7JPZ

Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*.

Yang, K.S.Ma, X.R.Ma, Y.Alugubelli, Y.R.Scott, D.A.Vatansever, E.C.Drelich, A.K.Sankaran, B.Geng, Z.Z.Blankenship, L.R.Ward, H.E.Sheng, Y.J.Hsu, J.C.Kratch, K.C.Zhao, B.Hayatshahi, H.S.Liu, J.Li, P.Fierke, C.A.Tseng, C.K.Xu, S.Liu, W.R.

(2021) ChemMedChem 16: 942-948

  • DOI: https://doi.org/10.1002/cmdc.202000924
  • Primary Citation of Related Structures:  
    7JPY, 7JPZ, 7JQ0, 7JQ1, 7JQ2, 7JQ3, 7JQ4, 7JQ5

  • PubMed Abstract: 

    The COVID-19 pathogen, SARS-CoV-2, requires its main protease (SC2M Pro ) to digest two of its translated long polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replicating in infected cells and therefore provides a potential COVID-19 treatment option. Guided by previous medicinal chemistry studies about SARS-CoV-1 main protease (SC1M Pro ), we have designed and synthesized a series of SC2M Pro inhibitors that contain β-(S-2-oxopyrrolidin-3-yl)-alaninal (Opal) for the formation of a reversible covalent bond with the SC2M Pro active-site cysteine C145. All inhibitors display high potency with K i values at or below 100 nM. The most potent compound, MPI3, has as a K i value of 8.3 nM. Crystallographic analyses of SC2M Pro bound to seven inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS-CoV-2-induced cytopathogenic effect in both Vero E6 and A549/ACE2 cells. Two inhibitors, MPI5 and MPI8, completely prevented the SARS-CoV-2-induced cytopathogenic effect in Vero E6 cells at 2.5-5 μM and A549/ACE2 cells at 0.16-0.31 μM. Their virus inhibition potency is much higher than that of some existing molecules that are under preclinical and clinical investigations for the treatment of COVID-19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2M Pro inhibitors with ultra-high antiviral potency.


  • Organizational Affiliation

    Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe 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
GHX (Subject of Investigation/LOI)
Query on GHX

Download Ideal Coordinates CCD File 
B [auth A](phenylmethyl) N-[(2S)-1-oxidanylidene-1-[[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-3-phenyl-propan-2-yl]carbamate
C24 H29 N3 O5
SDSQZWABGUFEMG-ACRUOGEOSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.24α = 90
b = 53.79β = 101.31
c = 45.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
pointlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM121584

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2024-10-16
    Changes: Structure summary