Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18005.56 
• Atom Count: 1303 
• Residue Count: 166 
• Unique protein chains: 1

3R59

Human Cyclophilin D Complexed with a Fragment

• DOI: 10.2210/pdb3R59/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2011-03-18 Released: 2012-03-21 
• Deposition Author(s): Colliandre, L., Ahmed-Belkacem, H., Bessin, Y., Pawlotsky, J.M., Guichou, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å
• R-Value Free: 0.153 
• R-Value Work: 0.134 

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

• PubMed: 27652979 
• DOI: 10.1038/ncomms12777
• Primary Citation of Related Structures:  
  4J5E, 4J5D, 4J5C, 4J5B, 4J59, 4J58, 3RDD, 3RDB, 3RDA, 3RD9, 3RCL, 3RCK, 3RCI, 3RCG, 3RCF, 3R57, 3R56, 3R54, 3R4G, 3R49
• 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 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.

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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: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A	166	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
3AO	A	1-(3-aminophenyl)ethanone C8 H9 N O CKQHAYFOPRIUOM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å
• R-Value Free: 0.153 
• R-Value Work: 0.134 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 57.379	α = 90.00
b = 57.379	β = 90.00
c = 87.784	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
DNA	data collection
X-PLOR	phasing
X-PLOR	model building
SCALA	data scaling
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-18 
• Released Date: 2012-03-21 
• Deposition Author(s): Colliandre, L., Ahmed-Belkacem, H., Bessin, Y., Pawlotsky, J.M., Guichou, J.F.

Revision History 

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