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- PDB-29ct: Crystal structure of enterovirus D68-3Cpro in complex with RK-384 -

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Basic information

Entry
Database: PDB / ID: 29ct
TitleCrystal structure of enterovirus D68-3Cpro in complex with RK-384
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / 3Cpro / enterovirus / inhibitor
Function / homology
Function and homology information


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 ...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 / RNA helicase activity / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / DNA-templated transcription / 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
: / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsEl Kilani, H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: Commun Chem / Year: 2026
Title: Structure-based macrocyclization of alpha-ketoamides leads to potent inhibitors of coronaviral and enteroviral proteases.
Authors: Akula, R.K. / El Kilani, H. / Metzen, A. / Joshi, S. / Durmaz, H. / Veenstra, R. / Roske, J. / Hurdiss, D.L. / Van Kuppeveld, F.J.M. / Rox, K. / Hilgenfeld, R. / Bronstrup, M.
History
DepositionMar 6, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 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: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5882
Polymers21,0251
Non-polymers5631
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.430, 56.430, 170.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Genome polyprotein


Mass: 21024.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus / Production host: Escherichia coli (E. coli)
References: UniProt: A1E4A3, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Chemical ChemComp-A1JTS / ~{N}-[(3~{S},6~{S},7~{R})-7-oxidanyl-4,8-bis(oxidanylidene)-6-[[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]methyl]-5,9-diazabicyclo[14.3.1]icosa-1(19),16(20),17-trien-3-yl]-3-phenyl-propanamide / RK-384


Mass: 562.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.73 Å3/Da / Density % sol: 67.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 7.8, 0.2 M Ammoniumacetat, 25 % w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 9, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.91→46.98 Å / Num. obs: 25274 / % possible obs: 99.47 % / Redundancy: 9.9 % / CC1/2: 0.999 / Net I/σ(I): 11.53
Reflection shellResolution: 1.91→1.978 Å / Num. unique obs: 2358 / CC1/2: 0.323

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→46.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.886 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2755 1262 5.006 %
Rwork0.2301 23949 -
all0.232 --
obs-25211 99.467 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 76.362 Å2
Baniso -1Baniso -2Baniso -3
1-2.433 Å21.216 Å20 Å2
2--2.433 Å2-0 Å2
3----7.892 Å2
Refinement stepCycle: LAST / Resolution: 1.91→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 41 16 1526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121548
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161442
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.8252098
X-RAY DIFFRACTIONr_angle_other_deg0.6531.763308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.085187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.262513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46810242
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.382101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.2671071
X-RAY DIFFRACTIONr_chiral_restr0.0930.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
X-RAY DIFFRACTIONr_nbd_refined0.2060.2271
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.21319
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2749
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.2838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.231
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2630.27
X-RAY DIFFRACTIONr_nbd_other0.1740.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0360.21
X-RAY DIFFRACTIONr_mcbond_it7.757.371751
X-RAY DIFFRACTIONr_mcbond_other7.7467.374752
X-RAY DIFFRACTIONr_mcangle_it9.71113.23938
X-RAY DIFFRACTIONr_mcangle_other9.71313.229938
X-RAY DIFFRACTIONr_scbond_it8.6398.252797
X-RAY DIFFRACTIONr_scbond_other8.6288.253797
X-RAY DIFFRACTIONr_scangle_it11.95514.7461160
X-RAY DIFFRACTIONr_scangle_other11.9514.7441161
X-RAY DIFFRACTIONr_lrange_it14.65570.5211593
X-RAY DIFFRACTIONr_lrange_other14.65270.531594
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.91-1.9590.657880.62816590.6318310.750.72195.41230.633
1.959-2.0130.631890.53916920.54317890.7540.77699.55280.529
2.013-2.0710.562870.54616500.54717460.6230.65599.48450.534
2.071-2.1350.513850.47816020.4816870.7410.7161000.443
2.135-2.2050.507810.43815470.44116340.8250.80999.63280.393
2.205-2.2820.415790.42715080.42615930.7850.81199.62340.388
2.282-2.3680.408780.3814740.38115580.8590.8499.61490.336
2.368-2.4640.313740.35914040.35614810.9010.88299.79740.321
2.464-2.5740.413720.30613700.31114420.8890.9181000.261
2.574-2.6990.376680.29112900.29513590.9110.93999.92640.246
2.699-2.8440.305640.24812230.25112890.9440.96299.84480.219
2.844-3.0160.286620.22911710.23212330.9430.9661000.203
3.016-3.2230.297590.21611160.2211750.9410.971000.201
3.223-3.480.244550.21110620.21211170.9630.9711000.202
3.48-3.810.279510.2329500.23410020.9380.96899.90020.226
3.81-4.2570.237460.198880.1929350.9570.9899.8930.198
4.257-4.9080.203420.1387850.1428290.9740.98899.75870.162
4.908-5.9950.275350.1746750.1787100.970.9841000.202
5.995-8.410.187290.2065420.2055720.9770.97799.82520.232
8.41-46.980.201180.183410.1813610.9740.97999.4460.232

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