Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


FK-506-binding protein: three-dimensional structure of the complex with the antagonist L-685,818.

Becker, J.W.Rotonda, J.McKeever, B.M.Chan, H.K.Marcy, A.I.Wiederrecht, G.Hermes, J.D.Springer, J.P.

(1993) J Biol Chem 268: 11335-11339

  • Primary Citation of Related Structures:  
    1FKD, 2FKE

  • PubMed Abstract: 

    L-685,818 differs only slightly in structure from the immunosuppressive drug FK-506, and both compounds bind with comparable affinity to the 12-kDa FK-506-binding protein (FKBP12), the major intracellular receptor for the drug. Despite these similarities, L-685,818 is a potent antagonist of both the immunosuppressive and toxic effects of the drug. Here, we present a structural analysis of this problem. Although FK-506 and L-685,818 differ greatly in pharmacology, we have found that the three-dimensional structures of their complexes with FKBP12 are essentially identical. Approximately half of each ligand is in contact with the receptor protein, and half is exposed to solvent; the exposed region includes the two sites where the compounds differ. These results indicate that the profound differences in the pharmacology of these two compounds are not caused by any difference in their interaction with FKBP12. Rather, these effects arise because relatively minor changes in the exposed part of a bound ligand have a strong effect on how FKBP12-ligand complexes interact with calcineurin, their putative intracellular target. In addition, FK-506 complexes with FKBP12 proteins from several species all inhibit mammalian calcineurin. Analysis of the three-dimensional structure of the complex with respect to residues conserved among these proteins suggests a small number of surface residues near the bound ligands that may play a critical role in interactions between the protein-drug complex and calcineurin.

  • Organizational Affiliation

    Department of Biophysical Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065-0900.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FK506 BINDING PROTEIN107Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
PHAROS:  P62942
GTEx:  ENSG00000088832 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62942
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FK5

Download Ideal Coordinates CCD File 
C44 H69 N O12
Binding Affinity Annotations 
IDSourceBinding Affinity
FK5 BindingDB:  2FKE Ki: 0.4 (nM) from 1 assay(s)
Kd: 0.2 (nM) from 1 assay(s)
IC50: min: 2.3, max: 1000 (nM) from 3 assay(s)
EC50: 0.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.72 Å
  • R-Value Observed: 0.180 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.154α = 90
b = 58.154β = 90
c = 55.445γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations