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- PDB-9pal: Crystal structure of HCoV-HKU1 3CLpro with ALG-097655 (Inhibitor 2) -

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Basic information

Entry
Database: PDB / ID: 9pal
TitleCrystal structure of HCoV-HKU1 3CLpro with ALG-097655 (Inhibitor 2)
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / Hydrolase/Inhibitor / HCoV-HKU1 / 3CL pro / Mpro / Nsp5 / ALG-097655 / Inhibitor 2 / pan coronavirus drug
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 / 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 / RNA-directed RNA polymerase activity / proteolysis / zinc ion binding
Similarity search - Function
Coronavirus Nsp3 DPUP domain / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / NSP3, DPUP domain, murine hepatitis virus-like / Non-structural protein 2, MHV-like / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / NSP1, C-terminal domain, betacoronavirus ...Coronavirus Nsp3 DPUP domain / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / NSP3, DPUP domain, murine hepatitis virus-like / Non-structural protein 2, MHV-like / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / 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 (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 speciesHuman coronavirus HKU1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.54 Å
AuthorsReddem, E.R. / Forouhar, F. / Shapiro, L. / Stoycheva, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)MAVDA-1U19AI1711401 United States
Bill & Melinda Gates FoundationINV-016167 United States
CitationJournal: Structure / Year: 2026
Title: Structural basis for pan-coronavirus inhibition of 3CL protease.
Authors: Reddem, E.R. / Forouhar, F. / Liu, C. / Stevens, S.K. / Jekle, A. / Chang, C.W. / Oswal, N. / McGowan, D.C. / Vandyck, K. / Smith, D.B. / Raboisson, P. / Beigelman, L.N. / Katsamba, P.S. / ...Authors: Reddem, E.R. / Forouhar, F. / Liu, C. / Stevens, S.K. / Jekle, A. / Chang, C.W. / Oswal, N. / McGowan, D.C. / Vandyck, K. / Smith, D.B. / Raboisson, P. / Beigelman, L.N. / Katsamba, P.S. / Bahna, F. / Mannepalli, S. / Blatt, L. / Perlin, D. / Symons, J.A. / Shapiro, L. / Stoycheva, A.D.
History
DepositionJun 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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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)67,6034
Polymers66,4442
Non-polymers1,1592
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein exits as a homodimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-18 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.642, 107.796, 131.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-564-

HOH

21B-584-

HOH

31B-587-

HOH

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Components

#1: Protein 3C-like proteinase nsp5 / 3CL-PRO / 3CLp / M-PRO / nsp5 / p27


Mass: 33222.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus HKU1 / Gene: 1a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0C6U3, SARS coronavirus main proteinase
#2: Chemical ChemComp-A1CHJ / (1R,2S,3S,6R,7S)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-[(2S)-4,4,4-trifluoro-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-4-azatricyclo[5.2.1.0~2,6~]dec-8-ene-3-carboxamide (non-preferred name)


Mass: 579.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H31F6N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium thiocyanate, 0.1 M Bis-Tris pH 8.5 and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.51→34.66 Å / Num. obs: 23414 / % possible obs: 98.3 % / Redundancy: 13.5 % / CC1/2: 0.95 / Net I/σ(I): 2.5
Reflection shellResolution: 2.51→2.53 Å / Num. unique obs: 3000 / CC1/2: 0.35

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MIRAS / Resolution: 2.54→34.41 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2889 1083 4.63 %
Rwork0.2088 --
obs0.2125 23414 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 80 174 4850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084794
X-RAY DIFFRACTIONf_angle_d1.0576545
X-RAY DIFFRACTIONf_dihedral_angle_d16.5011697
X-RAY DIFFRACTIONf_chiral_restr0.054753
X-RAY DIFFRACTIONf_plane_restr0.007821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.660.41291340.30932780X-RAY DIFFRACTION100
2.66-2.80.35381480.27862726X-RAY DIFFRACTION100
2.8-2.970.33971260.23992760X-RAY DIFFRACTION100
2.97-3.20.33491160.22522774X-RAY DIFFRACTION100
3.2-3.520.29821490.21032757X-RAY DIFFRACTION100
3.52-4.030.24981210.17782790X-RAY DIFFRACTION100
4.03-5.080.22161590.16322799X-RAY DIFFRACTION100
5.08-34.410.26821300.18692945X-RAY DIFFRACTION100

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