2FKE

FK-506-BINDING PROTEIN: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX WITH THE ANTAGONIST L-685,818


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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:  

  • 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 similari ...

    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.


    Related Citations: 
    • Structure of a New Macrocyclic Antibiotic
      Taga, T.,Tanaka, H.,Goto, T.,Tada, S.
      (1987) Acta Crystallogr.,Sect.C 43: 751


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FK506 BINDING PROTEIN
A
107Homo sapiensGene Names: FKBP1A (FKBP1, FKBP12)
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Go to Gene View: FKBP1A
Go to UniProtKB:  P62942
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

Download SDF File 
Download CCD File 
A
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
K506
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FK5Kd: 0.2 nM (100) BINDINGDB
FK5Ki: 0.4 nM (100) BINDINGDB
FK5IC50: 2.3 - 1000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.154α = 90.00
b = 58.154β = 90.00
c = 55.445γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other