1F40

SOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A NEUROTROPHIC LIGAND


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of a neurotrophic ligand bound to FKBP12 and its effects on protein dynamics.

Sich, C.Improta, S.Cowley, D.J.Guenet, C.Merly, J.P.Teufel, M.Saudek, V.

(2000) Eur.J.Biochem. 267: 5342-5354


  • PubMed Abstract: 
  • The structure of a recently reported neurotrophic ligand, 3-(3-pyridyl)-1-propyl(2S)-1-(3,3-dimethyl-1, 2-dioxopentyl)-2-pyrrolidinecarboxylate, in complex with FKBP12 was determined using heteronuclear NMR spectroscopy. The inhibitor exhibits a bind ...

    The structure of a recently reported neurotrophic ligand, 3-(3-pyridyl)-1-propyl(2S)-1-(3,3-dimethyl-1, 2-dioxopentyl)-2-pyrrolidinecarboxylate, in complex with FKBP12 was determined using heteronuclear NMR spectroscopy. The inhibitor exhibits a binding mode analogous to that observed for the macrocycle FK506, used widely as an immunosuppressant, with the prolyl ring replacing the pipecolyl moiety and the amide bond in a trans conformation. However, fewer favourable protein-ligand interactions are detected in the structure of the complex, suggesting weaker binding compared with the immunosuppressant drug. Indeed, a micromolar dissociation constant was estimated from the NMR ligand titration profile, in contrast to the previously published nanomolar inhibition activity. Although the inhibitor possesses a remarkable structural simplicity with respect to FK506, 15N relaxation studies show that it induces similar effects on the protein dynamics, stabilizing the conformation of solvent-exposed residues which are important for mediating the interaction of immunophilin/ligand complexes with molecular targets and potentially for the transmission of the neurotrophic action of FKBP12 inhibitors.


    Related Citations: 
    • Neurotrophic Immunophilin Ligands Stimulate Structural and Functional Recovery in Neurodegenerative Animal Models
      Steiner, J.P.,Hamilton, G.S.,Ross, D.T.,Valentine, H.L.,Guo, H.,Connolly, M.A.,Liang, S.,Ramsey, C.,Li, J.H.,Huang, W.,Howorth, P.,Soni, R.,Fuller, M.,Sauer, H.,Nowotnik, A.C.,Suzdak, P.D.
      (1997) Proc.Natl.Acad.Sci.USA 94: 2019
    • Atomic Structure of FKBP-FK506, an Immunophilin-immunosuppressant Complex
      van Duyne, G.D.,Staendert, R.F.,Karplus, P.A.,Schreiber, S.L.,Clardy, J.
      (1991) Science 252: 839
    • Design, Synthesis, and Kinetic Evaluation of high-affinity FKBP Ligands and the X-ray Structure of their Complexes with FKBP12
      Holt, D.A.,Luengo, J.I.,Yamashita, D.S.,Oh, H.-J.,Konalian, A.L.,Yen, H.-K.,Rozamus, L.W.,Brandt, M.,Bossard, M.J.,Levy, M.A.,Eggleston, D.S.,Lian, J.,Schultz, L.W.,Stout, T.J.,Clardy, J.
      (1993) J.Am.Chem.Soc. 115: 9925
    • 15N NMR Relaxation Studies of the FK506 Binding Protein: Dynamic Effects of Ligand Binding and Implications for Calcinerin Inhibition
      Cheng, J.W.,Lepre, C.A.,Moore, J.M.
      (1994) Biochemistry 33: 4093


    Organizational Affiliation

    Department of Structural Biology and Cheminformatics, Department of Biotechnology, Sanofi-Synthelabo, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FK506 BINDING PROTEIN (FKBP12)
A
107Homo sapiensMutation(s): 0 
Gene 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
GPI
Query on GPI

Download SDF File 
Download CCD File 
A
(2S)-[3-PYRIDYL-1-PROPYL]-1-[3,3-DIMETHYL-1,2-DIOXOPENTYL]-2-PYRROLIDINECARBOXYLATE
GPI-1046
C20 H28 N2 O4
OQAHHWOPVDDWHD-INIZCTEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GPIIC50: 1240 nM (100) BINDINGDB
GPIKi: 0 - 7.5 nM (100) BINDINGDB
GPIKd: 1000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance