8CAE | pdb_00008cae

Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with nirmatrelvir

PDB DOI: https://doi.org/10.2210/pdb8CAE/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia
Mutation(s): Yes

Deposited: 2023-01-24 Released: 2025-08-06
Deposition Author(s): El Kilani, H., Hilgenfeld, R.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.258 (Depositor), 0.261 (DCC)
R-Value Work:
0.176 (Depositor), 0.184 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

13b-K and Nirmatrelvir Resistance Mutations of SARS-CoV-2 Main Protease: Structural, Biochemical, and Biophysical Characterization of Free Enzymes and Inhibitor Complexes

El Kilani, H., Sun, X., Ibrahim, M.F., Curth, U., Hilgenfeld, R.

(2025) Crystals (Basel) 15

DOI: https://doi.org/10.3390/cryst15090758

Macromolecule Content

Total Structure Weight: 33.98 kDa
Atom Count: 2,402
Modeled Residue Count: 303
Deposited Residue Count: 303
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 11	A	303	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4WI (Subject of Investigation/LOI) Query on 4WI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C₂₃ H₃₄ F₃ N₅ O₄ WDVIRQQKRMIXGS-XIFHJVQQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.258 (Depositor), 0.261 (DCC)
R-Value Work: 0.176 (Depositor), 0.184 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.208	α = 90
b = 53.761	β = 101.585
c = 45.551	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Funding Organization	Location	Grant Number
European Commission	European Union	--

Revision History (Full details and data files)

Version 1.0: 2025-08-06
Type: Initial release
Version 1.1: 2025-09-03
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.