3R4G

Human Cyclophilin D Complexed with a Fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 
    0.139 (Depositor), 0.140 (DCC) 
  • R-Value Work: 
    0.118 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 
    0.119 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4SOClick on this verticalbar to view details

This is version 1.2 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, mitochondrial166Homo sapiensMutation(s): 1 
Gene Names: PPIFCYP3
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free:  0.139 (Depositor), 0.140 (DCC) 
  • R-Value Work:  0.118 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 0.119 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.252α = 90
b = 57.252β = 90
c = 87.172γ = 90
Software Package:
Software NamePurpose
DNAdata collection
X-PLORmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4SOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations