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)

• PDB DOI: https://doi.org/10.2210/pdb5NH0/pdb

• Classification: HYDROLASE
• Organism(s): Human coronavirus NL63
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-21 Released: 2018-05-16 
• Deposition Author(s): Zhang, L., Hilgenfeld, R.
• Funding Organization(s): German Center for Infection Research (DZIF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.232 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Starting Model: other

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 98.82 kDa 
• Atom Count: 7,396 
• Modelled Residue Count: 898 
• Deposited Residue Count: 900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B, C	300	Human coronavirus NL63	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22
UniProt
Find proteins for P0C6X5 (Human coronavirus NL63) Explore P0C6X5  Go to UniProtKB:  P0C6X5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8X8	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	I [auth C], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	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 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.65	α = 90
b = 211.29	β = 90
c = 118.26	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
SCALA	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Zhang, L., Hilgenfeld, R.

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Funding Organization	Location	Grant Number
German Center for Infection Research (DZIF)	Germany	TTU 01.803

Revision History  

• 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