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- PDB-7ur9: SARS-Cov2 Main protease in complex with inhibitor CDD-1845 -

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Basic information

Entry
Database: PDB / ID: 7ur9
TitleSARS-Cov2 Main protease in complex with inhibitor CDD-1845
Components3C-like proteinase nsp5
KeywordsHYDROLASE/INHIBITOR / SARS-Cov2 / Main protease / inhibitor / Non-covalent / VIRAL PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease 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 toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / viral protein processing / lyase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Trypsin-like serine proteases / 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 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 / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus replicase NSP1 / 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 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. / : / :
Similarity search - Domain/homology
Chem-O5F / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsLu, S. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P20CA221729 United States
CitationJournal: Commun Chem / Year: 2023
Title: DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors.
Authors: Jimmidi, R. / Chamakuri, S. / Lu, S. / Ucisik, M.N. / Chen, P.J. / Bohren, K.M. / Moghadasi, S.A. / Versteeg, L. / Nnabuife, C. / Li, J.Y. / Qin, X. / Chen, Y.C. / Faver, J.C. / Nyshadham, P. ...Authors: Jimmidi, R. / Chamakuri, S. / Lu, S. / Ucisik, M.N. / Chen, P.J. / Bohren, K.M. / Moghadasi, S.A. / Versteeg, L. / Nnabuife, C. / Li, J.Y. / Qin, X. / Chen, Y.C. / Faver, J.C. / Nyshadham, P. / Sharma, K.L. / Sankaran, B. / Judge, A. / Yu, Z. / Li, F. / Pollet, J. / Harris, R.S. / Matzuk, M.M. / Palzkill, T. / Young, D.W.
History
DepositionApr 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)68,7344
Polymers67,6512
Non-polymers1,0832
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-15 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.720, 100.460, 104.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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
Gene: rep, 1a-1b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-O5F / (2P)-2-(isoquinolin-4-yl)-1-[4-(methylamino)-4-oxobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide


Mass: 541.642 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H31N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium chloride, 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.16→56.83 Å / Num. obs: 38932 / % possible obs: 99.95 % / Redundancy: 5.8 % / Biso Wilson estimate: 19.74 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 8.2
Reflection shellResolution: 2.16→2.237 Å / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 19638

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Processing

Software
NameVersionClassification
MOSFLM1.17.1_3660data reduction
PHENIX1.17.1_3660refinement
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K3T

7k3t


Resolution: 2.16→56.83 Å / SU ML: 0.1843 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9588
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 1962 5.04 %
Rwork0.1606 36970 -
obs0.1626 38932 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.85 Å2
Refinement stepCycle: LAST / Resolution: 2.16→56.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 0 533 5349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074948
X-RAY DIFFRACTIONf_angle_d0.85336733
X-RAY DIFFRACTIONf_chiral_restr0.0512746
X-RAY DIFFRACTIONf_plane_restr0.0055957
X-RAY DIFFRACTIONf_dihedral_angle_d15.975746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.24341100.17722612X-RAY DIFFRACTION99.96
2.21-2.270.24681510.17742601X-RAY DIFFRACTION100
2.27-2.340.24131400.17872611X-RAY DIFFRACTION100
2.34-2.420.22811210.17722621X-RAY DIFFRACTION99.96
2.42-2.50.23491620.18412581X-RAY DIFFRACTION100
2.5-2.60.23261360.17882607X-RAY DIFFRACTION100
2.6-2.720.21431310.17332642X-RAY DIFFRACTION100
2.72-2.860.221610.1752590X-RAY DIFFRACTION99.96
2.86-3.040.24871290.1672642X-RAY DIFFRACTION100
3.04-3.280.20751040.16492679X-RAY DIFFRACTION99.86
3.28-3.610.17261640.14712614X-RAY DIFFRACTION99.96
3.61-4.130.16071580.1392639X-RAY DIFFRACTION99.89
4.13-5.20.16251270.12632727X-RAY DIFFRACTION100
5.21-56.830.17841680.1742804X-RAY DIFFRACTION99.83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.190287130630.01538978745051.035851448960.495174197571-0.09679346735381.76906979718-0.02057569268760.1358443101630.0767246710799-0.0165711336743-0.0491953607272-0.0891564592893-0.1212028752910.2839636094360.04170224530780.113828395288-0.03129200129420.004740312169670.09468883318070.008827696943490.13275088824718.83669498486.4086928660724.4236893239
22.04404932341-0.151230858071-0.4098466337561.986756938590.2207842009892.35793765432-0.00621216398180.1385182904650.0868115023082-0.127435112559-0.000657138850173-0.01126999303470.0165653814243-0.0003107911161590.01272611031720.06606810770320.004433574309940.01360317113420.158045742247-0.00404801907890.115731883942-12.15602324237.8049544203132.1783791368
31.38259144280.4909752041960.3028683400440.5467846577170.08242157224061.88627330308-0.1196300918350.04706597752790.202488880777-0.05180310974390.0393378413623-0.0242145586877-0.506369733785-0.04414398286850.04366489208060.1918085672780.01101760014270.009721679615210.0780590286186-0.001848689877910.114037399116-0.44776367662411.0221094571.67147995338
44.073728726590.4468096388891.497096203880.5497058654690.3436688969542.163643861960.1462633546020.6849632137590.86362327784-0.202990293629-0.1469620103510.316754681002-0.992691805319-0.7128668978550.07098404653520.6072086771990.2764757811510.02818492612260.427493182230.201855648820.359377908823-14.18341076318.4479593611-10.1027619191
52.086753544290.478915392091-0.09226803027010.844609553626-0.2287895904632.898769179170.02200802446070.09003639450740.129861224144-0.05144389224790.0225762084058-0.086740415758-0.3751040481460.0818146099988-0.01237784472240.1586843754210.003606151528260.006101696044970.06773068641920.003600511603610.125843224018-1.251051703597.371075086830.284508030993
60.839735935109-0.2412168924950.3678426353671.88681351409-1.042864745851.94712197880.0574497367209-0.0429915843163-0.129265158678-0.04692675006030.07065483414580.06701781873160.262508507109-0.313618850983-0.108641100650.155694200873-0.0225807165233-0.03373425729630.106706947982-0.00236675498890.130891370158-8.8100715377-10.08007719119.29586718234
72.174789380220.1299863210071.973888875574.023130146790.9861298434542.880217923180.1428089984210.158787871324-0.261694163279-0.07485386151920.0757802282977-0.3879882910570.4870406933480.284526165375-0.07901572625610.2591672130130.0299389755715-0.02417851310560.15130462579-0.01040646609830.2167537688140.160621274263-16.068827381916.451597164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 200 )
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 306 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 43 )
4X-RAY DIFFRACTION4chain 'B' and (resid 44 through 70 )
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 155 )
6X-RAY DIFFRACTION6chain 'B' and (resid 156 through 243 )
7X-RAY DIFFRACTION7chain 'B' and (resid 244 through 306 )

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