3RCL

Human Cyclophilin D Complexed with a Fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

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
  • Structures With Same Primary Citation

  • 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 ...

    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 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, mitochondrialA166Homo sapiensMutation(s): 1 
Gene Names: PPIFCYP3
EC: 5.2.1.8
Find proteins for P30405 (Homo sapiens)
Explore P30405 
Go to UniProtKB:  P30405
NIH Common Fund Data Resources
PHAROS  P30405
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P4C
Query on P4C

Download CCD File 
A
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
C14 H28 O8
CTLLATPOKUEFSQ-UHFFFAOYSA-N
 Ligand Interaction
5AO
Query on 5AO

Download CCD File 
A
3-(1,3-oxazol-5-yl)aniline
C9 H8 N2 O
AIELNJDAOGTASK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.055α = 90
b = 57.055β = 90
c = 87.459γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
X-PLORmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references