5N19

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.200
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C6X7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D03 Query on D03 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.200
R-Value Work: 0.172
R-Value Observed: 0.174
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.