8A4Q

crystal structures of diastereomer (R,S,S)-13b (13b-H) in complex with the SARS-CoV-2 Mpro.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 2.3 of the entry. See complete history


Literature

Diastereomeric Resolution Yields Highly Potent Inhibitor of SARS-CoV-2 Main Protease.

Cooper, M.S.Zhang, L.Ibrahim, M.Zhang, K.Sun, X.Roske, J.Gohl, M.Bronstrup, M.Cowell, J.K.Sauerhering, L.Becker, S.Vangeel, L.Jochmans, D.Neyts, J.Rox, K.Marsh, G.P.Maple, H.J.Hilgenfeld, R.

(2022) J Med Chem 65: 13328-13342

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01131
  • Primary Citation of Related Structures:  
    8A4Q, 8A4T

  • PubMed Abstract: 

    SARS-CoV-2 is the causative agent behind the COVID-19 pandemic. The main protease (M pro , 3CL pro ) of SARS-CoV-2 is a key enzyme that processes polyproteins translated from the viral RNA. M pro is therefore an attractive target for the design of inhibitors that block viral replication. We report the diastereomeric resolution of the previously designed SARS-CoV-2 M pro α-ketoamide inhibitor 13b . The pure ( S,S,S )-diastereomer, 13b-K , displays an IC 50 of 120 nM against the M pro and EC 50 values of 0.8-3.4 μM for antiviral activity in different cell types. Crystal structures have been elucidated for the M pro complexes with each of the major diastereomers, the active ( S,S,S )-13b ( 13b-K ), and the nearly inactive ( R,S,S )-13b ( 13b-H ); results for the latter reveal a novel binding mode. Pharmacokinetic studies show good levels of 13b-K after inhalative as well as after peroral administration. The active inhibitor ( 13b-K ) is a promising candidate for further development as an antiviral treatment for COVID-19.


  • Organizational Affiliation

    Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V9R (Subject of Investigation/LOI)
Query on V9R

Download Ideal Coordinates CCD File 
B [auth A]~{tert}-butyl ~{N}-[1-[(2~{R})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate
C31 H41 N5 O7
FRACPXUHUTXLCX-CGBRIMPHSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.908α = 90
b = 53.672β = 101.42
c = 44.777γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 2.0: 2023-03-08
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-03-22
    Changes: Advisory
  • Version 2.2: 2023-08-23
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.3: 2024-02-07
    Changes: Refinement description