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- PDB-9zjb: Crystal structure of MERS 3CL protease in complex with inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 9zjb
TitleCrystal structure of MERS 3CL protease in complex with inhibitor IKR-I-46
Components3C-like proteinase nsp5
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell membrane / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / viral genome replication / methyltransferase activity / endonuclease activity / methylation / SARS coronavirus main proteinase / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation ...host cell membrane / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / viral genome replication / methyltransferase activity / endonuclease activity / methylation / SARS coronavirus main proteinase / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / 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 / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / 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 / proteolysis / zinc ion binding
Similarity search - Function
Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / Coronavirus replicase NSP2, C-terminal / 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 ...Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / Coronavirus replicase NSP2, C-terminal / 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 / 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. / 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 replicase NSP7 / 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
: / Replicase polyprotein 1a
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsUng, A.R. / Lovell, S. / Battaile, K.P. / Ilesinghe, I.K.R.S. / Groutas, W.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI130092 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 nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8353
Polymers34,3141
Non-polymers5212
Water1,69394
1
A: 3C-like proteinase nsp5
hetero molecules

A: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6706
Polymers68,6282
Non-polymers1,0414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2690 Å2
ΔGint-32 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.677, 57.830, 49.760
Angle α, β, γ (deg.)90.00, 112.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3C-like proteinase nsp5 / 3CL-PRO / 3CLp / nsp5


Mass: 34314.242 Da / Num. of mol.: 1 / Fragment: UNP residues 3248-3553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Gene: 1a / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: K9N638, SARS coronavirus main proteinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A1C2K / N~2~-[(2S,4S)-3-benzyl-4-methyl-2-oxo-1,3,2lambda~5~-oxazaphospholidin-2-yl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide


Mass: 480.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H37N4O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: (25% (w/v) PEG 6000, 100 mM Hepes pH 7.0, 200 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 1, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.88→47.11 Å / Num. obs: 21817 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.057 / Rrim(I) all: 0.149 / Χ2: 1.03 / Net I/σ(I): 9.5 / Num. measured all: 149245
Reflection shellResolution: 1.88→1.92 Å / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 1.384 / Num. measured all: 10104 / Num. unique obs: 1409 / CC1/2: 0.726 / Rpim(I) all: 0.556 / Rrim(I) all: 1.493 / Χ2: 1.05 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5875: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→41.71 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 1103 5.06 %
Rwork0.1668 --
obs0.1693 21801 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 34 94 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012429
X-RAY DIFFRACTIONf_angle_d1.0543315
X-RAY DIFFRACTIONf_dihedral_angle_d16.064870
X-RAY DIFFRACTIONf_chiral_restr0.058377
X-RAY DIFFRACTIONf_plane_restr0.008419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.970.31091120.2692595X-RAY DIFFRACTION100
1.97-2.070.28651210.21052590X-RAY DIFFRACTION100
2.07-2.20.24761470.18452559X-RAY DIFFRACTION100
2.2-2.370.21481440.17272580X-RAY DIFFRACTION100
2.37-2.610.25161470.16692567X-RAY DIFFRACTION100
2.61-2.980.20311570.16642565X-RAY DIFFRACTION100
2.98-3.760.25051380.162611X-RAY DIFFRACTION100
3.76-41.710.16691370.14672631X-RAY DIFFRACTION99
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)
10.3666-0.1702-0.50730.45420.30240.7689-0.0596-0.001-0.0092-0.02770.06550.0302-0.0482-0.1117-0.00010.2645-0.0009-0.03530.26010.02050.2378-12.19476.721711.555
20.2587-0.29210.13210.3915-0.24010.1939-0.04380.15640.07880.07-0.04160.159-0.2259-0.4841-0.00030.39550.0254-0.04270.40430.02970.3087-19.694712.9188-1.433
30.0464-0.048-0.18040.5477-0.38911.218-0.03910.0272-0.0047-0.09950.0318-0.0245-0.0154-0.0377-00.1934-0.0082-0.01310.23460.00870.233-9.38892.11259.0869
40.0058-0.0225-0.01570.12370.02430.04870.10820.1865-0.0864-0.3682-0.11530.220.2118-0.13250.00010.3989-0.0235-0.03030.3707-0.05150.34-10.7674-11.03970.6678
50.59640.30060.20060.9611-0.1960.8138-0.0069-0.1603-0.1274-0.1545-0.0624-0.13590.28420.0940.00010.29880.04230.02560.270.03350.29586.2331-19.807218.5992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 183 )
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 203 )
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 303 )

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