8IGN

Crystal structure of SARS-CoV-2 main protease in complex with RAY1216


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Preclinical evaluation of the SARS-CoV-2 M pro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir.

Chen, X.Huang, X.Ma, Q.Kuzmic, P.Zhou, B.Zhang, S.Chen, J.Xu, J.Liu, B.Jiang, H.Zhang, W.Yang, C.Wu, S.Huang, J.Li, H.Long, C.Zhao, X.Xu, H.Sheng, Y.Guo, Y.Niu, C.Xue, L.Xu, Y.Liu, J.Zhang, T.Spencer, J.Zhu, Z.Deng, W.Chen, X.Chen, S.H.Zhong, N.Xiong, X.Yang, Z.

(2024) Nat Microbiol 9: 1075-1088

  • DOI: https://doi.org/10.1038/s41564-024-01618-9
  • Primary Citation of Related Structures:  
    8IGN, 8IGO

  • PubMed Abstract: 

    Although vaccines are available for SARS-CoV-2, antiviral drugs such as nirmatrelvir are still needed, particularly for individuals in whom vaccines are less effective, such as the immunocompromised, to prevent severe COVID-19. Here we report an α-ketoamide-based peptidomimetic inhibitor of the SARS-CoV-2 main protease (M pro ), designated RAY1216. Enzyme inhibition kinetic analysis shows that RAY1216 has an inhibition constant of 8.4 nM and suggests that it dissociates about 12 times slower from M pro compared with nirmatrelvir. The crystal structure of the SARS-CoV-2 M pro :RAY1216 complex shows that RAY1216 covalently binds to the catalytic Cys145 through the α-ketoamide group. In vitro and using human ACE2 transgenic mouse models, RAY1216 shows antiviral activities against SARS-CoV-2 variants comparable to those of nirmatrelvir. It also shows improved pharmacokinetics in mice and rats, suggesting that RAY1216 could be used without ritonavir, which is co-administered with nirmatrelvir. RAY1216 has been approved as a single-component drug named 'leritrelvir' for COVID-19 treatment in China.


  • Organizational Affiliation

    School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5A [auth B],
B [auth A]
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7ON (Subject of Investigation/LOI)
Query on 7ON

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
(3~{S},3~{a}~{S},6~{a}~{R})-2-[(2~{S})-2-cyclohexyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]ethanoyl]-~{N}-[(2~{S})-4-(cyclopentylamino)-3,4-bis(oxidanylidene)-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide
C31 H44 F3 N5 O6
ICGMMLTUQDVAST-HEZDJTGRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.829α = 80.03
b = 60.935β = 68.34
c = 64.037γ = 70.67
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82341085
National Key Research and Development Program of ChinaChina2021YFA1300903
National Natural Science Foundation of China (NSFC)China82341099
National Key Research and Development Program of ChinaChina2021YFA1300904
National Key Research and Development Program of ChinaChina2022YFC0868700
Ministry of Science and Technology (MoST, China)China2021YFA1300900

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2024-04-10
    Changes: Database references
  • Version 1.3: 2024-04-17
    Changes: Database references