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- PDB-9zj2: Crystal structure of SARS-CoV-2 3CL protease in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 9zj2
TitleCrystal structure of SARS-CoV-2 3CL protease in complex with inhibitor AMJ-II-122
Components3C-like proteinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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 ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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 / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / 5'-3' DNA helicase activity / mRNA guanylyltransferase / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / mRNA guanylyltransferase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA helicase / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / symbiont-mediated suppression of host NF-kappaB cascade / SARS-CoV-2 modulates host translation machinery / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell Golgi apparatus / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lyase activity / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / 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 / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
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 / : ...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. / 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.
Similarity search - Domain/homology
: / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLovell, S. / Cooper, A. / Battaile, K.P. / Jesri, A.R.M. / Groutas, W.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI161085 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2026
Title: Structure-guided design of broad-spectrum inhibitors of coronaviral proteases embodying a 1,3,2-oxazaphospholidin-3-one scaffold as a versatile design element.
Authors: Nguyen, H.N. / Ranasinghe, P.S. / Ilesinghe, I.K.R.S. / Dampalla, C.S. / Rathnayake, A.D. / Liska, Z. / Jesri, A.M. / Azmi, Z. / Nevonen, D.E. / Kim, Y. / Ung, A.R. / Taylor, K.E. / Cooper, ...Authors: Nguyen, H.N. / Ranasinghe, P.S. / Ilesinghe, I.K.R.S. / Dampalla, C.S. / Rathnayake, A.D. / Liska, Z. / Jesri, A.M. / Azmi, Z. / Nevonen, D.E. / Kim, Y. / Ung, A.R. / Taylor, K.E. / Cooper, A. / Liu, L. / Battaile, K.P. / Thurman, H.A. / Gusachenko, E. / Lovell, S. / Groutas, W.C. / Chang, K.O.
History
DepositionDec 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 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
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5575
Polymers68,1382
Non-polymers1,4193
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.569, 98.817, 59.070
Angle α, β, γ (deg.)90.00, 108.22, 90.00
Int Tables number4
Space group name H-MP1211

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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: 34068.805 Da / Num. of mol.: 2 / Fragment: Full Length
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-A1C2R / N~2~-({[(2S,4S)-2-[(4-fluorophenyl)methoxy]-3-(2-methylpropyl)-2-oxo-1,3,2lambda~5~-oxazaphospholidin-4-yl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide


Mass: 612.627 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H42FN4O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG 3350, 200 mM sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97956 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 27, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 1.5→49.41 Å / Num. obs: 96668 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Rrim(I) all: 0.067 / Χ2: 0.99 / Net I/σ(I): 13 / Num. measured all: 666718
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.125 / Num. measured all: 32629 / Num. unique obs: 4772 / CC1/2: 0.793 / Rpim(I) all: 0.461 / Rrim(I) all: 1.217 / Χ2: 1.06 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.41 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 4890 5.06 %
Rwork0.1634 --
obs0.1646 96620 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 97 491 5134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094914
X-RAY DIFFRACTIONf_angle_d1.0096715
X-RAY DIFFRACTIONf_dihedral_angle_d12.2651822
X-RAY DIFFRACTIONf_chiral_restr0.058769
X-RAY DIFFRACTIONf_plane_restr0.009882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.28071660.26673048X-RAY DIFFRACTION100
1.52-1.530.30391420.2573057X-RAY DIFFRACTION100
1.53-1.550.27271590.253074X-RAY DIFFRACTION100
1.55-1.570.26571770.23793015X-RAY DIFFRACTION100
1.57-1.590.24981610.22493049X-RAY DIFFRACTION100
1.59-1.620.27281550.24433031X-RAY DIFFRACTION100
1.62-1.640.26511790.23323081X-RAY DIFFRACTION100
1.64-1.660.27021430.22592993X-RAY DIFFRACTION100
1.66-1.690.22641870.20973101X-RAY DIFFRACTION100
1.69-1.720.22761600.19613000X-RAY DIFFRACTION100
1.72-1.750.23741850.18483039X-RAY DIFFRACTION100
1.75-1.780.22921360.18223069X-RAY DIFFRACTION100
1.78-1.810.21371530.17323081X-RAY DIFFRACTION100
1.81-1.850.20741720.16563049X-RAY DIFFRACTION100
1.85-1.890.18651560.16833018X-RAY DIFFRACTION100
1.89-1.930.18061830.17553073X-RAY DIFFRACTION100
1.93-1.980.20121610.17213076X-RAY DIFFRACTION100
1.98-2.040.19411740.15523013X-RAY DIFFRACTION100
2.04-2.10.1711540.16363068X-RAY DIFFRACTION100
2.1-2.160.17981700.15463028X-RAY DIFFRACTION100
2.16-2.240.19221720.15893049X-RAY DIFFRACTION100
2.24-2.330.21231440.15783086X-RAY DIFFRACTION100
2.33-2.440.18651520.15693078X-RAY DIFFRACTION100
2.44-2.560.19421600.15653077X-RAY DIFFRACTION100
2.56-2.730.18931740.16123031X-RAY DIFFRACTION100
2.73-2.940.19281560.16073092X-RAY DIFFRACTION100
2.94-3.230.16471530.16153068X-RAY DIFFRACTION100
3.23-3.70.17281590.153097X-RAY DIFFRACTION100
3.7-4.660.14631780.13113071X-RAY DIFFRACTION100
4.66-49.410.18441690.16363118X-RAY DIFFRACTION100
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)
12.45690.85550.03611.4813-0.58540.7348-0.0411-0.13530.05210.0804-0.0428-0.0699-0.02120.0530.00020.1796-0.0024-0.00870.20670.01140.180211.805610.739724.1968
20.8182-0.0297-0.60911.1394-0.27551.19250.03060.0444-0.1424-0.2258-0.0261-0.09130.1907-0.4888-0.0010.2876-0.081-0.00560.32080.03440.18691.676215.0699-6.6401
30.614-0.18630.11842.5175-0.65360.5712-0.03620.0698-0.0449-0.23350.10360.18940.0168-0.0260.00240.1689-0.0168-0.00450.15730.00880.1697-17.2326-5.481316.2766
40.3095-0.525-0.01430.7420.01890.4656-0.01760.0258-0.0709-0.36950.16630.27910.00080.08290.3080.266-0.0302-0.09280.18450.03010.2628-22.581913.13711.067
50.43080.0356-0.07110.45330.36350.35250.0485-0.02020.1293-0.08870.0130.2043-0.1076-0.067-0.00010.2118-0.0313-0.03030.21970.03230.2662-23.137729.186518.6283
60.63950.51370.07430.60970.53730.6355-0.03530.0216-0.0733-0.19320.17990.0291-0.04960.24010.00010.2505-0.0298-0.01760.2341-0.00210.2063-15.313727.641314.9316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 200 )
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 300 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 180 )
4X-RAY DIFFRACTION4chain 'B' and (resid 181 through 213 )
5X-RAY DIFFRACTION5chain 'B' and (resid 214 through 260 )
6X-RAY DIFFRACTION6chain 'B' and (resid 261 through 302 )

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