proteins have been implicated in prostate cancer. Furthermore, 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 that bind to these proteins indiscriminately but with nanomolar affinity. We here report the cocrystal structure of FKBP51 with a simplified α-ketoamide analogue derived from FK506 and the first structure-activity relationship analysis for FKBP51 and FKBP52 based on this compound. In particular, the tert-pentyl group of this ligand was systematically replaced by a cyclohexyl ring system, which more closely resembles the pyranose ring in the high-affinity ligands rapamycin and FK506. The interaction with FKBPs was found to be surprisingly tolerant to the stereochemistry of the attached cyclohexyl substituents. The molecular basis for this tolerance was elucidated by X-ray cocrystallography.

  • Organizational Affiliation

    Max Planck Institute of Psychiatry, Kraepelinstrasse 2, 80804 Munich, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5128Homo sapiensMutation(s): 0 
Gene Names: AIG6FKBP5FKBP51
UniProt & NIH Common Fund Data Resources
Find proteins for Q13451 (Homo sapiens)
Explore Q13451 
Go to UniProtKB:  Q13451
GTEx:  ENSG00000096060 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13451
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0MD

Download Ideal Coordinates CCD File 
B [auth A]{3-[(1R)-3-(3,4-dimethoxyphenyl)-1-({[(2S)-1-{[(1R,2S)-2-ethyl-1-hydroxycyclohexyl](oxo)acetyl}piperidin-2-yl]carbonyl}oxy)propyl]phenoxy}acetic acid
C35 H45 N O10
Binding Affinity Annotations 
IDSourceBinding Affinity
0MD BindingDB:  4DRO IC50: 3900 (nM) from 1 assay(s)
PDBBind:  4DRO IC50: 3900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.19α = 90
b = 54.785β = 90
c = 56.735γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description