1QPF

FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

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, 1QPL

  • 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 comple ...

    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: 
    • 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., H Sigal, N., Williamson, A.R., Parsons, W.H., Wyvratt, M.
      (1998) Transplantation 65: 18
    • 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
    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (FK506-BINDING PROTEIN) A, D107Homo sapiensMutation(s): 0 
Gene Names: FKBP1A, FKBP1, FKBP12
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
NIH Common Fund Data Resources
PHAROS:  P62942
GTEx:  ENSG00000088832
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
858
Query on 858
Download Ideal Coordinates CCD File 
A, D
C32-O-(1-ETHYL-INDOL-5-YL)ASCOMYCIN
C53 H78 N2 O12
CXVGRMOIFTUTMT-IUQQQLKSSA-N		 Ligand Interaction
B7G
Query on B7G
Download Ideal Coordinates CCD File 
A
heptyl beta-D-glucopyranoside
C13 H26 O6
NIDYWHLDTIVRJT-UJPOAAIJSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
858IC50:  27   nM  Binding MOAD
858IC50 :  27   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.26α = 90
b = 74.26β = 90
c = 236.45γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-GENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary