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

Validation slider image for 8CAE

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.