5WKL

1.85 A resolution structure of MERS 3CL protease in complex with piperidine-based peptidomimetic inhibitor 17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element.

Galasiti Kankanamalage, A.C.Kim, Y.Damalanka, V.C.Rathnayake, A.D.Fehr, A.R.Mehzabeen, N.Battaile, K.P.Lovell, S.Lushington, G.H.Perlman, S.Chang, K.O.Groutas, W.C.

(2018) Eur J Med Chem 150: 334-346


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orf1a protein
A
313Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)Mutation(s): 0 
Find proteins for K9N638 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Go to UniProtKB:  K9N638
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AVY
Query on AVY

Download SDF File 
Download CCD File 
A
(1R,2S)-2-{[N-({[4-benzyl-1-(tert-butoxycarbonyl)piperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
bound form
C31 H48 N4 O10 S
PJEUBFINPIVQHS-IPVQETTRSA-N
 Ligand Interaction
B3J
Query on B3J

Download SDF File 
Download CCD File 
A
(1S,2S)-2-{[N-({[4-benzyl-1-(tert-butoxycarbonyl)piperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
C31 H48 N4 O10 S
PJEUBFINPIVQHS-TTZMFTMZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.253α = 90.00
b = 58.099β = 112.00
c = 49.734γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

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 General Medical SciencesUnited StatesP30GM110761

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release