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- PDB-7lmg: SARS-CoV-1 3CLPro in complex with N-(4-(1H-imidazol-4-yl)phenyl)-... -

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Basic information

Entry
Database: PDB / ID: 7lmg
TitleSARS-CoV-1 3CLPro in complex with N-(4-(1H-imidazol-4-yl)phenyl)-2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(thiophen-3-ylmethyl)acetamide
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Hydrolase/Inhibitor / 3CLPro / SARS-CoV-1 Main Protease / Inhibitor Complex / Protease / Hydrolase-Inhibitor complex
Function / homology
Function and homology information


Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / endonuclease activity / 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 / methylation / omega peptidase activity / host cell Golgi apparatus / 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 / lyase activity / 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 / RNA-directed RNA polymerase activity / proteolysis / zinc ion binding / identical protein binding / membrane
Similarity search - Function
Non-structural protein 3, SUD-N macrodomain, SARS-CoV / 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 ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / 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 / 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
DI(HYDROXYETHYL)ETHER / Chem-Y6G / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsArya, T. / Goins, C.M. / Macdonald, J.D. / Stauffer, S.R.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro ).
Authors: Han, S.H. / Goins, C.M. / Arya, T. / Shin, W.J. / Maw, J. / Hooper, A. / Sonawane, D.P. / Porter, M.R. / Bannister, B.E. / Crouch, R.D. / Lindsey, A.A. / Lakatos, G. / Martinez, S.R. / ...Authors: Han, S.H. / Goins, C.M. / Arya, T. / Shin, W.J. / Maw, J. / Hooper, A. / Sonawane, D.P. / Porter, M.R. / Bannister, B.E. / Crouch, R.D. / Lindsey, A.A. / Lakatos, G. / Martinez, S.R. / Alvarado, J. / Akers, W.S. / Wang, N.S. / Jung, J.U. / Macdonald, J.D. / Stauffer, S.R.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5815
Polymers33,8771
Non-polymers7054
Water6,287349
1
AAA: 3C-like proteinase
hetero molecules

AAA: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,16310
Polymers67,7532
Non-polymers1,4108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4110 Å2
ΔGint0 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.406, 81.915, 53.308
Angle α, β, γ (deg.)90.000, 104.981, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-526-

HOH

21AAA-808-

HOH

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Components

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


Mass: 33876.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: 1a / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P0C6U8, SARS coronavirus main proteinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-Y6G / 2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-imidazol-4-yl)phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide


Mass: 414.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N6OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 10% PEG 6000, 0.1M MES, 1mM DTT, 1mM EDTA, 3% DMSO, 10% Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.55→32.281 Å / Num. obs: 64988 / % possible obs: 96.98 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.08478 / Net I/σ(I): 7.38
Reflection shellResolution: 1.55→1.606 Å / Num. unique obs: 6356 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VB3

3vb3


Resolution: 1.6→32.281 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.665 / SU ML: 0.057 / Cross valid method: NONE / ESU R: 0.069 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2078 3275 5.04 %
Rwork0.1845 61710 -
all0.186 --
obs-64985 99.666 %
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: 28.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.001 Å2
2---0.002 Å2-0 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 49 349 2769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132510
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172322
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.6613410
X-RAY DIFFRACTIONr_angle_other_deg1.5161.5865338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.365313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29122.951122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75815401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0291512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022894
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02600
X-RAY DIFFRACTIONr_nbd_refined0.2240.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.22226
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21223
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.217
X-RAY DIFFRACTIONr_nbd_other0.1980.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0960.214
X-RAY DIFFRACTIONr_mcbond_it2.1782.7321243
X-RAY DIFFRACTIONr_mcbond_other2.1762.7311242
X-RAY DIFFRACTIONr_mcangle_it2.8764.0991559
X-RAY DIFFRACTIONr_mcangle_other2.8754.0991560
X-RAY DIFFRACTIONr_scbond_it4.0713.1241267
X-RAY DIFFRACTIONr_scbond_other4.0693.1241268
X-RAY DIFFRACTIONr_scangle_it5.3834.5351851
X-RAY DIFFRACTIONr_scangle_other5.3824.5351852
X-RAY DIFFRACTIONr_lrange_it6.73534.8452872
X-RAY DIFFRACTIONr_lrange_other6.43733.7472776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6340.322440.2994466X-RAY DIFFRACTION99.9788
1.634-1.6810.3312200.2724353X-RAY DIFFRACTION100
1.681-1.7330.2742140.2524166X-RAY DIFFRACTION99.9772
1.733-1.790.2482460.2274079X-RAY DIFFRACTION100
1.79-1.8530.2692120.2053908X-RAY DIFFRACTION100
1.853-1.9230.2191830.1953832X-RAY DIFFRACTION100
1.923-2.0010.2211980.1853671X-RAY DIFFRACTION100
2.001-2.090.222050.1883477X-RAY DIFFRACTION100
2.09-2.1920.1991840.1773361X-RAY DIFFRACTION100
2.192-2.310.1951670.1723191X-RAY DIFFRACTION100
2.31-2.450.2291680.1743007X-RAY DIFFRACTION100
2.45-2.6190.2191380.1772877X-RAY DIFFRACTION99.9668
2.619-2.8280.2061170.1822685X-RAY DIFFRACTION100
2.828-3.0980.1911270.1742435X-RAY DIFFRACTION100
3.098-3.4620.1921240.1742212X-RAY DIFFRACTION99.8717
3.462-3.9960.1841010.181953X-RAY DIFFRACTION99.5637
3.996-4.890.175920.151655X-RAY DIFFRACTION99.4875
4.89-6.8950.206680.1931281X-RAY DIFFRACTION99.7044
6.895-32.2810.18350.176724X-RAY DIFFRACTION97.0588

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