5NH0

Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide tert-Butyl ((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)b- utan-2-yl)carbamate (tert-butyl -GlnLactam-CO-CO-NH-benzyl)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8X8Click on this verticalbar to view details

This is version 2.2 of the entry. See complete history


Literature

Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication

Lin, D.Zhang, L.Kusov, Y.Nian, Y.Ma, Q.Wang, J.Leyssen, P.Lanko, K.Neyts, J.de Wilde, A.Snijder, E.J.Liu, H.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, C
300Human coronavirus NL63Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22
UniProt
Find proteins for P0C6X5 (Human coronavirus NL63)
Explore P0C6X5 
Go to UniProtKB:  P0C6X5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8X8
Query on 8X8

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth C]
~{tert}-butyl ~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]carbamate
C20 H29 N3 O5
NGJBFZBVEKPTLR-HRCADAONSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth C],
J [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
K [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.65α = 90
b = 211.29β = 90
c = 118.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8X8Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Center for Infection Research (DZIF)GermanyTTU 01.803

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 2.0: 2021-04-28
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2024-11-13
    Changes: Structure summary