12WC | pdb_000012wc

Room Temperature X-Ray Structure of SARS-CoV-2 Main Protease in Complex with noncovalent inhibitor KK-7

• PDB DOI: https://doi.org/10.2210/pdb12WC/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-04-20 Released: 2026-09-09 
• Deposition Author(s): Bhandari, D., Kovalevsky, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Noncovalent SARS-CoV-2 main protease inhibitors targeting the catalytic dyad and primed substrate binding subsites.

Bhandari, D., Kovalevskaya, K., Coates, L., Jonsson, C.B., Parvathareddy, J., Weiss, K.L., Aniana, A., Louis, J.M., Bonnesen, P.V., Kovalevsky, A.

(2026) RSC Med Chem 

• PubMed: 42657162 
• DOI: https://doi.org/10.1039/d6md00401f
• Primary Citation Related Structures: 
  12QH, 12SV, 12TA, 12WC, 12XD, 12YF, 12ZG, 12ZL, 13BW, 13CL, 13FA, 13HO


• PubMed Abstract: 
  

  SARS-CoV-2 main protease (MPro) is a proven target for drug discovery of small-molecule antiviral agents due to its crucial role in viral polyprotein processing, high structural conservation across numerous divergent variants, and the lack of similar human enzymes. Unlike covalent compounds, noncovalent inhibitors of MPro do not modify the enzyme's active site, and may offer improved safety profiles, greater chemical tractability, and better oral bioavailability without the need for pharmacokinetic enhancement. In this study, we designed, synthesized and characterized thirteen noncovalent nonpeptidic SARS-CoV-2 MPro inhibitors clustered into two series (KK and KB) of compounds. The inhibitors were designed based on our recently discovered Mcule-5948770040 and its analogue HL-3-68 designed through the structure-activity relationship study. To obtain atomic details of the inhibitors' binding we solved room-temperature X-ray structures of the MPro/inhibitor complexes, and to quantify their binding and antiviral properties we performed in vitro DSF and ITC measurements and TCID ₅₀ antiviral assays. In addition, a room-temperature neutron structure of the MPro/KB-5 complex allowed direct determination of hydrogen positions, mapping intermolecular interactions and directly visualizing the protonation states and hydrogen bonding. Improved binding affinities of KK-7 and KB-3 through KB-6 could be attributed to the observed nonconventional S-H⋯F hydrogen bond and an additional conventional hydrogen bond between the carboxamide moieties and Q189. Our study provides binding details for the designed compounds and demonstrates the feasibility of our joint X-ray/neutron structure-assisted drug design approach to generate more potent noncovalent nonpeptidic MPro inhibitors.

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Organizational Affiliation: 
• Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge TN 37831 USA [e-mail].
Department of Chemistry, Berea College Berea KY 40404 USA.
Second Target Station, Oak Ridge National Laboratory Oak Ridge TN 37831 USA.
Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center Memphis TN 38103 USA.
Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center Memphis TN USA.
Regional Biocontainment Laboratory, The University of Tennessee Health Science Center Memphis TN 38105 USA.
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS Bethesda MD 20892-0520 USA.
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory Oak Ridge TN 37831 USA [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.27 kDa 
• Atom Count: 2,543 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1DCQ( Subject of Investigation/LOI)	B [auth A]	5-fluoro-6-[4-(3,4,5-trichlorophenyl)piperazine-1-carbonyl]pyrimidine-2,4(1H,3H)-dione C15 H12 Cl3 F N4 O3 JEAJYPLXDUDMDF-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.259	α = 90
b = 82.121	β = 95.65
c = 91.386	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data collection
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-09 
Deposition Author(s): Bhandari, D., Kovalevsky, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-09-09
  Type: Initial release