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- PDB-9gmq: Crystal structure of the Mpro of SARS COV-2 in complex with the M... -

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Entry
Database: PDB / ID: 9gmq
TitleCrystal structure of the Mpro of SARS COV-2 in complex with the MG-87 inhibitor
Components3C-like proteinase nsp5
KeywordsANTIVIRAL PROTEIN / Inhibitor / Complex
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / 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 ...viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / 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 / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / 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 / membrane
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 / Carbamoyl-phosphate synthase subdomain signature 2. ...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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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 / Betacoronavirus single-stranded poly(A) binding domain / 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 / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-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 replicase NSP7 / Coronavirus 3Ecto domain 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 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
Chem-MXU / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsEl Kilani, H. / Hilgenfeld, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: J.Med.Chem. / Year: 2025
Title: Structure-Based Optimization of Pyridone alpha-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease.
Authors: Akula, R.K. / El Kilani, H. / Metzen, A. / Roske, J. / Zhang, K. / Gohl, M. / Arisetti, N. / Marsh, G.P. / Maple, H.J. / Cooper, M.S. / Karadogan, B. / Jochmans, D. / Neyts, J. / Rox, K. / ...Authors: Akula, R.K. / El Kilani, H. / Metzen, A. / Roske, J. / Zhang, K. / Gohl, M. / Arisetti, N. / Marsh, G.P. / Maple, H.J. / Cooper, M.S. / Karadogan, B. / Jochmans, D. / Neyts, J. / Rox, K. / Hilgenfeld, R. / Bronstrup, M.
History
DepositionAug 29, 2024Deposition site: PDBE / Processing site: PDBE
SupersessionJan 29, 2025ID: 8AIQ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 2.0Feb 26, 2025Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_nonpoly_scheme.auth_seq_num

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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)68,6985
Polymers67,6512
Non-polymers1,0473
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area25250 Å2
Unit cell
Length a, b, c (Å)45.941, 63.773, 103.513
Angle α, β, γ (deg.)90.000, 91.251, 90.000
Int Tables number4
Space group name H-MP1211

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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-MXU / ~{tert}-butyl ~{N}-[1-[(2~{S})-1-[[(2~{S},3~{R})-4-azanyl-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-3-cyclopropyl-1-oxidanylidene-propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate


Mass: 505.564 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H35N5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.02 M sodium/potassium phosphate, 0.1 M Bis Tris propane pH8.5, 20 % w/v PEG 3350

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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: Nov 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.19→45.972 Å / Num. obs: 30543 / % possible obs: 98.6 % / Redundancy: 6.9 % / CC1/2: 0.996 / Net I/σ(I): 10.9
Reflection shellResolution: 2.19→2.26 Å / Num. unique obs: 2505 / CC1/2: 0.852

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→45.972 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.384 / SU ML: 0.137 / Cross valid method: FREE R-VALUE / ESU R: 0.274 / ESU R Free: 0.202
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2184 1411 4.62 %
Rwork0.1664 29132 -
all0.169 --
obs-30543 98.58 %
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: 26.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20.086 Å2
2--0.061 Å20 Å2
3---0.915 Å2
Refinement stepCycle: LAST / Resolution: 2.19→45.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4734 0 73 181 4988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0114918
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164560
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.6566688
X-RAY DIFFRACTIONr_angle_other_deg0.4721.57310472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6115610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.4876.56232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05810776
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg4.427102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.70810220
X-RAY DIFFRACTIONr_chiral_restr0.0660.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021168
X-RAY DIFFRACTIONr_nbd_refined0.2040.2840
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.24147
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22412
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22594
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2172
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.28
X-RAY DIFFRACTIONr_nbd_other0.190.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0580.28
X-RAY DIFFRACTIONr_mcbond_it2.2532.5572446
X-RAY DIFFRACTIONr_mcbond_other2.2522.5582446
X-RAY DIFFRACTIONr_mcangle_it3.4774.5833054
X-RAY DIFFRACTIONr_mcangle_other3.4814.5853055
X-RAY DIFFRACTIONr_scbond_it3.1662.9512472
X-RAY DIFFRACTIONr_scbond_other3.1652.9512473
X-RAY DIFFRACTIONr_scangle_it5.1065.2443628
X-RAY DIFFRACTIONr_scangle_other5.1065.2443629
X-RAY DIFFRACTIONr_lrange_it6.72524.7875213
X-RAY DIFFRACTIONr_lrange_other6.72624.6525193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.19-2.2470.333950.23120120.23522470.9360.96993.76950.205
2.247-2.3080.2551170.18520740.18922040.960.97999.41020.171
2.308-2.3750.271080.18920530.19321740.9560.97999.4020.176
2.375-2.4480.2461020.17819650.18120920.9620.98298.8050.166
2.448-2.5280.176700.15819370.15920270.9840.98599.01330.146
2.528-2.6160.241830.17118290.17419560.9630.98397.75050.161
2.616-2.7140.261740.17817870.18119100.9590.98197.43460.168
2.714-2.8250.212790.16617220.16818050.9680.98399.77840.156
2.825-2.950.2051010.15816590.16117630.9750.98599.82980.151
2.95-3.0930.234840.16416000.16716900.9680.98499.6450.155
3.093-3.260.228680.16415300.16616040.970.98499.62590.157
3.26-3.4570.211610.16914360.17115040.9730.98499.53460.163
3.457-3.6940.196680.15613450.15814300.9810.98898.81120.154
3.694-3.9870.188640.15912350.1613440.980.98696.65180.157
3.987-4.3650.184530.1411620.14212160.9780.98999.91780.14
4.365-4.8740.169460.12910660.13111230.9820.9999.02050.131
4.874-5.6180.175410.159460.1519930.980.98999.39580.15
5.618-6.8550.228460.2037760.2058320.9710.98398.79810.201
6.855-9.5890.209310.1746180.1766660.9780.98797.44740.175
9.589-45.9720.329200.2323800.2374000.8890.9711000.238

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