9C80 | pdb_00009c80

Co-structure of SARS-CoV-2 (COVID-19 with covalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.265 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9C80

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Identification of Potent, Broad-Spectrum Coronavirus Main Protease Inhibitors for Pandemic Preparedness.

Barkan, D.T.Garland, K.Zhang, L.Eastman, R.T.Hesse, M.Knapp, M.Ornelas, E.Tang, J.Cortopassi, W.A.Wang, Y.King, F.Jia, W.Nguyen, Z.Frank, A.O.Chan, R.Fang, E.Fuller, D.Busby, S.Carias, H.Donahue, K.Tandeske, L.Diagana, T.T.Jarrousse, N.Moser, H.Sarko, C.Dovala, D.Moquin, S.Marx, V.M.

(2024) J Med Chem 67: 17454-17471

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01404
  • Primary Citation Related Structures: 
    9C7W, 9C80, 9C8Q

  • PubMed Abstract: 

    The COVID-19 pandemic highlights the ongoing risk of zoonotic transmission of coronaviruses to global health. To prepare for future pandemics, it is essential to develop effective antivirals targeting a broad range of coronaviruses. Targeting the essential and clinically validated coronavirus main protease (M pro ), we constructed a structurally diverse M pro panel by clustering all known coronavirus sequences by M pro active site sequence similarity. Through screening, we identified a potent covalent inhibitor that engaged the catalytic cysteine of SARS-CoV-2 Mpro and used structure-based medicinal chemistry to develop compounds in the pyrazolopyrimidine sulfone series that exhibit submicromolar activity against multiple M pro homologues. Additionally, we solved the first X-ray cocrystal structure of M pro from the human-infecting OC43 coronavirus, providing insights into potency differences among compound-target pairs. Overall, the chemical compounds described in this study serve as starting points for the development of antivirals with broad-spectrum activity, enhancing our preparedness for emerging human-infecting coronaviruses.


  • Organizational Affiliation
    • Discovery Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States.

Macromolecule Content 

  • Total Structure Weight: 68.45 kDa 
  • Atom Count: 4,931 
  • Modeled Residue Count: 603 
  • Deposited Residue Count: 612 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AUX
(Subject of Investigation/LOI)

Query on A1AUX



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
(5R,7S,8R)-7-(2-fluorophenyl)-3-[(2-fluorophenyl)carbamoyl]-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-5-carboxylic acid
C20 H16 F2 N4 O3
RVBNUMVALXTMOF-SJORKVTESA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.265 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.78α = 90
b = 53.866β = 101.3
c = 114.04γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Database references