1F40

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

DOI: 10.2210/pdb1F40/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-06-07 Released: 2000-11-08
Deposition Author(s): Sich, C., Improta, S., Cowley, D.J., Guenet, C., Merly, J.P., Teufel, M., Saudek, V.

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: 10951192 Search on PubMed
DOI: 10.1046/j.1432-1327.2000.01551.x
Primary Citation of Related Structures:
1F40

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 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 U S A 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:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FK506 BINDING PROTEIN (FKBP12)	A	107	Homo sapiens	Mutation(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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GPI Query on GPI Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	(2S)-[3-PYRIDYL-1-PROPYL]-1-[3,3-DIMETHYL-1,2-DIOXOPENTYL]-2-PYRROLIDINECARBOXYLATE C₂₀ H₂₈ N₂ O₄ OQAHHWOPVDDWHD-INIZCTEOSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GPI	Kd : 1000 nM PDBBind
GPI	Ki: 0.009999999776482582 nM BindingDB
GPI	Ki: 7.5 nM BindingDB
GPI	IC50: 1240 nM BindingDB
GPI	Ki: 7.5 nM BindingDB

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
OLDERADO: 1F40 Olderado