Human Cyclophilin D Complexed with an Inhibitor

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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.

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
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens)
Explore P30405 
Go to UniProtKB:  P30405
GTEx:  ENSG00000108179 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30405
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6B4

Download Ideal Coordinates CCD File 
B [auth A]1-(4-aminobenzyl)-3-(2-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-2-oxoethyl)urea
C21 H26 N4 O2 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.818α = 90
b = 57.818β = 90
c = 88.755γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOSFLMdata reduction

Structure Validation

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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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations