4J58

Human Cyclophilin D Complexed with an Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/10.1038/ncomms12777
  • Primary Citation of Related Structures:  
    3R49, 3R4G, 3R54, 3R56, 3R57, 3R59, 3RCF, 3RCG, 3RCI, 3RCK, 3RCL, 3RD9, 3RDA, 3RDB, 3RDD, 4J58, 4J59, 4J5B, 4J5C, 4J5D, 4J5E

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase F, mitochondrial164Homo sapiensMutation(s): 1 
Gene Names: CYP3PPIF
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens)
Explore P30405 
Go to UniProtKB:  P30405
PHAROS:  P30405
GTEx:  ENSG00000108179 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30405
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
53Z
Query on 53Z

Download Ideal Coordinates CCD File 
B [auth A]1-(4-aminobenzyl)-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea
C14 H20 N4 O2
QDOWQYVYSCTSGP-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.244α = 90
b = 57.244β = 90
c = 87.621γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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