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- PDB-9sso: Crystal structure of SARS-CoV-2 Mpro in complex with RK-496 -

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Basic information

Entry
Database: PDB / ID: 9sso
TitleCrystal structure of SARS-CoV-2 Mpro in complex with RK-496
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Mpro / inhibitor / complex
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / endonuclease activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / methylation / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome ...viral genome replication / methyltransferase activity / endonuclease activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / methylation / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / G-quadruplex RNA binding / symbiont-mediated suppression of host ISG15-protein conjugation / mRNA guanylyltransferase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell Golgi apparatus / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding
Similarity search - Function
Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Coronavirus Nsp6 transmembrane protein profile. ...Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus replicase NSP2, N-terminal / : / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus Nsp3 ectodomain (3Ecto) profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus replicase NSP7 / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEl Kilani, H. / Hilgenfeld, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: Commun Chem / Year: 2026
Title: Structure-based macrocyclization of alpha-ketoamides leads to potent inhibitors of coronaviral and enteroviral proteases.
Authors: Akula, R.K. / El Kilani, H. / Metzen, A. / Joshi, S. / Durmaz, H. / Veenstra, R. / Roske, J. / Hurdiss, D.L. / Van Kuppeveld, F.J.M. / Rox, K. / Hilgenfeld, R. / Bronstrup, M.
History
DepositionSep 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase nsp5
B: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7624
Polymers67,6512
Non-polymers1,1112
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-9 kcal/mol
Surface area25090 Å2
Unit cell
Length a, b, c (Å)67.793, 100.178, 103.791
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3C-like proteinase nsp5 / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Chemical ChemComp-A1JQY / 1-[(3~{S},6~{S},7~{R})-7-oxidanyl-4,8-bis(oxidanylidene)-6-[[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]methyl]-5,9-diazabicyclo[14.3.1]icosa-1(19),16(20),17-trien-3-yl]-3-[2,2,2-tris(fluoranyl)ethyl]urea


Mass: 555.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H36F3N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium HEPES; MOPS (acid), 30% w/v (40% v/v PEG 500* MME; 20 % w/v PEG 20000), 0.1M Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→49.38 Å / Num. obs: 93746 / % possible obs: 99.94 % / Redundancy: 26.5 % / CC1/2: 0.999 / Net I/σ(I): 16.5
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 9284 / CC1/2: 0.567 / % possible all: 99.92

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→49.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.363 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2242 4654 4.965 %
Rwork0.1942 89088 -
all0.196 --
obs-93742 99.946 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.312 Å2
Baniso -1Baniso -2Baniso -3
1--1.728 Å2-0 Å20 Å2
2--2.569 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4707 0 78 269 5054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0114896
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164537
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6596652
X-RAY DIFFRACTIONr_angle_other_deg0.5421.57510428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1215607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.038530
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg6.41458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13410772
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.657102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.01510218
X-RAY DIFFRACTIONr_chiral_restr0.0820.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021164
X-RAY DIFFRACTIONr_nbd_refined0.210.2834
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.24208
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22404
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2201
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.26
X-RAY DIFFRACTIONr_nbd_other0.1960.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.210
X-RAY DIFFRACTIONr_mcbond_it2.6312.7392434
X-RAY DIFFRACTIONr_mcbond_other2.6152.7392434
X-RAY DIFFRACTIONr_mcangle_it3.6544.9123039
X-RAY DIFFRACTIONr_mcangle_other3.6544.9153040
X-RAY DIFFRACTIONr_scbond_it3.9563.1392462
X-RAY DIFFRACTIONr_scbond_other3.9573.1392460
X-RAY DIFFRACTIONr_scangle_it5.9325.5893613
X-RAY DIFFRACTIONr_scangle_other5.9325.5893614
X-RAY DIFFRACTIONr_lrange_it6.97927.0835217
X-RAY DIFFRACTIONr_lrange_other6.97926.8395179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.3443440.3266516X-RAY DIFFRACTION99.9126
1.642-1.6860.2923820.2926273X-RAY DIFFRACTION99.9549
1.686-1.7350.3213350.2676188X-RAY DIFFRACTION99.9234
1.735-1.7890.2753260.2515970X-RAY DIFFRACTION99.9048
1.789-1.8470.2493080.2325804X-RAY DIFFRACTION99.8693
1.847-1.9120.2612660.2225663X-RAY DIFFRACTION99.9157
1.912-1.9840.2442840.2025457X-RAY DIFFRACTION100
1.984-2.0650.2222510.1935271X-RAY DIFFRACTION99.9819
2.065-2.1570.2492680.1895040X-RAY DIFFRACTION100
2.157-2.2620.1972690.1764806X-RAY DIFFRACTION99.9803
2.262-2.3840.2212360.1864603X-RAY DIFFRACTION100
2.384-2.5280.2332260.1834376X-RAY DIFFRACTION100
2.528-2.7020.2261980.1954115X-RAY DIFFRACTION100
2.702-2.9180.2051810.1973826X-RAY DIFFRACTION99.8008
2.918-3.1950.221790.1943558X-RAY DIFFRACTION100
3.195-3.570.2351660.2013242X-RAY DIFFRACTION100
3.57-4.1190.21530.1742846X-RAY DIFFRACTION100
4.119-5.0360.1861340.1482437X-RAY DIFFRACTION99.8834
5.036-7.0850.228970.1961939X-RAY DIFFRACTION100
7.085-49.380.16510.1651158X-RAY DIFFRACTION100

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