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- PDB-9vkk: Crystal structure of EV71 3C protease in complex with bofutrelvir -

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Basic information

Entry
Database: PDB / ID: 9vkk
TitleCrystal structure of EV71 3C protease in complex with bofutrelvir
ComponentsProtease 3C
KeywordsHYDROLASE / Enterovirus / 3C protease / Complex / bofutrelvir
Function / homology
Function and homology information


symbiont-mediated suppression of host programmed cell death / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host programmed cell death / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / DNA replication / RNA helicase activity / 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 / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 ...: / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide / Chem-FHR / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, L. / Ye, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos Pathog. / Year: 2026
Title: A clinical SARS-CoV-2 Mpro inhibitor blocks replication of multiple enteroviruses and confers oral in vivo protection in animal models.
Authors: Ye, Z. / Dai, W. / Zhang, S. / Xiang, Y. / Wang, J. / Zhang, Y. / Cao, W. / Neyts, J. / Li, Z. / Feng, F. / Xiao, G. / Liu, H. / Cao, J. / Zhang, L.K.
History
DepositionJun 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6343
Polymers20,0891
Non-polymers5452
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint0 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.205, 46.617, 51.920
Angle α, β, γ (deg.)90.000, 106.640, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Protease 3C / Picornain 3C / P3C


Mass: 20089.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 (strain BRCR) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q66478, picornain 3C
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FHR / ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 452.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H32N4O4 / Feature type: SUBJECT OF INVESTIGATION
References: ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris (pH 8.5), 20% Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.3→39.58 Å / Num. obs: 7508 / % possible obs: 93 % / Redundancy: 4.5 % / Biso Wilson estimate: 19.27 Å2 / CC1/2: 0.995 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 767 / CC1/2: 0.948

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.92 Å / SU ML: 0.2147 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2197 357 4.78 %
Rwork0.1674 7114 -
obs0.1699 7471 92.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.87 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 6 101 1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881469
X-RAY DIFFRACTIONf_angle_d1.2761987
X-RAY DIFFRACTIONf_chiral_restr0.07228
X-RAY DIFFRACTIONf_plane_restr0.0083260
X-RAY DIFFRACTIONf_dihedral_angle_d16.5619533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.630.26041310.18372510X-RAY DIFFRACTION99.55
2.63-3.320.22911110.16512149X-RAY DIFFRACTION83.86
3.32-28.920.19361150.16162455X-RAY DIFFRACTION94.1

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