8IM6

Crystal structure of HCoV 229E main protease in complex with PF07304814


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural basis of main proteases of HCoV-229E bound to inhibitor PF-07304814 and PF-07321332.

Zhou, Y.Wang, W.Zeng, P.Feng, J.Li, D.Jing, Y.Zhang, J.Yin, X.Li, J.Ye, H.Wang, Q.

(2023) Biochem Biophys Res Commun 657: 16-23

  • DOI: https://doi.org/10.1016/j.bbrc.2023.03.043
  • Primary Citation of Related Structures:  
    7YRZ, 8IM6

  • PubMed Abstract: 

    PF-07321332 and PF-07304814, inhibitors against SARS-CoV-2 developed by Pfizer, exhibit broad-spectrum inhibitory activity against the main protease (M pro ) from various coronaviruses. Structures of PF-07321332 or PF-07304814 in complex with M pro s of various coronaviruses reveal their inhibitory mechanisms against different M pro s. However, the structural information on the lower pathogenic coronavirus M pro with PF-07321332 or PF-07304814 is currently scarce, which hinders our comprehensive understanding of the inhibitory mechanisms of these two inhibitors. Meanwhile, given that some immunocompromised individuals are still affected by low pathogenic coronaviruses, we determined the structures of lower pathogenic coronavirus HCoV-229E M pro with PF-07321332 and PF-07304814, respectively, and analyzed and defined in detail the structural basis for the inhibition of HCoV-229E M pro by both inhibitors. Further, we compared the crystal structures of multiple coronavirus M pro complexes with PF-07321332 or PF-07304814 to illustrate the differences in the interaction of M pro s, and found that the inhibition mechanism of lower pathogenic coronavirus M pro was more similar to that of moderately pathogenic coronaviruses. Our structural studies provide new insights into drug development for low pathogenic coronavirus M pro , and provide theoretical basis for further optimization of both inhibitors to contain potential future coronaviruses.


  • Organizational Affiliation

    College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
299Human coronavirus 229EMutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22
UniProt
Find proteins for P0C6X1 (Human coronavirus 229E)
Explore P0C6X1 
Go to UniProtKB:  P0C6X1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
80I (Subject of Investigation/LOI)
Query on 80I

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
[(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate
C24 H33 N4 O9 P
FQKALOFOWPDTED-WBAXXEDZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.522α = 90
b = 77.012β = 101.959
c = 74.626γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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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: 2024-03-06
    Type: Initial release