1QPL

FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-707,587


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

32-Indolyl ether derivatives of ascomycin: three-dimensional structures of complexes with FK506-binding protein.

Becker, J.W.Rotonda, J.Cryan, J.G.Martin, M.Parsons, W.H.Sinclair, P.J.Wiederrecht, G.Wong, F.

(1999) J.Med.Chem. 42: 2798-2804

  • DOI: 10.1021/jm9806042
  • Primary Citation of Related Structures:  1QPF

  • PubMed Abstract: 
  • 32-Indole ether derivatives of tacrolimus and ascomycin retain the potent immunosuppressive activity of their parent compounds but display reduced toxicity. In addition, their complexes with the 12-kDa FK506-binding protein (FKBP) form more stable co ...

    32-Indole ether derivatives of tacrolimus and ascomycin retain the potent immunosuppressive activity of their parent compounds but display reduced toxicity. In addition, their complexes with the 12-kDa FK506-binding protein (FKBP) form more stable complexes with the protein phosphatase calcineurin, the molecular target of these drugs. We have solved the three-dimensional structures of the FKBP complexes with two 32-indolyl derivatives of ascomycin. The structures of the protein and the macrolide are remarkably similar to those seen in the complexes with tacrolimus and ascomycin. The indole groups project away from the body of the complex, and multiple conformations are observed for the linkage to these groups as well as for a nearby peptide suggesting apparent flexibility in these parts of the structure. Comparison of these structures with that of the ternary complex of calcineurin, FKBP, and tacrolimus suggests that the indole groups interact with a binding site comprising elements of both the calcineurin alpha- and beta-chains and that this interaction is responsible for the increased stability of these complexes.


    Related Citations: 
    • Preparation and in Vitro Activities of Naphthyl and Indolyl Ether Derivatives of the Fk-506 Related Immunosuppressive Macrolide Ascomycin.
      Sinclair, P.J.,Wong, F.,Staruch, M.J.,Wiederrecht, G.,Parsons, W.H.,Dumont, F.,Wyvratt, M.
      (1996) Bioorg.Med.Chem.Lett. 6: 2193
    • A Tacrolimus-Related Immunosuppressant with Biochemical Properties Distinct from Those of Tacrolimus.
      Peterson, L.B.,Cryan, J.G.,Rosa, R.,Martin, M.M.,Wilusz, M.B.,Sinclair, P.J.,Wong, F.,Parsons, J.N.,O'Keefe, S.J.,Parsons, W.H.,Wyvratt, M.,Sigal, N.H.,Williamson, A.R.,Wiederrecht, G.J.
      (1998) Transplantation 65: 10
    • A Tacrolimus-Related Immunosuppressant with Reduced Toxicity.
      Dumont, F.J.,Koprak, S.,Staruch, M.J.,Talento, A.,Koo, G.,Dasilva, C.,Sinclair, P.J.,Wong, F.,Woods, J.,Barker, J.,Pivnichny, J.,Singer, I.,Sigal, N.H.,Williamson, A.R.,Parsons, W.H.,Wyvratt, M.
      (1998) Transplantation 65: 18


    Organizational Affiliation

    Departments of Endocrinology and Chemical Biology, Medicinal Chemistry, and Immunology Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065-0900, USA. beckerj@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (FK506-BINDING PROTEIN)
A, C
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
587
Query on 587

Download SDF File 
Download CCD File 
A, C
C32-O-(1-METHYL-INDOL-5-YL) 18-HYDROXY-ASCOMYCIN
L-709,587
C52 H76 N2 O13
APSPCHLQXFEUHG-CPBVNLROSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
587IC50: 3.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.223 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 119.740α = 90.00
b = 119.740β = 90.00
c = 57.210γ = 90.00
Software Package:
Software NamePurpose
X-GENdata scaling
FBSCALEdata scaling
MERLOTphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Database references