4ZRO

2.1 A X-Ray Structure of FIPV-3CLpro bound to covalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0566 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structure and inhibition of the feline infectious peritonitis virus 3C-like protease: Structural implications for drug design.

St John, S.E.Therkelsen, M.D.Nyalapatla, P.R.Osswald, H.L.Ghosh, A.K.Mesecar, A.D.

(2015) Bioorg.Med.Chem.Lett. 25: 5072-5077

  • DOI: 10.1016/j.bmcl.2015.10.023

  • PubMed Abstract: 
  • Feline infectious peritonitis (FIP) is a deadly disease that effects both domestic and wild cats and is caused by a mutation in feline coronavirus (FCoV) that allows the virus to replicate in macrophages. Currently, there are no treatments or vaccine ...

    Feline infectious peritonitis (FIP) is a deadly disease that effects both domestic and wild cats and is caused by a mutation in feline coronavirus (FCoV) that allows the virus to replicate in macrophages. Currently, there are no treatments or vaccines available for the treatment of FIP even though it kills approximately 5% of cats in multi-cat households per year. In an effort to develop small molecule drugs targeting FIP for the treatment of cats, we screened a small set of designed peptidomimetic inhibitors for inhibition of FIPV-3CL(pro), identifying two compounds with low to sub-micromolar inhibition, compound 6 (IC50=0.59±0.06 μM) and compound 7 (IC50=1.3±0.1 μM). We determined the first X-ray crystal structure of FIPV-3CL(pro) in complex with the best inhibitor identified, compound 6, to a resolution of 2.10 Å to better understand the structural basis for inhibitor specificity. Our study provides important insights into the structural requirements for the inhibition of FIPV-3CL(pro) by peptidomimetic inhibitors and expands the current structural knowledge of coronaviral 3CL(pro) architecture.


    Organizational Affiliation

    Departments of Biochemistry and Biological Sciences, Purdue University, West Lafayette, IN, USA; Centers for Cancer Research & Drug Discovery, Purdue University, West Lafayette, IN, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3C-like proteinase
A, B, C, D
299Feline coronavirus (strain FIPV WSU-79/1146)Mutation(s): 0 
Gene Names: rep
Find proteins for Q98VG9 (Feline coronavirus (strain FIPV WSU-79/1146))
Go to UniProtKB:  Q98VG9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bounded inhibitor of N-(tert-butoxycarbonyl)-L-seryl-L-valyl-N-{(2S)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-leucinamide
E, F, G, H
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0566 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.449α = 90.00
b = 101.896β = 90.00
c = 110.158γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI085089
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI26603

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations