5A0E

Crystal structure of cyclophilin D in complex with CsA analogue, JW47.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.098 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selective Inhibition of the Mitochondrial Permeability Transition Pore Protects Against Neuro-Degeneration in Experimental Multiple Sclerosis.

Warne, J.Pryce, G.Hill, J.Shi, X.Lenneras, F.Puentes, F.Kip, M.Hilditch, L.Walker, P.Simone, M.I.Chan, A.W.E.Towers, G.J.Coker, A.R.Duchen, M.R.Szabadkai, G.Baker, D.Selwood, D.L.

(2016) J.Biol.Chem. 291: 4356

  • DOI: 10.1074/jbc.M115.700385

  • PubMed Abstract: 
  • The mitochondrial permeability transition pore is a recognized drug target for neurodegenerative conditions such as multiple sclerosis and for ischemia-reperfusion injury in the brain and heart. The peptidylprolyl isomerase, cyclophilin D (CypD, PPIF ...

    The mitochondrial permeability transition pore is a recognized drug target for neurodegenerative conditions such as multiple sclerosis and for ischemia-reperfusion injury in the brain and heart. The peptidylprolyl isomerase, cyclophilin D (CypD, PPIF), is a positive regulator of the pore, and genetic down-regulation or knock-out improves outcomes in disease models. Current inhibitors of peptidylprolyl isomerases show no selectivity between the tightly conserved cyclophilin paralogs and exhibit significant off-target effects, immunosuppression, and toxicity. We therefore designed and synthesized a new mitochondrially targeted CypD inhibitor, JW47, using a quinolinium cation tethered to cyclosporine. X-ray analysis was used to validate the design concept, and biological evaluation revealed selective cellular inhibition of CypD and the permeability transition pore with reduced cellular toxicity compared with cyclosporine. In an experimental autoimmune encephalomyelitis disease model of neurodegeneration in multiple sclerosis, JW47 demonstrated significant protection of axons and improved motor assessments with minimal immunosuppression. These findings suggest that selective CypD inhibition may represent a viable therapeutic strategy for MS and identify quinolinium as a mitochondrial targeting group for in vivo use.


    Organizational Affiliation

    the Department of Cell and Developmental Biology, University College London, London WC1E 6BT, United Kingdom.,From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom, d.selwood@ucl.ac.uk.,the Medical Research Council Centre for Medical Molecular Biology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom.,Cyprotex Discovery Ltd., 100 Barbirolli Square, Manchester M2 3AB, United Kingdom, and.,From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom, the Neuroimmunology Unit, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, United Kingdom.,the Department of Cell and Developmental Biology, University College London, London WC1E 6BT, United Kingdom, the Department of Biomedical Sciences, University of Padua, Padua 35122, Italy.,the Neuroimmunology Unit, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, United Kingdom.,From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom.,the Neuroimmunology Unit, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, United Kingdom, david.baker@qmul.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
A, B
165Homo sapiensMutation(s): 1 
Gene Names: PPIF (CYP3)
EC: 5.2.1.8
Find proteins for P30405 (Homo sapiens)
Go to Gene View: PPIF
Go to UniProtKB:  P30405
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
JW47
C, E
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
C, E
L-PEPTIDE LINKINGC4 H9 N O2ALA
SAR
Query on SAR
C, E
PEPTIDE LINKINGC3 H7 N O2GLY
MLE
Query on MLE
C, E
L-PEPTIDE LINKINGC7 H15 N O2LEU
DAL
Query on DAL
C, E
D-PEPTIDE LINKINGC3 H7 N O2

--

AUX
Query on AUX
C, E
NON-POLYMERC21 H29 N2 O3

--

MVA
Query on MVA
C, E
L-PEPTIDE LINKINGC6 H13 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.098 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.120α = 90.00
b = 69.510β = 90.00
c = 109.170γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references
  • Version 1.2: 2019-05-08
    Type: Data collection, Derived calculations, Experimental preparation, Other