2YNB

Crystal structure of the main protease of coronavirus HKU4 in complex with a Michael acceptor SG85


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibitor for the Main Protease of Coronavirus Hku4

Ma, Q.Xiao, Y.Hilgenfeld, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-LIKE PROTEINASE
A, B
306Tylonycteris bat coronavirus HKU4Mutation(s): 0 
EC: 3.4.22.69
UniProt
Find proteins for P0C6T4 (Bat coronavirus HKU4)
Explore P0C6T4 
Go to UniProtKB:  P0C6T4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6T4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G85
Query on G85

Download Ideal Coordinates CCD File 
E [auth B]N-[(benzyloxy)carbonyl]-O-tert-butyl-L-seryl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-phenylalaninamide
C35 H48 N4 O8
JRBUWNJDFCUWEM-CRNKYVSFSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.35α = 90
b = 79.35β = 90
c = 178.67γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
XDSdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.2: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary