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- PDB-7wku: Structure of PDCoV Mpro in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 7wku
TitleStructure of PDCoV Mpro in complex with an inhibitor
Components
  • N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
  • Peptidase C30
KeywordsVIRAL PROTEIN / virus / viral protease / drug design / inhibitor / broad-spectrum antivirals
Function / homology
Function and homology information


RNA exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / methylation / endonuclease activity / membrane => GO:0016020 ...RNA exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / methylation / endonuclease activity / membrane => GO:0016020 / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Non-structural protein 5, deltacoronavirus / Nonstructural protein 14, deltacoronavirus / Nonstructural protein 15, middle domain, deltacoronavirus / Nonstructural protein 15, N-terminal, deltacoronavirus / RNA-dependent RNA polymerase, deltacoronavirus / Non-structural protein 6, deltacoronavirus / Non-structural protein 2, IBV-like / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus ...Non-structural protein 5, deltacoronavirus / Nonstructural protein 14, deltacoronavirus / Nonstructural protein 15, middle domain, deltacoronavirus / Nonstructural protein 15, N-terminal, deltacoronavirus / RNA-dependent RNA polymerase, deltacoronavirus / Non-structural protein 6, deltacoronavirus / Non-structural protein 2, IBV-like / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / 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 / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / 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. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 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-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE / ORF1ab polyprotein
Similarity search - Component
Biological speciesPorcine deltacoronavirus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, F.H. / Yang, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81772204 China
CitationJournal: Viruses / Year: 2022
Title: The Structure of the Porcine Deltacoronavirus Main Protease Reveals a Conserved Target for the Design of Antivirals.
Authors: Wang, F. / Chen, C. / Wang, Z. / Han, X. / Shi, P. / Zhou, K. / Liu, X. / Xiao, Y. / Cai, Y. / Huang, J. / Zhang, L. / Yang, H.
History
DepositionJan 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase C30
B: Peptidase C30
C: Peptidase C30
D: Peptidase C30
E: Peptidase C30
F: Peptidase C30
H: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
I: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
J: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
K: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
L: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
M: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Theoretical massNumber of molelcules
Total (without water)212,10112
Polymers212,10112
Non-polymers00
Water8,305461
1
A: Peptidase C30
J: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Theoretical massNumber of molelcules
Total (without water)35,3502
Polymers35,3502
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area13840 Å2
MethodPISA
2
B: Peptidase C30
K: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Theoretical massNumber of molelcules
Total (without water)35,3502
Polymers35,3502
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-8 kcal/mol
Surface area14090 Å2
MethodPISA
3
C: Peptidase C30
L: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Theoretical massNumber of molelcules
Total (without water)35,3502
Polymers35,3502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6 kcal/mol
Surface area14220 Å2
MethodPISA
4
D: Peptidase C30
M: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Theoretical massNumber of molelcules
Total (without water)35,3502
Polymers35,3502
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-7 kcal/mol
Surface area14040 Å2
MethodPISA
5
E: Peptidase C30
H: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Theoretical massNumber of molelcules
Total (without water)35,3502
Polymers35,3502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-6 kcal/mol
Surface area13430 Å2
MethodPISA
6
F: Peptidase C30
I: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Theoretical massNumber of molelcules
Total (without water)35,3502
Polymers35,3502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-5 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.292, 122.292, 289.754
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Peptidase C30 / Main protease


Mass: 34669.426 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine deltacoronavirus / Gene: ORF1ab / Production host: Escherichia coli (E. coli) / References: UniProt: A0A166XB12
#2: Protein/peptide
N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Type: Peptide-like / Class: Inhibitor / Mass: 680.791 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 291 K / Method: batch mode
Details: 0.1M sodium citrate (pH 5.1), 4% (w/v) polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 75173 / % possible obs: 99.6 % / Redundancy: 20.5 % / Biso Wilson estimate: 49.56 Å2 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.049 / Rrim(I) all: 0.176 / Χ2: 0.525 / Net I/σ(I): 2.6 / Num. measured all: 1541176
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.6-2.6420.337330.7060.5380.44599.3
2.64-2.6920.337230.7730.3720.53499.3
2.69-2.7419.937450.8090.3490.44499.4
2.74-2.819.537420.8760.2930.44899.4
2.8-2.8618.737650.8810.2570.44499.4
2.86-2.9319.837190.9050.2130.4499.40.9270.951
2.93-32037840.9340.1790.43799.60.7830.804
3-3.0821.937200.9620.1450.44999.50.6690.684
3.08-3.1721.837550.9780.1210.45399.60.5590.572
3.17-3.2821.737620.9840.0970.49699.60.4430.453
3.28-3.3921.537630.9870.0810.48599.70.3710.38
3.39-3.5321.137410.9920.0650.60499.70.2950.303
3.53-3.6920.937710.9940.0590.78999.60.2670.273
3.69-3.8820.337480.9950.0450.71299.70.1980.203
3.88-4.1318.737750.9970.0330.64599.70.1410.145
4.13-4.4519.437620.9980.0230.52999.70.0990.102
4.45-4.8921.837830.9990.0190.53499.80.0870.089
4.89-5.621.737890.9990.020.50899.80.0910.093
5.6-7.0520.737620.9990.020.49699.70.0880.091
7.05-5019.938310.9990.0130.60199.70.0580.059

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHENIXmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GWZ

5gwz


Resolution: 2.6→49.74 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 3733 4.97 %
Rwork0.1905 71354 -
obs0.1929 75087 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.95 Å2 / Biso mean: 57.2077 Å2 / Biso min: 13.63 Å2
Refinement stepCycle: final / Resolution: 2.6→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14100 0 294 461 14855
Biso mean--69.01 47.07 -
Num. residues----1798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.630.35751530.28552563271698
2.63-2.660.2931340.27352663279799
2.66-2.70.29861100.26482651276199
2.7-2.740.31771800.24812586276699
2.74-2.780.29571200.26292702282299
2.78-2.820.32491390.25442591273099
2.82-2.870.28931120.24542670278299
2.87-2.920.31461550.237726402795100
2.92-2.970.28681340.230326252759100
2.97-3.030.28781600.227726032763100
3.03-3.090.28121480.227926212769100
3.09-3.160.27131340.22622650278499
3.16-3.230.32921420.222726552797100
3.23-3.310.29991360.224126592795100
3.31-3.40.25971680.22426032771100
3.4-3.50.25391330.190626402773100
3.5-3.610.24831370.193126702807100
3.61-3.740.26131160.186426472763100
3.74-3.890.26041230.174526682791100
3.89-4.070.21891260.170626742800100
4.07-4.280.19931860.152225882774100
4.28-4.550.18461320.145326692801100
4.55-4.90.20991130.146726842797100
4.9-5.40.19591390.158426522791100
5.4-6.180.22841280.182926692797100
6.18-7.770.21331250.180126822807100
7.78-49.740.17511500.17082629277998

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