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- PDB-9pad: Crystal structure of IBV-3CLpro with ALG-097608 (Inhibitor 1) -

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Basic information

Entry
Database: PDB / ID: 9pad
TitleCrystal structure of IBV-3CLpro with ALG-097608 (Inhibitor 1)
ComponentsORF1ab polyprotein
KeywordsVIRAL PROTEIN / Hydrolase/Inhibitor / 3CL Protease / Nsp5 / Pan coronavirus durg / ALG-097608 / IBV 3CL
Function / homology
Function and homology information


endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / omega peptidase activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / lyase activity ...endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / omega peptidase activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / lyase activity / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Viral superfamily 1 RNA helicase core domain ...Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Viral superfamily 1 RNA helicase core domain / NSP15, NendoU domain, 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 / : / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Papain-like viral protease, palm and finger domains, 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 replicase NSP7 / : / : / 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 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.
Similarity search - Domain/homology
: / ORF1ab polyprotein
Similarity search - Component
Biological speciesInfectious bronchitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsReddem, E.R. / Forouhad, 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 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 15, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF1ab polyprotein
B: ORF1ab polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0414
Polymers66,9182
Non-polymers1,1232
Water13,745763
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein exists as a dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-14 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.355, 101.355, 162.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ORF1ab polyprotein


Mass: 33459.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bronchitis virus / Gene: 1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1P8SSX4
#2: Chemical ChemComp-A1CHF / (1R,2R,3S,6S,7S)-4-[(2S)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-10,10-difluoro-N-{(1E,2R)-1-imino-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propan-2-yl}-4-azatricyclo[5.2.1.0~2,6~]decane-3-carboxamide (non-preferred name)


Mass: 561.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H32F5N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M Bis-Tris pH5.5 and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.902 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.902 Å / Relative weight: 1
ReflectionResolution: 1.4→43.02 Å / Num. obs: 188824 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.058 / Rrim(I) all: 0.367 / Χ2: 0.97 / Net I/σ(I): 10.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 15 % / Rmerge(I) obs: 1.75 / Num. unique obs: 9102 / CC1/2: 0.386 / Rpim(I) all: 0.589 / Rrim(I) all: 0.07 / Χ2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→43.02 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1869 9377 4.97 %
Rwork0.1758 --
obs0.1763 188824 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 78 763 5538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054996
X-RAY DIFFRACTIONf_angle_d1.0326824
X-RAY DIFFRACTIONf_dihedral_angle_d13.9531755
X-RAY DIFFRACTIONf_chiral_restr0.093773
X-RAY DIFFRACTIONf_plane_restr0.006865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.34243110.33515942X-RAY DIFFRACTION100
1.42-1.440.34772690.32435923X-RAY DIFFRACTION100
1.44-1.450.30573170.30755939X-RAY DIFFRACTION100
1.45-1.470.30723100.28675893X-RAY DIFFRACTION100
1.47-1.490.27983310.27365951X-RAY DIFFRACTION100
1.49-1.510.27123180.2555928X-RAY DIFFRACTION100
1.51-1.530.26223180.24445900X-RAY DIFFRACTION100
1.53-1.560.24113280.23675907X-RAY DIFFRACTION100
1.56-1.580.23962900.22655963X-RAY DIFFRACTION100
1.58-1.610.23992930.22235983X-RAY DIFFRACTION100
1.61-1.630.21713070.20995902X-RAY DIFFRACTION100
1.63-1.660.24283300.20445969X-RAY DIFFRACTION100
1.66-1.70.22392550.19385965X-RAY DIFFRACTION100
1.7-1.730.21272950.18855963X-RAY DIFFRACTION100
1.73-1.770.20823290.18525922X-RAY DIFFRACTION100
1.77-1.810.20783320.19785953X-RAY DIFFRACTION100
1.81-1.850.19343640.18255898X-RAY DIFFRACTION100
1.85-1.90.17992950.16935981X-RAY DIFFRACTION100
1.9-1.960.17162690.16566024X-RAY DIFFRACTION100
1.96-2.020.17662830.16025990X-RAY DIFFRACTION100
2.02-2.10.18793080.16115978X-RAY DIFFRACTION100
2.1-2.180.18013160.16136010X-RAY DIFFRACTION100
2.18-2.280.17063020.16116002X-RAY DIFFRACTION100
2.28-2.40.19153420.16535961X-RAY DIFFRACTION100
2.4-2.550.18323270.16816005X-RAY DIFFRACTION100
2.55-2.750.16692920.16976064X-RAY DIFFRACTION100
2.75-3.020.17393140.16356031X-RAY DIFFRACTION100
3.02-3.460.18073070.16516088X-RAY DIFFRACTION100
3.46-4.360.15063730.13756087X-RAY DIFFRACTION100
4.36-43.020.14673520.15216325X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -58.9148 Å / Origin y: 25.3502 Å / Origin z: 14.2027 Å
111213212223313233
T0.0986 Å20.0267 Å20.0013 Å2-0.1103 Å20.0145 Å2--0.0999 Å2
L0.1026 °2-0.0569 °20.0399 °2-0.1527 °20.0024 °2--0.2604 °2
S0.0044 Å °0.0336 Å °0.0072 Å °0.0179 Å °-0.0075 Å °-0.007 Å °-0.0032 Å °0.0189 Å °-0.0125 Å °
Refinement TLS groupSelection details: all

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