8W1T

SARS-CoV-2 Main protease bound to a non-covalent non-peptidic HTS hit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

An oral non-covalent non-peptidic inhibitor of SARS-CoV-2 Mpro ameliorates viral replication and pathogenesis in vivo.

Zhou, N.E.Tang, S.Bian, X.Parai, M.K.Krieger, I.V.Flores, A.Jaiswal, P.K.Bam, R.Wood, J.L.Shi, Z.Stevens, L.J.Scobey, T.Diefenbacher, M.V.Moreira, F.R.Baric, T.J.Acharya, A.Shin, J.Rathi, M.M.Wolff, K.C.Riva, L.Bakowski, M.A.McNamara, C.W.Catanzaro, N.J.Graham, R.L.Schultz, D.C.Cherry, S.Kawaoka, Y.Halfmann, P.J.Baric, R.S.Denison, M.R.Sheahan, T.P.Sacchettini, J.C.

(2024) Cell Rep 43: 114929-114929

  • DOI: https://doi.org/10.1016/j.celrep.2024.114929
  • Primary Citation of Related Structures:  
    8W1T, 8W1U

  • PubMed Abstract: 

    Safe, effective, and low-cost oral antiviral therapies are needed to treat those at high risk for developing severe COVID-19. To that end, we performed a high-throughput screen to identify non-peptidic, non-covalent inhibitors of the SARS-CoV-2 main protease (Mpro), an essential enzyme in viral replication. NZ-804 was developed from a screening hit through iterative rounds of structure-guided medicinal chemistry. NZ-804 potently inhibits SARS-CoV-2 Mpro (0.009 μM IC 50 ) as well as SARS-CoV-2 replication in human lung cell lines (0.008 μM EC 50 ) and primary human airway epithelial cell cultures. Antiviral activity is maintained against distantly related sarbecoviruses and endemic human CoV OC43. In SARS-CoV-2 mouse and hamster disease models, NZ-804 therapy given once or twice daily significantly diminished SARS-CoV-2 replication and pathogenesis. NZ-804 synthesis is low cost and uncomplicated, simplifying global production and access. These data support the exploration of NZ-804 as a therapy for COVID-19 and future emerging sarbecovirus infections.


  • Organizational Affiliation

    Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77840, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A21 (Subject of Investigation/LOI)
Query on A1A21

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]
(5-bromopyridin-3-yl){4-[(R)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}methanone
C23 H21 Br Cl N3 O
HUHIPWIDNVSBFL-JOCHJYFZSA-N
A1AFD (Subject of Investigation/LOI)
Query on A1AFD

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B]
(5-bromopyridin-3-yl){4-[(S)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}methanone
C23 H21 Br Cl N3 O
HUHIPWIDNVSBFL-QFIPXVFZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B],
K [auth B],
L [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.146α = 79.6
b = 54.223β = 70.18
c = 59.906γ = 88.46
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release