5N19 | pdb_00005n19

Structure of SARS coronavirus main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide

• PDB DOI: https://doi.org/10.2210/pdb5N19/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-05 Released: 2018-02-28 
• Deposition Author(s): Zhang, L., Ma, Q., Hilgenfeld, R.
• Funding Organization(s): German Center for Infection Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.200 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.172 (Depositor) 
• R-Value Observed: 
  0.174 (Depositor) 

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 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 34.52 kDa 
• Atom Count: 2,852 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS coronavirus main protease	A	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D03	B [auth A]	(S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide C33 H36 N4 O5 ZTFAWEJBUOCZIL-NHTHZNHESA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.200 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.172 (Depositor) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.196	α = 90
b = 82.284	β = 103.95
c = 53.435	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Zhang, L., Ma, Q., Hilgenfeld, R.

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

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 2.0: 2024-05-01
  Changes: Advisory, Atomic model, Data collection, Database references, Refinement description
• Version 2.1: 2024-10-23
  Changes: Structure summary