5NH0 | pdb_00005nh0

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.232 (Depositor), 0.229 (DCC)
R-Value Work:
0.190 (Depositor)
R-Value Observed:
0.192 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6X5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8X8 Query on 8X8 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C]	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		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C]	I [auth C], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain I [auth C] Focus chain J [auth C]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth A], K [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.232 (Depositor), 0.229 (DCC)
R-Value Work: 0.190 (Depositor)
R-Value Observed: 0.192 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Zhang, L.

Hilgenfeld, R.

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