6FFS

Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors

• PDB DOI: https://doi.org/10.2210/pdb6FFS/pdb

• Classification: HYDROLASE
• Organism(s): rhinovirus A2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-09 Released: 2018-02-21 
• Deposition Author(s): Wiesmann, C., Farady, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.172 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 

Starting Model: experimental

Literature

Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors.

Namoto, K., Sirockin, F., Sellner, H., Wiesmann, C., Villard, F., Moreau, R.J., Valeur, E., Paulding, S.C., Schleeger, S., Schipp, K., Loup, J., Andrews, L., Swale, R., Robinson, M., Farady, C.J.

(2018) Bioorg Med Chem Lett 28: 906-909

• PubMed: 29433930 
• DOI: https://doi.org/10.1016/j.bmcl.2018.01.064
• Primary Citation of Related Structures:  
  6FFN, 6FFS


• PubMed Abstract: 
  

  The design and synthesis of macrocyclic inhibitors of human rhinovirus 3C protease is described. A macrocyclic linkage of the P1 and P3 residues, and the subsequent structure-based optimization of the macrocycle conformation and size led to the identification of a potent biochemical inhibitor 10 with sub-micromolar antiviral activity.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 20.75 kDa 
• Atom Count: 1,718 
• Modelled Residue Count: 182 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C Protease	A	182	rhinovirus A2	Mutation(s): 0  EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data)
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936  Go to UniProtKB:  P04936

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D8E (Subject of Investigation/LOI)	B [auth A]	~{N}-[(2~{S},5~{S},14~{S})-2-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-9-methyl-3,8,15-tris(oxidanylidene)-1,4,9-triazacyclopentadec-14-yl]-5-methyl-1,2-oxazole-3-carboxamide C26 H34 F N5 O6 NMKVYCKPYPCEGS-ACRUOGEOSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.172 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.657	α = 90
b = 77.657	β = 90
c = 87.855	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Wiesmann, C., Farady, C.

Revision History  

• Version 1.0: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2018-03-14
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary