3RD9 | pdb_00003rd9

Human Cyclophilin D Complexed with a Fragment

• PDB DOI: https://doi.org/10.2210/pdb3RD9/pdb

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


• Deposited: 2011-04-01 Released: 2012-03-21 
• Deposition Author(s): Colliandre, L., Ahmed-Belkacem, H., Bessin, Y., Pawlotsky, J.M., Guichou, J.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.150 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1038/ncomms12777
• Primary Citation 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.
CNRS UMR5048, Centre de Biochimie Structurale, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France.
INSERM U1054, Centre de Biochimie Structurale, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France.
Institut des Sciences Analytiques, CNRS UMR5280, Université Lyon 1, École Nationale Supérieure de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.
National Reference Center for Viral Hepatitis B, C and Delta, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, 51 avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 18.23 kDa 
• Atom Count: 1,772 
• Modeled Residue Count: 164 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A [auth X]	166	Homo sapiens	Mutation(s): 1  Gene Names: PPIF, CYP3 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MSY	B [auth X]	3-(3-methyl-5-oxo-4,5-dihydro-1H-pyrazol-1-yl)benzenesulfonamide C10 H11 N3 O3 S ASVVGQURNHNITH-UHFFFAOYSA-N
PEG	C [auth X]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.150 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.214	α = 90
b = 57.214	β = 90
c = 87.198	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description