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- PDB-7lmh: SARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-... -

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Basic information

Entry
Database: PDB / ID: 7lmh
TitleSARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(4-(pyridin-3-yl)phenyl)-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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / host cell endoplasmic reticulum / 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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / host cell endoplasmic reticulum / 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 / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / methylation / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / single-stranded RNA binding / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / 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. / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-Y6D / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)34,4864
Polymers33,8771
Non-polymers6103
Water4,918273
1
AAA: 3C-like proteinase
hetero molecules

AAA: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9738
Polymers67,7532
Non-polymers1,2196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3490 Å2
ΔGint-4 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.685, 82.471, 53.297
Angle α, β, γ (deg.)90.000, 105.228, 90.000
Int Tables number5
Space group name H-MC121

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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-Y6D / 2-(benzotriazol-1-yl)-~{N}-(4-pyridin-3-ylphenyl)-~{N}-(thiophen-3-ylmethyl)ethanamide


Mass: 425.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19N5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 63.51 %
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: 1.85→40 Å / Num. obs: 38249 / % possible obs: 99.42 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.019 / Net I/σ(I): 5.77
Reflection shellResolution: 1.85→1.916 Å / Num. unique obs: 3632 / CC1/2: 0.985 / % possible all: 94.9

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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: 1.85→32.319 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.381 / SU ML: 0.073 / Cross valid method: NONE / ESU R: 0.11 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2152 1905 4.981 %
Rwork0.179 36344 -
all0.181 --
obs-38249 98.973 %
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: 34.883 Å2
Baniso -1Baniso -2Baniso -3
1--0.095 Å20 Å2-0.293 Å2
2--0.042 Å2-0 Å2
3---0.185 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 43 273 2687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132494
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172298
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.6613391
X-RAY DIFFRACTIONr_angle_other_deg1.511.5865281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5415311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96822.951122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50115396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7441512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022881
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02599
X-RAY DIFFRACTIONr_nbd_refined0.2160.2456
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22214
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21237
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2196
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.213
X-RAY DIFFRACTIONr_nbd_other0.2530.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0870.216
X-RAY DIFFRACTIONr_mcbond_it3.13.3481238
X-RAY DIFFRACTIONr_mcbond_other3.0993.3471237
X-RAY DIFFRACTIONr_mcangle_it3.7925.011551
X-RAY DIFFRACTIONr_mcangle_other3.7925.0111552
X-RAY DIFFRACTIONr_scbond_it4.8523.8251256
X-RAY DIFFRACTIONr_scbond_other4.853.8271257
X-RAY DIFFRACTIONr_scangle_it6.6635.5541840
X-RAY DIFFRACTIONr_scangle_other6.6625.5561841
X-RAY DIFFRACTIONr_lrange_it8.08541.4512817
X-RAY DIFFRACTIONr_lrange_other840.7572753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8940.2511070.2152387X-RAY DIFFRACTION87.4474
1.894-1.9460.2711450.232594X-RAY DIFFRACTION99.5638
1.946-2.0030.2751290.1962573X-RAY DIFFRACTION100
2.003-2.0640.2381360.1892486X-RAY DIFFRACTION100
2.064-2.1320.2421290.1892423X-RAY DIFFRACTION99.8826
2.132-2.2060.1951390.1762292X-RAY DIFFRACTION100
2.206-2.290.2321320.1892234X-RAY DIFFRACTION99.8312
2.29-2.3830.2381310.1782138X-RAY DIFFRACTION100
2.383-2.4890.2491010.1782123X-RAY DIFFRACTION100
2.489-2.610.2541000.1841978X-RAY DIFFRACTION100
2.61-2.7510.2511090.1911900X-RAY DIFFRACTION100
2.751-2.9180.27710.1851799X-RAY DIFFRACTION100
2.918-3.1190.21830.1831702X-RAY DIFFRACTION100
3.119-3.3680.238980.191574X-RAY DIFFRACTION99.9402
3.368-3.6880.198870.1891430X-RAY DIFFRACTION100
3.688-4.1220.179670.1661319X-RAY DIFFRACTION99.9279
4.122-4.7560.184520.1491165X-RAY DIFFRACTION100
4.756-5.8170.163390.1631005X-RAY DIFFRACTION100
5.817-8.1940.181270.18788X-RAY DIFFRACTION100
8.194-32.3190.189230.162434X-RAY DIFFRACTION97.4414

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