4J59

Human Cyclophilin D Complexed with an Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities.

Ahmed-Belkacem, A.Colliandre, L.Ahnou, N.Nevers, Q.Gelin, M.Bessin, Y.Brillet, R.Cala, O.Douguet, D.Bourguet, W.Krimm, I.Pawlotsky, J.M.Guichou, J.F.

(2016) Nat Commun 7: 12777-12777

  • DOI: 10.1038/ncomms12777
  • Primary Citation of Related Structures:  
  • Also Cited By: 3RDC

  • PubMed Abstract: 
  • Cyclophilins are peptidyl-prolyl cis/trans isomerases (PPIase) that catalyse the interconversion of the peptide bond at proline residues. Several cyclophilins play a pivotal role in the life cycle of a number of viruses. The existing cyclophilin inhi ...

    Cyclophilins are peptidyl-prolyl cis/trans isomerases (PPIase) that catalyse the interconversion of the peptide bond at proline residues. Several cyclophilins play a pivotal role in the life cycle of a number of viruses. The existing cyclophilin inhibitors, all derived from cyclosporine A or sanglifehrin A, have disadvantages, including their size, potential for side effects unrelated to cyclophilin inhibition and drug-drug interactions, unclear antiviral spectrum and manufacturing issues. Here we use a fragment-based drug discovery approach using nucleic magnetic resonance, X-ray crystallography and structure-based compound optimization to generate a new family of non-peptidic, small-molecule cyclophilin inhibitors with potent in vitro PPIase inhibitory activity and antiviral activity against hepatitis C virus, human immunodeficiency virus and coronaviruses. This family of compounds has the potential for broad-spectrum, high-barrier-to-resistance treatment of viral infections.


    Organizational Affiliation

    INSERM U955 'Pathophysiology and Therapy of Chronic Viral Hepatitis and Related Cancers', Hôpital Henri Mondor, Université Paris-Est, 51 avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France.,National Reference Center for Viral Hepatitis B, C and Delta, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, 51 avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France.,Institut des Sciences Analytiques, CNRS UMR5280, Université Lyon 1, École Nationale Supérieure de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.,CNRS UMR5048, Centre de Biochimie Structurale, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France.,INSERM U1054, Centre de Biochimie Structurale, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase F, mitochondrial
A
164Homo 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
671
Query on 671

Download SDF File 
Download CCD File 
A
1-(4-aminobenzyl)-3-{2-[(2R)-2-(naphthalen-1-yl)pyrrolidin-1-yl]-2-oxoethyl}urea
C24 H26 N4 O2
MRLPPIJHRIIWJS-JOCHJYFZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.150 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.068α = 90.00
b = 57.068β = 90.00
c = 87.421γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references