5E0J

1.20 A resolution structure of Norovirus 3CL protease in complex with a triazole-based macrocyclic (21-mer) inhibitor

PDB DOI: https://doi.org/10.2210/pdb5E0J/pdb

Classification: PROTEASE/PROTEASE INHIBITOR
Organism(s): Norovirus Hu/1968/US
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2015-09-28 Released: 2016-05-04
Deposition Author(s): Lovell, S., Battaile, K.P., Mehzabeen, N., Weerawarna, P.M., Kim, Y., Kankanamalage, A.C.G., Damalanka, V.C., Lushington, G.H., Alliston, K.R., Chang, K.-O., Groutas, W.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.165
R-Value Work: 0.137
R-Value Observed: 0.138

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure-based design and synthesis of triazole-based macrocyclic inhibitors of norovirus protease: Structural, biochemical, spectroscopic, and antiviral studies.

Weerawarna, P.M., Kim, Y., Galasiti Kankanamalage, A.C., Damalanka, V.C., Lushington, G.H., Alliston, K.R., Mehzabeen, N., Battaile, K.P., Lovell, S., Chang, K.O., Groutas, W.C.

(2016) Eur J Med Chem 119: 300-318

PubMed: 27235842 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.ejmech.2016.04.013
Primary Citation of Related Structures:
5E0G, 5E0H, 5E0J

PubMed Abstract:
Outbreaks of acute gastroenteritis caused by noroviruses constitute a public health concern worldwide. To date, there are no approved drugs or vaccines for the management and prophylaxis of norovirus infections. A potentially effective strategy for the development of norovirus therapeutics entails the discovery of inhibitors of norovirus 3CL protease, an enzyme essential for noroviral replication. We describe herein the structure-based design of the first class of permeable, triazole-based macrocyclic inhibitors of norovirus 3C-like protease, as well as pertinent X-ray crystallographic, biochemical, spectroscopic, and antiviral studies.

Organizational Affiliation

Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.

Macromolecule Content

Total Structure Weight: 20.87 kDa
Atom Count: 1,514
Modelled Residue Count: 174
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Norovirus 3C-like protease	A	188	Norovirus Hu/1968/US	Mutation(s): 0 Gene Names: ORF1 EC: 3.4.22.66
UniProt
Find proteins for Q83883 (Norovirus (strain Human/NoV/United States/Norwalk/1968/GI)) Explore Q83883 Go to UniProtKB: Q83883
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q83883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5LJ Query on 5LJ Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	(phenylmethyl) ~{N}-[(12~{S},15~{S},18~{S})-15-(cyclohexylmethyl)-12-(hydroxymethyl)-9,14,17-tris(oxidanylidene)-1,8,13,16,21,22-hexazabicyclo[18.2.1]tricosa-20(23),21-dien-18-yl]carbamate C₃₃ H₄₉ N₇ O₆ ITOVOSDUKDWVAY-ZXRKZBAXSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002203 (5LJ) Query on PRD_002203	E [auth A]	(phenylmethyl) ~{N}-[(12~{S},15~{S},18~{S})-15-(cyclohexylmethyl)-12-(hydroxymethyl)-9,14,17-tris(oxidanylidene)-1,8,13,16,21,22-hexazabicyclo[18.2.1]tricosa-20(23),21-dien-18-yl]carbamate	Polypeptide / Inhibitor		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.165
R-Value Work: 0.137
R-Value Observed: 0.138
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.666	α = 90
b = 37.159	β = 110.04
c = 61.859	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Kankanamalage, A.C.G.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R01AI109039

Revision History (Full details and data files)

Version 1.0: 2016-05-04
Type: Initial release
Version 1.1: 2016-06-15
Changes: Database references
Version 1.2: 2017-09-13
Changes: Author supporting evidence, Database references, Derived calculations
Version 1.3: 2019-12-11
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description