Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-68

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.

Kneller, D.W.Li, H.Galanie, S.Phillips, G.Labbe, A.Weiss, K.L.Zhang, Q.Arnould, M.A.Clyde, A.Ma, H.Ramanathan, A.Jonsson, C.B.Head, M.S.Coates, L.Louis, J.M.Bonnesen, P.V.Kovalevsky, A.

(2021) J Med Chem 64: 17366-17383

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01475
  • Primary Citation of Related Structures:  
    7N8C, 7RLS, 7RM2, 7RMB, 7RME, 7RMT, 7RMZ, 7RN4, 7RNH, 7RNK

  • PubMed Abstract: 

    Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (M pro ) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of M pro complexed with Mcule-5948770040 (compound 1 ), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1 . In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on M pro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.

  • Organizational Affiliation

    Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.

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
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5YN (Subject of Investigation/LOI)
Query on 5YN

Download Ideal Coordinates CCD File 
B [auth A]6-[4-(3,4,5-trichlorophenyl)piperazine-1-carbonyl]pyrimidine-2,4(1H,3H)-dione
C15 H13 Cl3 N4 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.205α = 90
b = 82.175β = 95.5
c = 91.33γ = 90
Software Package:
Software NamePurpose
CrysalisProdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description