5FX6

Novel inhibitors of human rhinovirus 3C protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Design and Structure-Activity Relationships of Novel Inhibitors of Human Rhinovirus 3C Protease.

Kawatkar, S.P.Gagnon, M.Hoesch, V.Tiong-Yip, C.Johnson, K.Ek, M.Nilsson, E.Lister, T.Olsson, L.Patel, J.Yu, Q.

(2016) Bioorg Med Chem Lett 26: 3248

  • DOI: 10.1016/j.bmcl.2016.05.066
  • Primary Citation of Related Structures:  
    5FX6, 5FX5

  • PubMed Abstract: 
  • Human rhinovirus (HRV) is a primary cause of common cold and is linked to exacerbation of underlying respiratory diseases such as asthma and COPD. HRV 3C protease, which is responsible for cleavage of viral polyprotein in to proteins essential for viral life-cycle, represents an important target ...

    Human rhinovirus (HRV) is a primary cause of common cold and is linked to exacerbation of underlying respiratory diseases such as asthma and COPD. HRV 3C protease, which is responsible for cleavage of viral polyprotein in to proteins essential for viral life-cycle, represents an important target. We have designed proline- and azetidine-based analogues of Rupintrivir that target the P2 pocket of the binding site. Potency optimization, aided with X-ray crystallography and quantum mechanical calculations, led to compounds with activity against a broad spectrum of HRV serotypes. Altogether, these compounds represent alternative starting points to identify promising leads in our continual efforts to treat HRV infections.


    Organizational Affiliation

    AstraZeneca Infection Innovative Medicines Unit, 35 Gatehouse Drive, Waltham, MA, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RHINOVIRUS 3C PROTEASE A182Human rhinovirus A2Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P04936 (Human rhinovirus 2)
Explore P04936 
Go to UniProtKB:  P04936
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6OY
Query on 6OY

Download Ideal Coordinates CCD File 
A
ethyl (4R)-4-[[(2S,4S)-1-[(2S)-3-methyl-2-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]butanoyl]-4-phenyl-pyrrolidin-2-yl]carbonylamino]-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pentanoate
C32 H43 N5 O7
VXYKULSXGSKGQQ-OSKYGDQXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.046α = 90
b = 77.641β = 104.99
c = 34.112γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release